http://hydrodictyon.eeb.uconn.edu/eebedia/api.php?action=feedcontributions&user=PaulLewis&feedformat=atomEEBedia - User contributions [en]2024-03-29T06:29:53ZUser contributionsMediaWiki 1.25.2http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20492Systematics Seminar2012-01-24T17:52:23Z<p>PaulLewis: /* Monday, 23 January 2012 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
Images created from the data sets provided online showing extent of missing data. The color red indicates new data collected for this study, black indicates existing data, white indicates missing data. Note, if you choose to display these in your browser (rather than downloading them and using Preview or Photoshop to view them), you should be aware that they are very wide but not very tall, so you will have to zoom your browser to see anything (unless you have really good eyes).<br />
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]<br />
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_200x216402.png large_200x216402.png]<br />
<br />
=== Monday, 30 January 2012 &lArr; ===<br />
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion on the following shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
Your name here...<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20491Systematics Seminar2012-01-24T17:47:15Z<p>PaulLewis: /* Monday, 23 January 2012 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
Images created from the data sets provided online showing extent of missing data. The color red indicates new data collected for this study, black indicates existing data, white indicates missing data.<br />
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]<br />
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_200x216402.png large_200x216402.png]<br />
<br />
=== Monday, 30 January 2012 &lArr; ===<br />
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion on the following shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
Your name here...<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20490Systematics Seminar2012-01-24T17:45:31Z<p>PaulLewis: /* Monday, 23 January 2012 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
Images created from the data sets provided online showing extent of missing data. The color red indicates new data collected for this study, black indicates existing data, white indicates missing data.<br />
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_200x216402.png large_200x216402.png]<br />
<br />
=== Monday, 30 January 2012 &lArr; ===<br />
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion on the following shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
Your name here...<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20485Systematics Seminar2012-01-24T15:33:34Z<p>PaulLewis: /* Monday, 30 January 2012 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
=== Monday, 30 January 2012 &lArr; ===<br />
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion on the following shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
Your name here...<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20484Systematics Seminar2012-01-24T15:29:59Z<p>PaulLewis: /* Monday, 30 January 2012 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
=== Monday, 30 January 2012 ===<br />
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion on the following shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
Your name here...<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20480Systematics Seminar2012-01-23T23:20:42Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
=== Monday, 30 January 2012 ===<br />
Continuing on the phylogenomic theme, let's examine a shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
Your name here...<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20479Systematics Seminar2012-01-23T23:17:39Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
=== Monday, 30 January 2012 ===<br />
Continuing on the phylogenomic theme, let's examine a shakeup in the green plant tree:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
TBA<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20478Systematics Seminar2012-01-23T22:58:37Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 January 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
=== Monday, 30 January 2012 ===<br />
Continuing on the phylogenomic theme, let's examine a shakeup in the green plant tree:<br />
PDF coming soon... Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.<br />
<br />
=== Monday, 6 February 2012 ===<br />
TBA<br />
<br />
=== Monday, 13 February 2012 ===<br />
Brigette Zacharczenko<br />
<br />
=== Monday, 20 February 2012 ===<br />
Emily Ellis<br />
<br />
=== Monday, 27 February 2012 ===<br />
Beth Timpe<br />
<br />
=== Monday, 5 March 2012 ===<br />
Ursula King<br />
<br />
=== Monday, 12 March 2012 ===<br />
'''SPRING BREAK''' - no meeting this week<br />
<br />
=== Monday, 19 March 2012 ===<br />
Lily Lewis<br />
<br />
=== Monday, 26 March 2012 ===<br />
Rus Meister<br />
<br />
=== Monday, 2 April 2012 ===<br />
Veronica Bueno<br />
<br />
=== Monday, 9 April 2012 ===<br />
Timothy Moore<br />
<br />
=== Monday, 16 April 2012 ===<br />
<br />
=== Monday, 23 April 2012 ===<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20428Systematics Seminar2012-01-19T18:16:18Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 Jan 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20427Systematics Seminar2012-01-19T18:16:04Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 Jan 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs<br />
with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20426Systematics Seminar2012-01-19T18:08:56Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
=== Monday, 23 Jan 2012 ===<br />
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling, I have uploaded a short Nature paper for us to discuss:<br />
<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20423Systematics Seminar2012-01-19T16:35:12Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
First meeting: Monday, 23 Jan 2012 (at this meeting we will discuss possible themes for this semester's seminar)<br />
<br />
== Past Systematics Seminars ==<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar_Fall_2011&diff=20422Systematics Seminar Fall 20112012-01-19T16:34:00Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
=== Tuesday, September 27, 2011 ===<br />
Chris Owen will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.<br />
I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form. <br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.<br />
<br />
===Tuesday, October 4th, 2011===<br />
Beth Timpe will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br><br />
''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br><br />
<br />
===Tuesday, October 11th, 2011===<br />
Don Les will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br><br />
''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br><br />
<br />
===Tuesday, October 18th, 2011===<br />
<br />
Hamid Razifard will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br><br />
"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br><br />
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.<br />
<br />
===Tuesday, October 25th, 2011===<br />
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.<br />
The following paper gives some background information:<br />
<br />
Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf<br />
<br />
===Tuesday, November 1st, 2011===<br />
<br />
Russ Meister will lead a discussion on the following paper:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf<br />
<br />
And possibly talk about his proposed doctorate work.<br />
<br />
===Tuesday, November 8th, 2011===<br />
Chris Owen will lead a discussion of the following paper:<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Townsend%202007%20PhyloInform.pdf}}Townsend. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56(2):222-231<br />
<br />
===Tuesday, November 15th, 2011===<br />
Karolina Fučíková will lead a discussion about the ITS2 species concept, particularly the emphasis on compensatory base changes. There are a number of relevant papers, but here is a short one to look at by Wolf et al. 2005 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/CBCAnalyzer.pdf}}<br />
<br />
=== Tuesday, November 29, 2011 ===<br />
<br />
Dan Rosauer will be visiting. Here are his suggestions for reading: "I’ve attached 2 papers, and suggest that people could choose one of them to read. The Rosauer et al paper describes the phylogenetic endemism concept – which is one of the measures implemented in Biodiverse, while the Laffan et al paper focuses on the Biodiverse software and what it can do."<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rosaueretal2009PhylogeneticEndemism_opt.pdf}} Rosauer et al. 2009<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laffanetal2010Biodiverse.pdf}}Laffan et al. 2010<br />
<br />
=== Tuesday, December 6, 2011 ===<br />
<br />
For our last meeting of the semester we have two readings. Both are on diversification rates and, if true, call into question major macroevolutionary patterns that you may have been taught in evolution or my entomology course.<br />
<br />
Our primary reading will be Stadler (2007). Don’t get bogged down in the math unless you are so inclined. It is our last class meeting: be happy. I am only sorry that Paul is not going to be with us (to interrogate). Note that Olin Silander, John’s son, was a reader (who works on viral evolution).<br />
<br />
The core text of the second paper on beetle radiations (Hunt et al. 2007) is less than two pages (length mostly figures), and you can skip the paragraphs that delve into the details of beetle classification on page 1914.<br />
<br />
Thought these would be interesting, not too long, and address two big patterns that are discussed in evolutionary texts, classes, etc.<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PNAS-2011-Stadler-6187-92.pdf}}PNAS-2011-Stadler<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Science-2007-Hunt-1913-6.pdf}}Science-2007-Hunt<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20278Systematics Seminar2012-01-17T18:26:34Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
First meeting: Monday, 23 Jan 2012 (at this meeting we will discuss possible themes for this semester's seminar)<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2011|Fall 2011]]<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar_Fall_2011&diff=20277Systematics Seminar Fall 20112012-01-17T18:24:45Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
=== Tuesday, September 27, 2011 ===<br />
Chris Owen will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.<br />
I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form. <br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.<br />
<br />
===Tuesday, October 4th, 2011===<br />
Beth Timpe will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br><br />
''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br><br />
<br />
===Tuesday, October 11th, 2011===<br />
Don Les will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br><br />
''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br><br />
<br />
===Tuesday, October 18th, 2011===<br />
<br />
Hamid Razifard will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br><br />
"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br><br />
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.<br />
<br />
===Tuesday, October 25th, 2011===<br />
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.<br />
The following paper gives some background information:<br />
<br />
Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf<br />
<br />
===Tuesday, November 1st, 2011===<br />
<br />
Russ Meister will lead a discussion on the following paper:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf<br />
<br />
And possibly talk about his proposed doctorate work.<br />
<br />
===Tuesday, November 8th, 2011===<br />
Chris Owen will lead a discussion of the following paper:<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Townsend%202007%20PhyloInform.pdf}}Townsend. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56(2):222-231<br />
<br />
===Tuesday, November 15th, 2011===<br />
Karolina Fučíková will lead a discussion about the ITS2 species concept, particularly the emphasis on compensatory base changes. There are a number of relevant papers, but here is a short one to look at by Wolf et al. 2005 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/CBCAnalyzer.pdf}}<br />
<br />
=== Tuesday, November 29, 2011 ===<br />
<br />
Dan Rosauer will be visiting. Here are his suggestions for reading: "I’ve attached 2 papers, and suggest that people could choose one of them to read. The Rosauer et al paper describes the phylogenetic endemism concept – which is one of the measures implemented in Biodiverse, while the Laffan et al paper focuses on the Biodiverse software and what it can do."<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rosaueretal2009PhylogeneticEndemism_opt.pdf}} Rosauer et al. 2009<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laffanetal2010Biodiverse.pdf}}Laffan et al. 2010<br />
<br />
=== Tuesday, December 6, 2011 ===<br />
<br />
For our last meeting of the semester we have two readings. Both are on diversification rates and, if true, call into question major macroevolutionary patterns that you may have been taught in evolution or my entomology course.<br />
<br />
Our primary reading will be Stadler (2007). Don’t get bogged down in the math unless you are so inclined. It is our last class meeting: be happy. I am only sorry that Paul is not going to be with us (to interrogate). Note that Olin Silander, John’s son, was a reader (who works on viral evolution).<br />
<br />
The core text of the second paper on beetle radiations (Hunt et al. 2007) is less than two pages (length mostly figures), and you can skip the paragraphs that delve into the details of beetle classification on page 1914.<br />
<br />
Thought these would be interesting, not too long, and address two big patterns that are discussed in evolutionary texts, classes, etc.<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PNAS-2011-Stadler-6187-92.pdf}}PNAS-2011-Stadler<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Science-2007-Hunt-1913-6.pdf}}Science-2007-Hunt<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar_Fall_2011&diff=20276Systematics Seminar Fall 20112012-01-17T18:23:50Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
=== Tuesday, September 27, 2011 ===<br />
Chris Owen will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.<br />
I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form. <br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.<br />
<br />
===Tuesday, October 4th, 2011===<br />
Beth Timpe will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br><br />
''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br><br />
<br />
===Tuesday, October 11th, 2011===<br />
Don Les will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br><br />
''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br><br />
<br />
===Tuesday, October 18th, 2011===<br />
<br />
Hamid Razifard will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br><br />
"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br><br />
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.<br />
<br />
===Tuesday, October 25th, 2011===<br />
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.<br />
The following paper gives some background information:<br />
<br />
Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf<br />
<br />
===Tuesday, November 1st, 2011===<br />
<br />
Russ Meister will lead a discussion on the following paper:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf<br />
<br />
And possibly talk about his proposed doctorate work.<br />
<br />
===Tuesday, November 8th, 2011===<br />
Chris Owen will lead a discussion of the following paper:<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Townsend%202007%20PhyloInform.pdf}}Townsend. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56(2):222-231<br />
<br />
===Tuesday, November 15th, 2011===<br />
Karolina Fučíková will lead a discussion about the ITS2 species concept, particularly the emphasis on compensatory base changes. There are a number of relevant papers, but here is a short one to look at by Wolf et al. 2005 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/CBCAnalyzer.pdf}}<br />
<br />
=== Tuesday, November 29, 2011 ===<br />
<br />
Dan Rosauer will be visiting. Here are his suggestions for reading: "I’ve attached 2 papers, and suggest that people could choose one of them to read. The Rosauer et al paper describes the phylogenetic endemism concept – which is one of the measures implemented in Biodiverse, while the Laffan et al paper focuses on the Biodiverse software and what it can do."<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rosaueretal2009PhylogeneticEndemism_opt.pdf}} Rosauer et al. 2009<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laffanetal2010Biodiverse.pdf}}Laffan et al. 2010<br />
<br />
=== Tuesday, December 6, 2011 ===<br />
<br />
For our last meeting of the semester we have two readings. Both are on diversification rates and, if true, call into question major macroevolutionary patterns that you may have been taught in evolution or my entomology course.<br />
<br />
Our primary reading will be Stadler (2007). Don’t get bogged down in the math unless you are so inclined. It is our last class meeting: be happy. I am only sorry that Paul is not going to be with us (to interrogate). Note that Olin Silander, John’s son, was a reader (who works on viral evolution).<br />
<br />
The core text of the second paper on beetle radiations (Hunt et al. 2007) is less than two pages (length mostly figures), and you can skip the paragraphs that delve into the details of beetle classification on page 1914.<br />
<br />
Thought these would be interesting, not too long, and address two big patterns that are discussed in evolutionary texts, classes, etc.<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PNAS-2011-Stadler-6187-92.pdf}}PNAS-2011-Stadler<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Science-2007-Hunt-1913-6.pdf}}Science-2007-Hunt<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar_Fall_2011&diff=20275Systematics Seminar Fall 20112012-01-17T18:22:44Z<p>PaulLewis: New page: == Schedule for Fall Semester 2011 == Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one. * Ancestral state reconstruction * Use ...</p>
<hr />
<div>== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
=== Tuesday, September 27, 2011 ===<br />
Chris Owen will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.<br />
I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form. <br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.<br />
<br />
===Tuesday, October 4th, 2011===<br />
Beth Timpe will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br><br />
''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br><br />
<br />
===Tuesday, October 11th, 2011===<br />
Don Les will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br><br />
''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br><br />
<br />
===Tuesday, October 18th, 2011===<br />
<br />
Hamid Razifard will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br><br />
"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br><br />
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.<br />
<br />
===Tuesday, October 25th, 2011===<br />
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.<br />
The following paper gives some background information:<br />
<br />
Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf<br />
<br />
===Tuesday, November 1st, 2011===<br />
<br />
Russ Meister will lead a discussion on the following paper:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf<br />
<br />
And possibly talk about his proposed doctorate work.<br />
<br />
===Tuesday, November 8th, 2011===<br />
Chris Owen will lead a discussion of the following paper:<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Townsend%202007%20PhyloInform.pdf}}Townsend. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56(2):222-231<br />
<br />
===Tuesday, November 15th, 2011===<br />
Karolina Fučíková will lead a discussion about the ITS2 species concept, particularly the emphasis on compensatory base changes. There are a number of relevant papers, but here is a short one to look at by Wolf et al. 2005 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/CBCAnalyzer.pdf}}<br />
<br />
=== Tuesday, November 29, 2011 ===<br />
<br />
Dan Rosauer will be visiting. Here are his suggestions for reading: "I’ve attached 2 papers, and suggest that people could choose one of them to read. The Rosauer et al paper describes the phylogenetic endemism concept – which is one of the measures implemented in Biodiverse, while the Laffan et al paper focuses on the Biodiverse software and what it can do."<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rosaueretal2009PhylogeneticEndemism_opt.pdf}} Rosauer et al. 2009<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laffanetal2010Biodiverse.pdf}}Laffan et al. 2010<br />
<br />
=== Tuesday, December 6, 2011 ===<br />
<br />
For our last meeting of the semester we have two readings. Both are on diversification rates and, if true, call into question major macroevolutionary patterns that you may have been taught in evolution or my entomology course.<br />
<br />
Our primary reading will be Stadler (2007). Don’t get bogged down in the math unless you are so inclined. It is our last class meeting: be happy. I am only sorry that Paul is not going to be with us (to interrogate). Note that Olin Silander, John’s son, was a reader (who works on viral evolution).<br />
<br />
The core text of the second paper on beetle radiations (Hunt et al. 2007) is less than two pages (length mostly figures), and you can skip the paragraphs that delve into the details of beetle classification on page 1914.<br />
<br />
Thought these would be interesting, not too long, and address two big patterns that are discussed in evolutionary texts, classes, etc.<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PNAS-2011-Stadler-6187-92.pdf}}PNAS-2011-Stadler<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Science-2007-Hunt-1913-6.pdf}}Science-2007-Hunt</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=20274Systematics Seminar2012-01-17T18:22:08Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''<br />
<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=19875Systematics Seminar2011-11-28T15:01:12Z<p>PaulLewis: /* Tuesday, November 29, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
=== Tuesday, September 27, 2011 ===<br />
Chris Owen will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.<br />
I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form. <br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.<br />
<br />
===Tuesday, October 4th, 2011===<br />
Beth Timpe will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br><br />
''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br><br />
<br />
===Tuesday, October 11th, 2011===<br />
Don Les will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br><br />
''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br><br />
<br />
===Tuesday, October 18th, 2011===<br />
<br />
Hamid Razifard will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br><br />
"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br><br />
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.<br />
<br />
===Tuesday, October 25th, 2011===<br />
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.<br />
The following paper gives some background information:<br />
<br />
Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf<br />
<br />
===Tuesday, November 1st, 2011===<br />
<br />
Russ Meister will lead a discussion on the following paper:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf<br />
<br />
And possibly talk about his proposed doctorate work.<br />
<br />
===Tuesday, November 8th, 2011===<br />
Chris Owen will lead a discussion of the following paper:<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Townsend%202007%20PhyloInform.pdf}}Townsend. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56(2):222-231<br />
<br />
===Tuesday, November 15th, 2011===<br />
Karolina Fučíková will lead a discussion about the ITS2 species concept, particularly the emphasis on compensatory base changes. There are a number of relevant papers, but here is a short one to look at by Wolf et al. 2005 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/CBCAnalyzer.pdf}}<br />
<br />
=== Tuesday, November 29, 2011 ===<br />
<br />
Dan Rosauer will be visiting. Here are his suggestions for reading: "I’ve attached 2 papers, and suggest that people could choose one of them to read. The Rosauer et al paper describes the phylogenetic endemism concept – which is one of the measures implemented in Biodiverse, while the Laffan et al paper focuses on the Biodiverse software and what it can do."<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rosaueretal2009PhylogeneticEndemism_opt.pdf}} Rosauer et al. 2009<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laffanetal2010Biodiverse.pdf}}Laffan et al. 2010<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=19874Systematics Seminar2011-11-28T14:58:39Z<p>PaulLewis: /* Tuesday, November 15th, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
=== Tuesday, September 27, 2011 ===<br />
Chris Owen will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.<br />
I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form. <br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.<br />
<br />
===Tuesday, October 4th, 2011===<br />
Beth Timpe will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br><br />
''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br><br />
<br />
===Tuesday, October 11th, 2011===<br />
Don Les will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br><br />
''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br><br />
<br />
===Tuesday, October 18th, 2011===<br />
<br />
Hamid Razifard will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br><br />
"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br><br />
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.<br />
<br />
===Tuesday, October 25th, 2011===<br />
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.<br />
The following paper gives some background information:<br />
<br />
Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf<br />
<br />
===Tuesday, November 1st, 2011===<br />
<br />
Russ Meister will lead a discussion on the following paper:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf<br />
<br />
And possibly talk about his proposed doctorate work.<br />
<br />
===Tuesday, November 8th, 2011===<br />
Chris Owen will lead a discussion of the following paper:<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Townsend%202007%20PhyloInform.pdf}}Townsend. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56(2):222-231<br />
<br />
===Tuesday, November 15th, 2011===<br />
Karolina Fučíková will lead a discussion about the ITS2 species concept, particularly the emphasis on compensatory base changes. There are a number of relevant papers, but here is a short one to look at by Wolf et al. 2005 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/CBCAnalyzer.pdf}}<br />
<br />
=== Tuesday, November 29, 2011 ===<br />
<br />
Dan Rosauer will be visiting. Here are his suggestions for reading: "I’ve attached 2 papers, and suggest that people could choose one of them to read. The Rosauer et al paper describes the phylogenetic endemism concept – which is one of the measures implemented in Biodiverse, while the Laffan et al paper focuses on the Biodiverse software and what it can do."<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rosaueretal2009PhylogeneticEndemism_opt.pdf}} Rosauer et al. 2009<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=File:Beforeps.jpg&diff=19817File:Beforeps.jpg2011-11-17T14:55:53Z<p>PaulLewis: </p>
<hr />
<div></div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Mammalogy_Class_Pictures&diff=19790Mammalogy Class Pictures2011-11-16T20:29:00Z<p>PaulLewis: </p>
<hr />
<div>__NOEDITSECTION__<br />
<br><br />
<h2 style="margin:0;background-color:#FFCC00;font-size:170%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">'''WHAT IS THIS PAGE?'''</h2><br />
<br><br><br />
This page is an extension of the mammalogy class page (link below). It serves as a place where mammal- and class-related images can be posted, including pictures from the class field trip to the Bronx Zoo, people and personal mammal encounters.<br />
<br><br><br />
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Mammalogy '''LINK TO MAMMALOGY CLASS PAGE (EEB 3254/5254)''']<br />
<br><br><br />
<h2 style="font-size:150%;font-weight:bold;color:#0000CC">HOW TO GET YOUR PICTURES POSTED HERE</h2><br />
<font color="#000000"><br />
<h2 style="font-size:125%"><br />
<br><br />
*you must be a member of the class (or at least a friend of Kurt's)<br />
<br><br />
*send your picture by email to Kurt (kurt.schwenk@uconn.edu)<br />
<br><br />
*if you have multiple images or large files, put them in a folder with an appropriate name, compress the folder (right click on it for compression option) and send the compressed file to the UConn 'drop box': [https://dropbox.uconn.edu/dropbox '''DROP BOX'''] - this will be faster if you do it from campus. Once uploaded, the drop box will provide you with a link where the file can be retrieved - EMAIL THE LINK TO KURT<br />
<br><br />
*if you want, provide captions for the photographs (make sure you give me enough info to be able to put match the captions with the photos)<br />
<br><br><br />
</h2><br />
<h2 style="font-size:150%;font-weight:bold;color:#0000CC">PICTURES!</h2><br />
<font color="#000000"><br />
<br><br />
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| [[Image:MammClassZoo11_11.jpg|center|thumb|Mammalogy class at the Bronx Zoo, 10 Nov. 2011 (Schwenk)]] || [[Image:Glaucomys_sabrinus1.jpg|center|thumb|Kurt's most recent encounter with a flying squirrel (''Glaucomys'') - on the hearth!]] || [[Image:Glaucomys_sabrinus2.jpg|center|thumb|...climbing]] || [[Image:Glaucomys_sabrinus3.jpg|center|thumb|...making his escape]] || [[Image:BobcatWindhamHerrick09.jpg|center|thumb|Bobcat (''Lynx rufus'') spotted by a colleague in her Windham backyard! (Susan Herrick)]]<br />
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| [[Image:3254BlurryClassZoo.jpg|center|thumb|Blurry class pic taken by friendly bystander at the zoo]] || [[Image:3254ZooClassMarching_LCisneros.jpg|center|thumb|Forced march (L. Cisneros)]] || [[Image:3254ZooStudentsLauraCisneros.jpg|center|thumb| Looking at zebras (L. Cisneros)]] || [[Image:3254KellyBillKatieLaura_LCisneros.jpg|center|thumb| Kelly, Bill, Katie and Laura (L. Cisneros]] || [[Image:3254LyndsayErika_LCisneros.jpg|center|thumb| Lyndsay and Erika (L. Cisneros)]]<br />
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| || [[Image:33254GorillaFace2LauraCisneros.jpg|center|thumb| Showing his teeth (L. Cisneros)]] || || || <br />
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[[Category:EEB Courses]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=File:TLSHornwort.jpg&diff=19783File:TLSHornwort.jpg2011-11-16T12:56:17Z<p>PaulLewis: Hornworts found growing beside Torrey Life Science building, UConn Storrs campus.</p>
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<div>Hornworts found growing beside Torrey Life Science building, UConn Storrs campus.</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Tobias_Landberg&diff=19728Tobias Landberg2011-11-11T23:56:23Z<p>PaulLewis: </p>
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<div><span style="font-size: large">PhD</span><br><br />
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'''E-mail:''' tlandberg@murraystate.edu <br><br />
I've now joined [http://campus.murraystate.edu/academic/faculty/hwhiteman/index.shtml Dr. Howard Whiteman's lab] as a post-doctoral researcher working on environmentally induced polyphenisms in Ambystoma salamanders. <br />
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[[Image:Barbouribaby.jpg |center]]<br><br />
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== '''About''' ==<br />
I recently earned my PhD in the Ecology & Evolutionary Biology department at the University of Connecticut, Storrs and then did my first post-doc with Dr. Karen Warkentin studying red-eyed treefrogs at the Smithsonian Tropical Research Institute in Gamboa, Panama<br><br />
PhD Co-advisors Drs. [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Kurt_Schwenk Kurt Schwenk] & [http://hydrodictyon.eeb.uconn.edu/people/schlichting/ Carl Schlichting] headed my committee– which also included Drs. [http://hydrodictyon.eeb.uconn.edu/people/jockusch/jockuschlab/ Elizabeth Jockusch] and [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Kentwood_Wells Kentwood Wells]. <br><br />
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== '''Research philosophy''' ==<br />
[[Image:Underwaterhellbender.jpg|left|frame|100px|Hellbender from Lycoming Creek, PA]][[Image:Ontogeny.jpg|right]]<br />
In a nutshell, it's about unraveling the mobius strip of how organisms perform their behaviors, how sources of variation affect that performance, and how that performance affects evolution. Raising related species under a set of different environments can reveal how developmental responses to the environment evolve. Together with an understanding of the organisms' natural environments and the results of a variety of performance tests, functional variation can be used to interpret evolution.<br />
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== '''Dissertation research''' ==<br />
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[[Image:BeaverDamPond.jpg|right]]<br />
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The broad goal of my dissertation is to see how maternal, developmental and environmental sources of variation contribute to species level diversity.<br />
The specifics include two types of experimental manipulations of environmental features. First, oxygen, because these salamander have an aquatic embryonic and larval phase to their life histories that spans a wide range of natural oxygen levels across streams and ponds. Second, maternal investment in yolk reserves, because female investment in egg size and number trade off. Investing in fewer offspring by the mother must gain an advantage for individual larvae. I'm looking at sister species that breed in ponds and streams (A. texanum & A. barbouri respectively). <br />
[[Image:Streamvspond.jpg|center]]<br />
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=== '''Oxygen plasticity''' ===<br />
[[Image:Newtbreathing.gif|left|]]<br />
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Dissolved oxygen can act as a resource, because it is required for aerobic metabolism, and as information, because it can indicate poor water quality and drying pond conditions. Embryos raised in low oxygen were smaller than those raised in high oxygen indicating oxygen limits growth. The pond species, that lives in low oxygen habitats, had a much smaller response to oxygen than the stream species that generally experiences high oxygen. This suggests that the response to oxygen increases evolutionarily with the availability of oxygen. Later in development, pond larvae reversed the direction of their response so that larvae raised in low oxygen were larger than those raised in high oxygen. This growth response to low oxygen is correlated with early metamorphosis which suggests the response is adaptive when ponds dry up. The stream dweller, however, did not developmentally reverse the direction of plasticity. It continued having the largest body size in high oxygen throughout development. This pattern appears adaptive as well because the streams dry up quickly almost every year. Together these results suggest that the ancestral condition in pond species is oxygen limitation in embryos followed by adaptive plasticity in larvae. The stream species has evolved two adaptations of their response, a larger magnitude response and an reversal of the ancestral developmental reversal. <br><br />
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=== '''Maternal investment''' ===<br />
[[Image:Salamander_larvae.jpg|left|frame|100px|Spotted salamander larvae: can you guess which one had yolk removed? Photo by Tobias Landberg]]<br />
[[Image:Spottedlarvadorsal.jpg|right]]<br />
Egg size is another feature that varies dramatically among amphibians living in different environments. Stream breeders typically have large eggs while pond breeders have relatively small eggs. This difference has important evolutionary consequences because females are resource limited and cannot both have large eggs and many of them. This trade-off and correlation with habitat strongly suggests that stream environments favor large eggs because of the high quality offspring they produce. <br />
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My approach to this question is experimental. By surgically removing small quantities of yolk from developing embryos, yolk reserves can be artificially manipulated. The strategy is to compare siblings who have had yolk removed to the sham operated group– those who were "poked" but no yolk actually removed. Tiny quantities of yolk can affect development from hatching all the way through metamorphosis.<br />
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== '''Other salamander projects''' ==<br />
<br>During my tenure here at UConn, I've engaged in a number of other fruitful projects. They are just for fun and as such are all collaborative efforts.<br />
[[Image:Bufometamorph2.jpg|left]]<br />
[[Image:Chorusfrogmetamorph.jpg|right]]<br />
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=== '''Predator induced plasticity''' ===<br />
One of the best-studied forms of adaptive plasticity in amphibians is their response to predators. Early hatching in response to egg predators is practically ubiquitous among amphibians, but what are the long term costs of leaving the egg early? How do predators that specialize on different life stages interact? Since metamorphosis is thought to be a particularly vulnerable life stage, is it responsive to the presence of predators? Has metamorphosis been selected to be as rapid as possible? Is it constrained physiologically by the demands of transformation? Together with [http://hydrodictyon.eeb.uconn.edu/people/schlichting/ Carl Schlichting], I have mentored two honors students who completed theses on some of these questions.<br />
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[[Image:Leah sm.jpg|left]]<br />
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[http://digitalcommons.uconn.edu/cgi/viewcontent.cgi?article=1043&context=srhonors_theses Leah Brown-Wilusz's honors thesis], was designed to address some of these questions in our local spotted salamander (''Ambystoma maculatum''). We raised embryos with and without egg predators (trichopteran larvae) and larval predators (marbled salamander larvae:''Ambystoma opacum'') to see if the early hatching response to one predator affected a future the response to larval predators. Presence of the egg predator caused early hatching regardless of the presence of the larval predator indicating that the immediate threat outweighs any future potential threat. Salamander embryos exposed to larval predators grew larger tail fins and survived longer with the predators but early hatching incurred a measurable cost. The effect of early hatching even extended to the adult life stage indicating that hatching early in response to an egg predator can make individuals smaller at metamorphosis. The early hatching response therefore looks to be maintained as a plastic strategy by costs in the larval period in terms of larval predator avoidance as well as potential fitness costs at metamorphosis.<br />
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[http://digitalcommons.uconn.edu/cgi/viewcontent.cgi?article=1075&context=srhonors_theses Laurel Dwyer's honors thesis] was designed to address several questions about the mysterious process of metamorphosis. We employed centrarchid sunfish (green sunfish: ''Lepomis cyanellus'' and bluegill sunfish: ''L. macrochirus'') to see if spotted salamander larvae ''Ambystoma maculatum'') can adaptively reduce their predation risk by reducing the amount of time they spend in the vulnerable process of metamorphosis. Behavioral trials indicated that predator exposed animals ate and weighed less explaining why they had lower survival despite only being exposed to chemical cues from the fish. Metamorphosis was approximately 25% shorter in duration for the salamanders exposed to predator cues compared to those not exposed. This suggests that salamanders assess their risk of predation and adaptively reduce the amount of time spent in the vulnerable metamorphic life stage. <br><br />
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=== '''Algae–salamander symbiosis''' ===<br />
[[Image:OophilaKYsmall.jpg|left]]<br />
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[[Image:OophilaCTsmall.jpg|right]]<br />
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With undergraduate Shawn Binns, and professor [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Louise_A._Lewis Louise Lewis], I am investigating algae-salamander mutualisms. Ambystomatid salamander eggs deposited in vernal ponds often develop a green hue. This is not just a coating of pond scum, but rather an alga that lives inside the egg capsule. Poetically named, ''Oophila'' means egg-lover. Research has previously shown that the salamander benefits from increased oxygen levels produced by the algae while the algae gets nitrogenous waste products from the embryos. Everybody wins!<br />
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Who are these little green invaders? Do all the eggs have the same strain or species of algae. Does this vary from year to year? The algae inside of Louisiana spotted salamanders looks morphologically different from Connecticut algae. Is it plasticity or the same species? We also noticed that Kentucky algae growing on a different species (Ambystoma texanum) grows in the jelly matrix rather than inside the egg capsule. They look similar to the Connecticut algae but bigger. It's fun to think of salamander embryos as a source of food for plants.<br />
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== '''Turtle research''' ==<br />
=== '''Breathing & locomotion''' ===<br />
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[[Image:Turtleanatomy.gif|250px|right]]With [http://www.brown.edu/Departments/EEB/brainerd_lab/ Elizabeth Brainerd] and Jeff Mailhot at the University of Massachusetts at Amherst, I studied turtle breathing and locomotion. Turtles can breathe using the limbs at rest... can they breathe during locomotion? Work done by [http://bms.brown.edu/mppb/faculty/facultypage.php?id=1100924384&type= Dr. Don Jackson] and colleagues showed that nesting green sea turtles (''Chelonia mydas'') don't breathe at all during terrestrial locomotion. Box turtles and red eared sliders do however. Surprisingly, there is no relationship between limb movement and when breaths occur. So they can't be using the limbs for breathing during locomotion. Both species appear to use specialized abdominal muscles for breathing during locomotion, but there is one difference. There was no measurable effect of locomotion on breathing in the box turtle, ''Terrapene carolina''- a species that has numerous adaptations for terrestriality. The red-eared slider, ''Trachemys scripta'' is much more typically semi-aquatic. When sliders pause between bouts of locomotion, they double the size of each breath indicating that locomotion interferes with breathing– by reducing the size of each breath. And the adult green sea turtle, of course, who has many highly derived features for aquatic locomotion, doesn't breathe during terrestrial locomotion. Three species–– three different life styles and three different patterns of interaction between breathing & locomotion. Makes you wonder...{{#ev:youtube|1fKBnE-_eC0}} <br />
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=== '''Snapping turtle ecology''' ===<br />
[[Image:HartfordCourant1.jpg|right|frame|Tobias frees "Jawless" a 39 pound snapping turtle from the net. Photo credit: Hartford Courant]]In conjunction with many generous private volunteers, several local Connecticut organizations including [http://www.opp.org/ Our Piece of the Pie], [http://www.riverfront.org/ Riverfront Recapture], [http://www.ctwater.com/CritterCamProject.htm Connecticut Water Company] as well as the [http://www.nationalgeographic.com/ National Geographic Society], I am working with high school students on a snapping turtle ecology. The goal is expose teenagers in Hartford, CT to nature, science and career options they might not otherwise see – and learn a thing or two about snappers.<br />
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'''Click the video below''' to see Shenipsit Lake, Connecticut from the shell of a 24 pound snapper!<br />
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{{#ev:youtube|EM2yj1_vBDE}}<br />
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Learn more about the [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Snapping_turtle_research_team snapping turtle research team]<br><br />
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== '''Publications''' ==<br />
[[Image:Babywoodflipsmall.gif|right]]<br />
'''Landberg, T.''' and Schwenk, K. (in press). Book review: Steyermark, A.C. Finkler, M.S. & Brooks, R.J. (editors) 2008. Biology of the snapping turtle (Chelydra serpentina). – Baltimore, The Johns Hopkins University Press. Palarch’s Journal of Vertebrate Palaeontology <br><br><br />
'''Landberg, T.''', [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Colin_Carlson Carlson, C. J.], Abernathy, K., Luginbuhl, C. Gemme, P. and Mergins, C. (2010) Natural History Notes: CHELYDRA SERPENTINA SERPENTINA L. (Eastern Snapping Turtle). SURVIVAL AFTER INJURY. Herpetological Review 41(1):70-71 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Image:Landbergetal2010Jawless.pdf}}<br><br><br />
'''Landberg T''' and Azizi, E. (2010) Ontogeny of escape swimming performance in the spotted salamander. Functional Ecology 24(3):576-586 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Image:Landberg%26Azizi%28inpress%29.pdf}}<br><br><br />
'''Landberg T'''., J. D. Mailhot and E. L. Brainerd (2009). Lung ventilation during treadmill locomotion in a semi-aquatic turtle, ''Trachemys scripta''. Journal of Experimental Zoology 311A(8):551-562. {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Image:Landbergetal08.pdf}}<br><br><br />
Azizi, E., '''T. Landberg''' and R. J. Wassersug (2007) Vertebral function during tadpole locomotion. Zoology 110:290-297. {{pdf|http://hydrodictyon.eeb.uconn.edu/people/schwenk/TadpoleLocoAziziLanderberg07.pdf}}<br><br><br />
'''Landberg, T.''', J. Mailhot and E.L. Brainerd (2003) Lung ventilation during treadmill locomotion in a terrestrial turtle, ''Terrapene carolina''. Journal of Experimental Biology 206:3391-3404. {{pdf|http://hydrodictyon.eeb.uconn.edu/people/schwenk/LandbergEAturtleVentilation03.pdf}}<br><br><br />
Azizi, E., and '''T. Landberg''' (2002) Effects of metamorphosis on the aquatic escape response of the two-lined salamander (''Eurycea bislineata''). Journal of Experimental Biology 205:841-849. {{pdf|http://hydrodictyon.eeb.uconn.edu/people/schwenk/AziziLandbergEuryceaEscape02.pdf}}<br><br><br />
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== '''Links''' ==<br />
The [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_Club Biology Club] is for anyone interested in undergraduate research in Biology at UConn.<br />
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My YouTube account has lots [http://www.youtube.com/Jobediah more videos] <br><br />
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My Facebook account has lots [http://uconn.new.facebook.com/profile.php?id=9025023 more photos]<br />
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[[Category:EEB Graduate Students|Landberg]] [[Category:EEB People|Landberg]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Web_site_FAQ&diff=19727Web site FAQ2011-11-11T21:40:56Z<p>PaulLewis: /* How do I connect to the web server using FileZilla? */</p>
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<div>This page contains frequently asked questions (and answers!) about the EEB department's web server.<br />
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== The web server (hydrodictyon) ==<br />
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=== What is hydrodictyon? ===<br />
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Hydrodictyon is the name of the computer that serves up all the web pages that together constitute the [http://hydrodictyon.eeb.uconn.edu/ EEB web site]. The term ''web server'' can refer to either the ''software'' that serves web pages ([http://httpd.apache.org/ Apache] in our case) or the computer that runs that software (a Dell Optiplex 755 in our case). Hydrodictyon runs the [http://fedoraproject.org/ Red Hat Fedora 9] Linux operating system.<br />
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=== Do I need an account on hydrodictyon? ===<br />
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You need an account on hydrodictyon if you want to create a traditional HTML-based web page for yourself or a course. Many find it much easier to create and maintain web pages using EEBedia than the traditional approach. This FAQ page, for example, was created in EEBedia. If you would like to try using EEBedia, click on the [[Help:Contents|Help]] link to your left to get started.<br />
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=== How do I get an account on hydrodictyon? ===<br />
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Just send an email request to the [mailto:eebwebmaster@uconn.edu EEB Webmaster]. Ordinarily, you must be a current member of the EEB department to obtain an account, but exceptions will be made under some circumstances.<br />
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=== What is the difference between my home directory and my web folder on hydrodictyon? ===<br />
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When your account is created, you automatically get a '''home directory'''. Your home directory is located within the <tt>/home</tt> directory on hydrodictyon. (For those unfamiliar with Linux, the root of the file system is "/", which is akin to "C:/" in Windows, so <tt>/home</tt> is one level up from the root of the file system.) Items you upload or create in your home directory will not be visible on the internet. Inside your home directory, you should find an an item named "html". While "html" looks and acts like a directory, it is actually an alias (or symbolic link, in Linux terminology) to a completely separate directory on the hard drive, your '''web folder'''. For example, my (Paul Lewis) home directory is <tt>/home/plewis</tt>, whereas my web folder is <tt>/var/www/html/people/plewis</tt>. Items placed in your web folder will be immediately visible on the internet at an address (URL) that looks like this:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
or, equivalently, <br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
Note that you should replace the "yourusername" part of the URL with your own username. <br />
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The "html" alias makes it easy for you to transfer files to your web folder. No matter how you connect to hydrodictyon, you will be dumped first in your home directory, where you should see the "html" alias staring you in the face. Just double-click that alias and you will be transported across the hard drive to your web folder.<br />
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Before you begin uploading files, read the next section entitled "Why you should name your home page index.html"<br />
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=== Why you should name your home page index.html ===<br />
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Suppose you name your home page <tt>MyHomePage.html</tt>. In order for someone to see your homepage, they must know the exact name of your home page file and append it to your base URL, as follows:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/MyHomePage.html<br />
If someone does not know the name of the file serving as your home page, they may try typing this URL into their browser instead:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
[[Image:Dirlisting.png|thumb|right]]If they were to do that, they would not see your home page. Instead, they would see a directory listing like the one shown on the right (click the thumbnail image to see the full size image if you want). Now they have to wade through all your web files and try to figure out which one is your home page. In the meantime, they might happen on some files you didn't plan on anyone viewing (e.g. <tt>junk_I_home_noone_ever_sees.html</tt>), perhaps because they represent works in progress or obsolete content that you just can't bring yourself to delete.<br />
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If you name your home page index.html, however, then users will always get your home page when they enter your base URL, i.e.<br />
<nowiki>http://hydrodictyon.eeb.uconn.edu/people/yourusername/</nowiki><br />
and they will never get an index showing all your files. This gives you a lot of control over what people see: they can only see the files you have linked to your home page or to other pages linked to your home page. It also gives you control over what will appear in searches conducted on Google (and other search sites) because the webbots used by the search engines also cannot get a listing of all your files.<br />
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=== Who is the EEB Webmaster? ===<br />
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The current EEB webmaster is [mailto:eebwebmaster@uconn.edu Paul Lewis].<br />
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=== What can the EEB Webmaster do for me? ===<br />
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The EEB Webmaster's duties include:<br />
* maintaining the web server (both hardward and software)<br />
* backing up the web content daily<br />
* creating accounts and providing edit access to EEBedia<br />
* creating and maintaining software for editing course, event and people information<br />
* maintaining and creating department-wide content, such as the flash display on the EEB home page<br />
* helping with problems involving access to the web server<br />
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The EEB Webmaster's duties do not, however, include helping you write web pages. You must create your own content, either as a traditional HTML web page or using EEBedia.<br />
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=== How do I change my password on hydrodictyon? ===<br />
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Use the [https://hydrodictyon.eeb.uconn.edu/password.php web form] to create your first password, or change your password. <br />
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'''<span style="color: red">Important!</span>''' If an account has '''just been created''' for you, or if your password has '''just been reset''' by the [[EEB Webmaster]], you should '''leave the field labeled ''Old password'' blank'''. <br />
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== The EEB home page ==<br />
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=== How do I get an image into the Flash display on the home page? ===<br />
Send the [mailto:eebwebmaster@uconn.edu webmaster] these three things:<br />
# A landscape-style image (e.g. jpeg format) at least 500 pixels wide and 350 pixels tall<br />
# An appropriate caption about 10 words long<br />
# The URL of an existing web page that can be linked to the image<br />
Keep in mind that the caption inside the purple rectangle will obscure part of the image, so try to compose your photo so that important parts are not hidden by the caption.<br />
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=== Why do I sometimes not see a particular image in the Flash presentation when I view the home page? ===<br />
To keep the file size of the Flash presentation low enough so that there is no noticeable delay when the home page is loaded, photos are grouped into casettes of about 4-5 images. The casette that will be shown is chosen randomly when the home page is loaded. If you want to see other casettes, simply refresh your browser to load another randomly-chosen group of photos.<br />
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[[#top|Back to top]]<br />
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== Transferring files ==<br />
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Hydrodictyon does not support FTP for security reasons (the old FTP protocol sends passwords across the network in plain text), but it does allow file transfers via the Secure Shell protocol (Secure FTP, or SFTP for short) or Samba-mediated Windows network shares. What means you use to move files back and forth depends on what operating system you use.<br />
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=== Mac users ===<br />
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If you use a MacIntosh running Mac OS 10.x, Fugu is probably the easiest means of transferring files back and forth from your own computer to hydrodictyon.<br />
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==== Fugu for MacOS 10.x ====<br />
[http://rsug.itd.umich.edu/software/fugu/ Fugu] provides a free secure file transfer solution for MacIntosh computers running MacOS X. Fugu is only for transferring files. It will not help you create or edit web pages. <br />
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==== How do I connect to the web server using Fugu? ====<br />
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To set up file transfer using Fugu (I'm using version 1.1), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
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# In the Connect to field, enter hydrodictyon.eeb.uconn.edu<br />
# In the Username field, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# In the Port field, enter 22 (this is the standard Secure Shell, or SSH, port)<br />
# Click the Add to Favorites button to make it easier to connect to hydrodictyon the next time<br />
# Click the Connect button to login to hydrodictyon. If you have never connected to hydrodictyon before, you will see a warning stating "The authenticity of host 'hydrodictyon.eeb.uconn.edu (137.99.88.31)' can't be established. Unable to get host key. Something is odd. Are you sure you want to continue connecting? " You can ignore this warning (the first time you see it, at least) and just press the Continue button.<br />
# You should now be asked for a password. Here is where Dr. Bunsen Honeydew would type his password, beaker (your password should be more secure than his!). After entering your password, click the button Authenticate.<br />
# At this point, you should see an alias (shortcut) named html in the righthand window labeled "hydrodictyon.eeb.uconn.edu". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, click the Disconnect button on the menu bar at the top<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Why does Fugu say <tt>@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @</tt>? ====<br />
<br />
You will get this warning whenever the machine serving as hydrodictyon is changed, which will happen once or twice per year. Fugu's warning is designed to make you think twice about connecting to hydrodictyon because the identity of hydrodictyon has changed. To stop this warning, choose Fugu &gt; Preferences... from the main menu, then click the Known Hosts tab. You should see an entry that looks like this<pre>hydrodictyon.eeb.uconn.edu.137.99.88.31</pre> Select this entry, then press the Delete button, and finally press the Save button before closing the Preferences dialog box. Now when you attempt to connect to hydrodictyon, it will present a different warning (''The authenticity of host...Something is odd. Are you sure you want to continue connecting?''), but it will at least let you continue connecting if you press the Continue button. Your Fugu client will now download a new host key from hydrodictyon, which it will use each time you connect to verify that you are indeed connecting to hydrodictyon (at least until hydrodictyon is changed again!).<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows users ===<br />
<br />
If you use Windows, you will probably want to use either Samba (if on campus) or FileZilla/CyberDuck (from off campus) to move files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Using Samba ====<br />
<br />
Hydrodictyon runs [http://www.samba.org/ Samba], which makes it possible for a Windows user to mount their home directory on hydrodictyon as if it were a network share on a Windows machine. Each person given an account on hydrodictyon is automatically set up to use this method, but be aware that UConn prevents the use of Windows file sharing from off-campus sites unless you log into the [http://security.uconn.edu/guides/vpn.html VPN (Virtual Private Network)]. <br />
<br />
To mount your home directory on hydrodictyon as (for example) drive Z: on your Windows XP machine, follow these steps (I will use the user name <nowiki>userid</nowiki> here, but you should of course '''substitute your own user name''' wherever <nowiki>userid</nowiki> appears):<br />
<br />
# Open My Computer<br />
# Choose Tools from the main menu, then Map Network Drive... <br />
# Choose Z: (or some other letter) as Drive<br />
# Specify <nowiki>\\hydrodictyon\userid</nowiki> for Folder (remember to replace <nowiki>plewis</nowiki> with your own user name (given to you when your account on hydrodictyon was created)<br />
# Check Reconnect at logon if you want your Windows machine to try to map this drive every time you start it up<br />
# Press the Finish button<br />
# In the dialog box that appears, type <nowiki>hydrodictyon\userid</nowiki> for the user name (note: no leading double backslash this time) and enter your password.<br />
# If all goes well, you should be able to access files on hydrodictyon using drive Z: on your Windows PC. If things don't go well, please feel free to ask for help from the [mailto:eebwebmaster@uconn.edu EEB Webmaster]<br />
<br />
Another approach is to simply open your Start menu, choose Run..., and type <nowiki>\\hydrodictyon\userid</nowiki> into the edit box labeled Open. You can also set up a network neighborhood shortcut to hydrodictyon. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== FileZilla for Windows ====<br />
<br />
[http://filezilla.sourceforge.net/ FileZilla] provides a free secure file transfer solution for Windows computers. FileZilla is a bit bewildering at first, but it is free. It is only for transferring files. It will not help you create or edit web pages. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#filezilla_setup "How do I connect to the web server using FileZilla?"] for help in setting up FileZilla.<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Cyberduck for Windows ====<br />
<br />
[http://cyberduck.ch/ Cyberduck] provides a free secure file transfer solution for Windows computers. Information about connecting to hydrodictyon using Cyberduck is forthcoming...<br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using FileZilla? ====<br />
<br />
To set up file transfer using FileZilla (I'm using version 2.2.18), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# Choose File, Site Manager... from the main menu (or press Ctrl-S)<br />
# Click the New Site button. You can change the name of the site now from "New FTP site" to something more appropriate, such as "Hydrodictyon" or "EEB Web Server "<br />
# For Host, enter hydrodictyon.eeb.uconn.edu<br />
# For Port, enter 22 (FileZilla defaults to using the old, insecure FTP port 21, but hydodictyon will not grant you an audience if you arrive at port 21; you want to dock at the Secure Shell SSH port 22 instead)<br />
# For Servertype, enter SFTP using SSH2<br />
# For Logontype, click Normal<br />
# For User, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# For Password, enter beaker (your password should be more secure than this one!)<br />
# I would prefer that you check Don't save password, but I know better than to ask<br />
# Now press the Connect button. If you have never connected to hydrodictyon before, you will see a warning starting "The server's host key is not cached in the registry." You can ignore this warning and just press the Yes button.<br />
# At this point, you should see an alias (shortcut) named html in the window labeled "Remote Site". If you don't, write to [mailto:paul.lewis@uconn.edu me]. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local Site window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, choose File, Disconnect from the main menu (or use the key combination Ctrl-D)<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows or Mac users ===<br />
<br />
==== Dreamweaver ====<br />
The [http://www.adobe.com/products/dreamweaver/ Adobe (formerly Macromedia) Dreamweaver] software is installed on many of the [http://hydrodictyon.eeb.uconn.edu/department/computerroom/installed%20software.pdf computers] in the McCarthy room computer lab. Dreamweaver allows you to edit web pages and upload them at any time to the web server with the click of a button. It is available for Windows or MacIntosh computers. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#dreamweaver_setup "How do I connect to the web server using Dreamweaver"] for help setting up Dreamweaver. You can also purchase Dreamweaver 8 from the Co-op. Note: do not just go to the Co-op and buy it off the shelf; you will pay way too much this way! Take a BO46 form (see Stephanie Balough in the Bio Central Services) to the bookstore after figuring out the price at the UConn Co-op's [http://www.bookstore.uconn.edu/howto.html Adobe and Macromedia Licensing] web page. As of this writing (30-Aug-2006), the Dreamweaver 8 software itself costs $100, with a media fee of $7.95.<br />
<br />
==== How do I connect to the web server using Dreamweaver? ====<br />
<br />
To set up file transfer using Dreamweaver MX 2004, follow the steps below:<br />
<br />
# Click Start, then navigate to Dreamweaver 2004 (you might need to go through a link named Macromedia to get there) to start Dreamweaver<br />
# If you have never used Dreamweaver before, you will be asked to choose which workspace setup you want (just choose one or the other).<br />
# Once the program is started, choose Site (from the main menu at the top), then Manage Sites...<br />
# Click the New... button, then choose Site, and finally click the Advanced tab (you will end up providing the same information whether you choose Basic or Advanced, but Advanced is faster given that you have these instructions)<br />
# For category (see left side) Local Info:<br />
#* For Site name, just make something up (e.g. mysite)<br />
#* For Local root folder, choose the folder where your web site files will be stored on the computer you are now sitting at. In my case, I chose \\dentata\faculty\plewis\My Documents\mysite\. The \\dentata part means that my files are actually stored on the server named dentata, which manages the new EEB domain. (Your folder path may start with \\matrix if you are still in the older EEB-NET domain, which is managed by the file server named matrix.)<br />
#* For HTTP address, I entered http://hydrodictyon.eeb.uconn.edu/people/plewis/. You should enter the same thing, except change the final plewis part to your own login name. If you do not yet have an account on hydrodictyon, you will need to send an email request to the EEB Webmaster to get one.<br />
# For category Remote Info:<br />
#* For Access, enter FTP<br />
#* For FTP Host, enter hydrodictyon.eeb.uconn.edu<br />
#* For Host directory, I entered /var/www/html/people/plewis/, but you would of course replace the plewis with the user name you use to login to hydrodictyon<br />
#* Now skip ahead and check the box beside Use Secure FTP (SFTP)<br />
#* Fill in your user name and password (these were assigned when you obtained your hydrodictyon account from the EEB Webmaster) and press the Test button. You may get a Windows Security Alert popping up. I was able to dismiss this, but if this turns out to be an insurmountable roadblock, please contact the computer room administrator to help you punch a hole in the firewall. Dreamweaver should indicate that it was able to log in to your site successfully. The EEB webmaster can help if something goes wrong at this point.<br />
# The defaults should work well for the remaining options. Once you close the dialog box, you can view your files on hydrodictyon by choosing Remote view in the Files window (if the Files window is not obvious, hit the F8 button to open it). Choosing Local view lets you see the files currently on your local computer. The up and down arrow buttons in the Files window allow you to upload selected files to (or download selected files from) hydrodictyon.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Miscellany ==<br />
<br />
==== How do I create a web page that will redirect users to my new site? ====<br />
<br />
Here is how to create a very basic redirect page using an HTML meta tag. This assumes your name is Jonathan and your new web site URL is <nowiki>http://www.uconn.edu/</nowiki>. Just create a file named <tt>index.html</tt> in your old web folder (and remove all other files), then add the following text to <tt>index.html</tt><pre><br />
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><br />
<html><br />
<head><br />
<title>Redirecting to Jonathan's new home page</title><br />
<META http-equiv="refresh" content="5;URL=http://www.uconn.edu/"><br />
</head><br />
<body><br />
<center><br />
You will be redirected to Jonathan's new home page automatically in 5 seconds.<br/> <br />
Please update any bookmarks to point to the new address, which is<br/><br />
<a href="http://www.uconn.edu/">http://www.uconn.edu/</a><br />
</center><br />
</body><br />
</html> <br />
</pre><br />
<br />
[[#top|Back to top]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Web_site_FAQ&diff=19726Web site FAQ2011-11-11T21:40:14Z<p>PaulLewis: /* How do I connect to the web server using FileZilla? */</p>
<hr />
<div>This page contains frequently asked questions (and answers!) about the EEB department's web server.<br />
<br />
== The web server (hydrodictyon) ==<br />
<br />
=== What is hydrodictyon? ===<br />
<br />
Hydrodictyon is the name of the computer that serves up all the web pages that together constitute the [http://hydrodictyon.eeb.uconn.edu/ EEB web site]. The term ''web server'' can refer to either the ''software'' that serves web pages ([http://httpd.apache.org/ Apache] in our case) or the computer that runs that software (a Dell Optiplex 755 in our case). Hydrodictyon runs the [http://fedoraproject.org/ Red Hat Fedora 9] Linux operating system.<br />
<br />
=== Do I need an account on hydrodictyon? ===<br />
<br />
You need an account on hydrodictyon if you want to create a traditional HTML-based web page for yourself or a course. Many find it much easier to create and maintain web pages using EEBedia than the traditional approach. This FAQ page, for example, was created in EEBedia. If you would like to try using EEBedia, click on the [[Help:Contents|Help]] link to your left to get started.<br />
<br />
=== How do I get an account on hydrodictyon? ===<br />
<br />
Just send an email request to the [mailto:eebwebmaster@uconn.edu EEB Webmaster]. Ordinarily, you must be a current member of the EEB department to obtain an account, but exceptions will be made under some circumstances.<br />
<br />
=== What is the difference between my home directory and my web folder on hydrodictyon? ===<br />
<br />
When your account is created, you automatically get a '''home directory'''. Your home directory is located within the <tt>/home</tt> directory on hydrodictyon. (For those unfamiliar with Linux, the root of the file system is "/", which is akin to "C:/" in Windows, so <tt>/home</tt> is one level up from the root of the file system.) Items you upload or create in your home directory will not be visible on the internet. Inside your home directory, you should find an an item named "html". While "html" looks and acts like a directory, it is actually an alias (or symbolic link, in Linux terminology) to a completely separate directory on the hard drive, your '''web folder'''. For example, my (Paul Lewis) home directory is <tt>/home/plewis</tt>, whereas my web folder is <tt>/var/www/html/people/plewis</tt>. Items placed in your web folder will be immediately visible on the internet at an address (URL) that looks like this:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
or, equivalently, <br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
Note that you should replace the "yourusername" part of the URL with your own username. <br />
<br />
The "html" alias makes it easy for you to transfer files to your web folder. No matter how you connect to hydrodictyon, you will be dumped first in your home directory, where you should see the "html" alias staring you in the face. Just double-click that alias and you will be transported across the hard drive to your web folder.<br />
<br />
Before you begin uploading files, read the next section entitled "Why you should name your home page index.html"<br />
<br />
=== Why you should name your home page index.html ===<br />
<br />
Suppose you name your home page <tt>MyHomePage.html</tt>. In order for someone to see your homepage, they must know the exact name of your home page file and append it to your base URL, as follows:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/MyHomePage.html<br />
If someone does not know the name of the file serving as your home page, they may try typing this URL into their browser instead:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
[[Image:Dirlisting.png|thumb|right]]If they were to do that, they would not see your home page. Instead, they would see a directory listing like the one shown on the right (click the thumbnail image to see the full size image if you want). Now they have to wade through all your web files and try to figure out which one is your home page. In the meantime, they might happen on some files you didn't plan on anyone viewing (e.g. <tt>junk_I_home_noone_ever_sees.html</tt>), perhaps because they represent works in progress or obsolete content that you just can't bring yourself to delete.<br />
<br />
If you name your home page index.html, however, then users will always get your home page when they enter your base URL, i.e.<br />
<nowiki>http://hydrodictyon.eeb.uconn.edu/people/yourusername/</nowiki><br />
and they will never get an index showing all your files. This gives you a lot of control over what people see: they can only see the files you have linked to your home page or to other pages linked to your home page. It also gives you control over what will appear in searches conducted on Google (and other search sites) because the webbots used by the search engines also cannot get a listing of all your files.<br />
<br />
=== Who is the EEB Webmaster? ===<br />
<br />
The current EEB webmaster is [mailto:eebwebmaster@uconn.edu Paul Lewis].<br />
<br />
=== What can the EEB Webmaster do for me? ===<br />
<br />
The EEB Webmaster's duties include:<br />
* maintaining the web server (both hardward and software)<br />
* backing up the web content daily<br />
* creating accounts and providing edit access to EEBedia<br />
* creating and maintaining software for editing course, event and people information<br />
* maintaining and creating department-wide content, such as the flash display on the EEB home page<br />
* helping with problems involving access to the web server<br />
<br />
The EEB Webmaster's duties do not, however, include helping you write web pages. You must create your own content, either as a traditional HTML web page or using EEBedia.<br />
<br />
=== How do I change my password on hydrodictyon? ===<br />
<br />
Use the [https://hydrodictyon.eeb.uconn.edu/password.php web form] to create your first password, or change your password. <br />
<br />
'''<span style="color: red">Important!</span>''' If an account has '''just been created''' for you, or if your password has '''just been reset''' by the [[EEB Webmaster]], you should '''leave the field labeled ''Old password'' blank'''. <br />
<br />
[[#top|Back to top]]<br />
<br />
== The EEB home page ==<br />
<br />
=== How do I get an image into the Flash display on the home page? ===<br />
Send the [mailto:eebwebmaster@uconn.edu webmaster] these three things:<br />
# A landscape-style image (e.g. jpeg format) at least 500 pixels wide and 350 pixels tall<br />
# An appropriate caption about 10 words long<br />
# The URL of an existing web page that can be linked to the image<br />
Keep in mind that the caption inside the purple rectangle will obscure part of the image, so try to compose your photo so that important parts are not hidden by the caption.<br />
<br />
=== Why do I sometimes not see a particular image in the Flash presentation when I view the home page? ===<br />
To keep the file size of the Flash presentation low enough so that there is no noticeable delay when the home page is loaded, photos are grouped into casettes of about 4-5 images. The casette that will be shown is chosen randomly when the home page is loaded. If you want to see other casettes, simply refresh your browser to load another randomly-chosen group of photos.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Transferring files ==<br />
<br />
Hydrodictyon does not support FTP for security reasons (the old FTP protocol sends passwords across the network in plain text), but it does allow file transfers via the Secure Shell protocol (Secure FTP, or SFTP for short) or Samba-mediated Windows network shares. What means you use to move files back and forth depends on what operating system you use.<br />
<br />
=== Mac users ===<br />
<br />
If you use a MacIntosh running Mac OS 10.x, Fugu is probably the easiest means of transferring files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Fugu for MacOS 10.x ====<br />
[http://rsug.itd.umich.edu/software/fugu/ Fugu] provides a free secure file transfer solution for MacIntosh computers running MacOS X. Fugu is only for transferring files. It will not help you create or edit web pages. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using Fugu? ====<br />
<br />
To set up file transfer using Fugu (I'm using version 1.1), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# In the Connect to field, enter hydrodictyon.eeb.uconn.edu<br />
# In the Username field, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# In the Port field, enter 22 (this is the standard Secure Shell, or SSH, port)<br />
# Click the Add to Favorites button to make it easier to connect to hydrodictyon the next time<br />
# Click the Connect button to login to hydrodictyon. If you have never connected to hydrodictyon before, you will see a warning stating "The authenticity of host 'hydrodictyon.eeb.uconn.edu (137.99.88.31)' can't be established. Unable to get host key. Something is odd. Are you sure you want to continue connecting? " You can ignore this warning (the first time you see it, at least) and just press the Continue button.<br />
# You should now be asked for a password. Here is where Dr. Bunsen Honeydew would type his password, beaker (your password should be more secure than his!). After entering your password, click the button Authenticate.<br />
# At this point, you should see an alias (shortcut) named html in the righthand window labeled "hydrodictyon.eeb.uconn.edu". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, click the Disconnect button on the menu bar at the top<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Why does Fugu say <tt>@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @</tt>? ====<br />
<br />
You will get this warning whenever the machine serving as hydrodictyon is changed, which will happen once or twice per year. Fugu's warning is designed to make you think twice about connecting to hydrodictyon because the identity of hydrodictyon has changed. To stop this warning, choose Fugu &gt; Preferences... from the main menu, then click the Known Hosts tab. You should see an entry that looks like this<pre>hydrodictyon.eeb.uconn.edu.137.99.88.31</pre> Select this entry, then press the Delete button, and finally press the Save button before closing the Preferences dialog box. Now when you attempt to connect to hydrodictyon, it will present a different warning (''The authenticity of host...Something is odd. Are you sure you want to continue connecting?''), but it will at least let you continue connecting if you press the Continue button. Your Fugu client will now download a new host key from hydrodictyon, which it will use each time you connect to verify that you are indeed connecting to hydrodictyon (at least until hydrodictyon is changed again!).<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows users ===<br />
<br />
If you use Windows, you will probably want to use either Samba (if on campus) or FileZilla/CyberDuck (from off campus) to move files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Using Samba ====<br />
<br />
Hydrodictyon runs [http://www.samba.org/ Samba], which makes it possible for a Windows user to mount their home directory on hydrodictyon as if it were a network share on a Windows machine. Each person given an account on hydrodictyon is automatically set up to use this method, but be aware that UConn prevents the use of Windows file sharing from off-campus sites unless you log into the [http://security.uconn.edu/guides/vpn.html VPN (Virtual Private Network)]. <br />
<br />
To mount your home directory on hydrodictyon as (for example) drive Z: on your Windows XP machine, follow these steps (I will use the user name <nowiki>userid</nowiki> here, but you should of course '''substitute your own user name''' wherever <nowiki>userid</nowiki> appears):<br />
<br />
# Open My Computer<br />
# Choose Tools from the main menu, then Map Network Drive... <br />
# Choose Z: (or some other letter) as Drive<br />
# Specify <nowiki>\\hydrodictyon\userid</nowiki> for Folder (remember to replace <nowiki>plewis</nowiki> with your own user name (given to you when your account on hydrodictyon was created)<br />
# Check Reconnect at logon if you want your Windows machine to try to map this drive every time you start it up<br />
# Press the Finish button<br />
# In the dialog box that appears, type <nowiki>hydrodictyon\userid</nowiki> for the user name (note: no leading double backslash this time) and enter your password.<br />
# If all goes well, you should be able to access files on hydrodictyon using drive Z: on your Windows PC. If things don't go well, please feel free to ask for help from the [mailto:eebwebmaster@uconn.edu EEB Webmaster]<br />
<br />
Another approach is to simply open your Start menu, choose Run..., and type <nowiki>\\hydrodictyon\userid</nowiki> into the edit box labeled Open. You can also set up a network neighborhood shortcut to hydrodictyon. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== FileZilla for Windows ====<br />
<br />
[http://filezilla.sourceforge.net/ FileZilla] provides a free secure file transfer solution for Windows computers. FileZilla is a bit bewildering at first, but it is free. It is only for transferring files. It will not help you create or edit web pages. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#filezilla_setup "How do I connect to the web server using FileZilla?"] for help in setting up FileZilla.<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Cyberduck for Windows ====<br />
<br />
[http://cyberduck.ch/ Cyberduck] provides a free secure file transfer solution for Windows computers. Information about connecting to hydrodictyon using Cyberduck is forthcoming...<br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using FileZilla? ====<br />
<br />
To set up file transfer using FileZilla (I'm using version 2.2.18), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# Choose File, Site Manager... from the main menu (or press Ctrl-S)<br />
# Click the New Site button. You can change the name of the site now from "New FTP site" to something more appropriate, such as "Hydrodictyon" or "EEB Web Server "<br />
# For Host, enter hydrodictyon.eeb.uconn.edu<br />
# For Port, enter 22 (FileZilla defaults to using the old, insecure FTP port 21, but hydodictyon will not grant you an audience if you arrive at port 21; you want to dock at the Secure Shell SSH port 22 instead)<br />
# For Servertype, enter SFTP using SSH2<br />
# For Logontype, click Normal<br />
# For User, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# For Password, enter beaker (your password should be more secure than this one!)<br />
# I would prefer that you check Don't save password, but I know better than to ask<br />
# Now press the Connect button. If you have never connected to hydrodictyon before, you will see a warning starting "The server's host key is not cached in the registry." You can ignore this warning and just press the Yes button.<br />
# At this point, you should see an alias (shortcut) named html in the window labeled "Remote Site". If you don't, write to [http://mailto:paul.lewis@uconn.edu me]. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local Site window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, choose File, Disconnect from the main menu (or use the key combination Ctrl-D)<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows or Mac users ===<br />
<br />
==== Dreamweaver ====<br />
The [http://www.adobe.com/products/dreamweaver/ Adobe (formerly Macromedia) Dreamweaver] software is installed on many of the [http://hydrodictyon.eeb.uconn.edu/department/computerroom/installed%20software.pdf computers] in the McCarthy room computer lab. Dreamweaver allows you to edit web pages and upload them at any time to the web server with the click of a button. It is available for Windows or MacIntosh computers. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#dreamweaver_setup "How do I connect to the web server using Dreamweaver"] for help setting up Dreamweaver. You can also purchase Dreamweaver 8 from the Co-op. Note: do not just go to the Co-op and buy it off the shelf; you will pay way too much this way! Take a BO46 form (see Stephanie Balough in the Bio Central Services) to the bookstore after figuring out the price at the UConn Co-op's [http://www.bookstore.uconn.edu/howto.html Adobe and Macromedia Licensing] web page. As of this writing (30-Aug-2006), the Dreamweaver 8 software itself costs $100, with a media fee of $7.95.<br />
<br />
==== How do I connect to the web server using Dreamweaver? ====<br />
<br />
To set up file transfer using Dreamweaver MX 2004, follow the steps below:<br />
<br />
# Click Start, then navigate to Dreamweaver 2004 (you might need to go through a link named Macromedia to get there) to start Dreamweaver<br />
# If you have never used Dreamweaver before, you will be asked to choose which workspace setup you want (just choose one or the other).<br />
# Once the program is started, choose Site (from the main menu at the top), then Manage Sites...<br />
# Click the New... button, then choose Site, and finally click the Advanced tab (you will end up providing the same information whether you choose Basic or Advanced, but Advanced is faster given that you have these instructions)<br />
# For category (see left side) Local Info:<br />
#* For Site name, just make something up (e.g. mysite)<br />
#* For Local root folder, choose the folder where your web site files will be stored on the computer you are now sitting at. In my case, I chose \\dentata\faculty\plewis\My Documents\mysite\. The \\dentata part means that my files are actually stored on the server named dentata, which manages the new EEB domain. (Your folder path may start with \\matrix if you are still in the older EEB-NET domain, which is managed by the file server named matrix.)<br />
#* For HTTP address, I entered http://hydrodictyon.eeb.uconn.edu/people/plewis/. You should enter the same thing, except change the final plewis part to your own login name. If you do not yet have an account on hydrodictyon, you will need to send an email request to the EEB Webmaster to get one.<br />
# For category Remote Info:<br />
#* For Access, enter FTP<br />
#* For FTP Host, enter hydrodictyon.eeb.uconn.edu<br />
#* For Host directory, I entered /var/www/html/people/plewis/, but you would of course replace the plewis with the user name you use to login to hydrodictyon<br />
#* Now skip ahead and check the box beside Use Secure FTP (SFTP)<br />
#* Fill in your user name and password (these were assigned when you obtained your hydrodictyon account from the EEB Webmaster) and press the Test button. You may get a Windows Security Alert popping up. I was able to dismiss this, but if this turns out to be an insurmountable roadblock, please contact the computer room administrator to help you punch a hole in the firewall. Dreamweaver should indicate that it was able to log in to your site successfully. The EEB webmaster can help if something goes wrong at this point.<br />
# The defaults should work well for the remaining options. Once you close the dialog box, you can view your files on hydrodictyon by choosing Remote view in the Files window (if the Files window is not obvious, hit the F8 button to open it). Choosing Local view lets you see the files currently on your local computer. The up and down arrow buttons in the Files window allow you to upload selected files to (or download selected files from) hydrodictyon.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Miscellany ==<br />
<br />
==== How do I create a web page that will redirect users to my new site? ====<br />
<br />
Here is how to create a very basic redirect page using an HTML meta tag. This assumes your name is Jonathan and your new web site URL is <nowiki>http://www.uconn.edu/</nowiki>. Just create a file named <tt>index.html</tt> in your old web folder (and remove all other files), then add the following text to <tt>index.html</tt><pre><br />
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><br />
<html><br />
<head><br />
<title>Redirecting to Jonathan's new home page</title><br />
<META http-equiv="refresh" content="5;URL=http://www.uconn.edu/"><br />
</head><br />
<body><br />
<center><br />
You will be redirected to Jonathan's new home page automatically in 5 seconds.<br/> <br />
Please update any bookmarks to point to the new address, which is<br/><br />
<a href="http://www.uconn.edu/">http://www.uconn.edu/</a><br />
</center><br />
</body><br />
</html> <br />
</pre><br />
<br />
[[#top|Back to top]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Web_site_FAQ&diff=19725Web site FAQ2011-11-11T21:38:59Z<p>PaulLewis: /* Cyberduck for Windows */</p>
<hr />
<div>This page contains frequently asked questions (and answers!) about the EEB department's web server.<br />
<br />
== The web server (hydrodictyon) ==<br />
<br />
=== What is hydrodictyon? ===<br />
<br />
Hydrodictyon is the name of the computer that serves up all the web pages that together constitute the [http://hydrodictyon.eeb.uconn.edu/ EEB web site]. The term ''web server'' can refer to either the ''software'' that serves web pages ([http://httpd.apache.org/ Apache] in our case) or the computer that runs that software (a Dell Optiplex 755 in our case). Hydrodictyon runs the [http://fedoraproject.org/ Red Hat Fedora 9] Linux operating system.<br />
<br />
=== Do I need an account on hydrodictyon? ===<br />
<br />
You need an account on hydrodictyon if you want to create a traditional HTML-based web page for yourself or a course. Many find it much easier to create and maintain web pages using EEBedia than the traditional approach. This FAQ page, for example, was created in EEBedia. If you would like to try using EEBedia, click on the [[Help:Contents|Help]] link to your left to get started.<br />
<br />
=== How do I get an account on hydrodictyon? ===<br />
<br />
Just send an email request to the [mailto:eebwebmaster@uconn.edu EEB Webmaster]. Ordinarily, you must be a current member of the EEB department to obtain an account, but exceptions will be made under some circumstances.<br />
<br />
=== What is the difference between my home directory and my web folder on hydrodictyon? ===<br />
<br />
When your account is created, you automatically get a '''home directory'''. Your home directory is located within the <tt>/home</tt> directory on hydrodictyon. (For those unfamiliar with Linux, the root of the file system is "/", which is akin to "C:/" in Windows, so <tt>/home</tt> is one level up from the root of the file system.) Items you upload or create in your home directory will not be visible on the internet. Inside your home directory, you should find an an item named "html". While "html" looks and acts like a directory, it is actually an alias (or symbolic link, in Linux terminology) to a completely separate directory on the hard drive, your '''web folder'''. For example, my (Paul Lewis) home directory is <tt>/home/plewis</tt>, whereas my web folder is <tt>/var/www/html/people/plewis</tt>. Items placed in your web folder will be immediately visible on the internet at an address (URL) that looks like this:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
or, equivalently, <br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
Note that you should replace the "yourusername" part of the URL with your own username. <br />
<br />
The "html" alias makes it easy for you to transfer files to your web folder. No matter how you connect to hydrodictyon, you will be dumped first in your home directory, where you should see the "html" alias staring you in the face. Just double-click that alias and you will be transported across the hard drive to your web folder.<br />
<br />
Before you begin uploading files, read the next section entitled "Why you should name your home page index.html"<br />
<br />
=== Why you should name your home page index.html ===<br />
<br />
Suppose you name your home page <tt>MyHomePage.html</tt>. In order for someone to see your homepage, they must know the exact name of your home page file and append it to your base URL, as follows:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/MyHomePage.html<br />
If someone does not know the name of the file serving as your home page, they may try typing this URL into their browser instead:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
[[Image:Dirlisting.png|thumb|right]]If they were to do that, they would not see your home page. Instead, they would see a directory listing like the one shown on the right (click the thumbnail image to see the full size image if you want). Now they have to wade through all your web files and try to figure out which one is your home page. In the meantime, they might happen on some files you didn't plan on anyone viewing (e.g. <tt>junk_I_home_noone_ever_sees.html</tt>), perhaps because they represent works in progress or obsolete content that you just can't bring yourself to delete.<br />
<br />
If you name your home page index.html, however, then users will always get your home page when they enter your base URL, i.e.<br />
<nowiki>http://hydrodictyon.eeb.uconn.edu/people/yourusername/</nowiki><br />
and they will never get an index showing all your files. This gives you a lot of control over what people see: they can only see the files you have linked to your home page or to other pages linked to your home page. It also gives you control over what will appear in searches conducted on Google (and other search sites) because the webbots used by the search engines also cannot get a listing of all your files.<br />
<br />
=== Who is the EEB Webmaster? ===<br />
<br />
The current EEB webmaster is [mailto:eebwebmaster@uconn.edu Paul Lewis].<br />
<br />
=== What can the EEB Webmaster do for me? ===<br />
<br />
The EEB Webmaster's duties include:<br />
* maintaining the web server (both hardward and software)<br />
* backing up the web content daily<br />
* creating accounts and providing edit access to EEBedia<br />
* creating and maintaining software for editing course, event and people information<br />
* maintaining and creating department-wide content, such as the flash display on the EEB home page<br />
* helping with problems involving access to the web server<br />
<br />
The EEB Webmaster's duties do not, however, include helping you write web pages. You must create your own content, either as a traditional HTML web page or using EEBedia.<br />
<br />
=== How do I change my password on hydrodictyon? ===<br />
<br />
Use the [https://hydrodictyon.eeb.uconn.edu/password.php web form] to create your first password, or change your password. <br />
<br />
'''<span style="color: red">Important!</span>''' If an account has '''just been created''' for you, or if your password has '''just been reset''' by the [[EEB Webmaster]], you should '''leave the field labeled ''Old password'' blank'''. <br />
<br />
[[#top|Back to top]]<br />
<br />
== The EEB home page ==<br />
<br />
=== How do I get an image into the Flash display on the home page? ===<br />
Send the [mailto:eebwebmaster@uconn.edu webmaster] these three things:<br />
# A landscape-style image (e.g. jpeg format) at least 500 pixels wide and 350 pixels tall<br />
# An appropriate caption about 10 words long<br />
# The URL of an existing web page that can be linked to the image<br />
Keep in mind that the caption inside the purple rectangle will obscure part of the image, so try to compose your photo so that important parts are not hidden by the caption.<br />
<br />
=== Why do I sometimes not see a particular image in the Flash presentation when I view the home page? ===<br />
To keep the file size of the Flash presentation low enough so that there is no noticeable delay when the home page is loaded, photos are grouped into casettes of about 4-5 images. The casette that will be shown is chosen randomly when the home page is loaded. If you want to see other casettes, simply refresh your browser to load another randomly-chosen group of photos.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Transferring files ==<br />
<br />
Hydrodictyon does not support FTP for security reasons (the old FTP protocol sends passwords across the network in plain text), but it does allow file transfers via the Secure Shell protocol (Secure FTP, or SFTP for short) or Samba-mediated Windows network shares. What means you use to move files back and forth depends on what operating system you use.<br />
<br />
=== Mac users ===<br />
<br />
If you use a MacIntosh running Mac OS 10.x, Fugu is probably the easiest means of transferring files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Fugu for MacOS 10.x ====<br />
[http://rsug.itd.umich.edu/software/fugu/ Fugu] provides a free secure file transfer solution for MacIntosh computers running MacOS X. Fugu is only for transferring files. It will not help you create or edit web pages. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using Fugu? ====<br />
<br />
To set up file transfer using Fugu (I'm using version 1.1), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# In the Connect to field, enter hydrodictyon.eeb.uconn.edu<br />
# In the Username field, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# In the Port field, enter 22 (this is the standard Secure Shell, or SSH, port)<br />
# Click the Add to Favorites button to make it easier to connect to hydrodictyon the next time<br />
# Click the Connect button to login to hydrodictyon. If you have never connected to hydrodictyon before, you will see a warning stating "The authenticity of host 'hydrodictyon.eeb.uconn.edu (137.99.88.31)' can't be established. Unable to get host key. Something is odd. Are you sure you want to continue connecting? " You can ignore this warning (the first time you see it, at least) and just press the Continue button.<br />
# You should now be asked for a password. Here is where Dr. Bunsen Honeydew would type his password, beaker (your password should be more secure than his!). After entering your password, click the button Authenticate.<br />
# At this point, you should see an alias (shortcut) named html in the righthand window labeled "hydrodictyon.eeb.uconn.edu". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, click the Disconnect button on the menu bar at the top<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Why does Fugu say <tt>@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @</tt>? ====<br />
<br />
You will get this warning whenever the machine serving as hydrodictyon is changed, which will happen once or twice per year. Fugu's warning is designed to make you think twice about connecting to hydrodictyon because the identity of hydrodictyon has changed. To stop this warning, choose Fugu &gt; Preferences... from the main menu, then click the Known Hosts tab. You should see an entry that looks like this<pre>hydrodictyon.eeb.uconn.edu.137.99.88.31</pre> Select this entry, then press the Delete button, and finally press the Save button before closing the Preferences dialog box. Now when you attempt to connect to hydrodictyon, it will present a different warning (''The authenticity of host...Something is odd. Are you sure you want to continue connecting?''), but it will at least let you continue connecting if you press the Continue button. Your Fugu client will now download a new host key from hydrodictyon, which it will use each time you connect to verify that you are indeed connecting to hydrodictyon (at least until hydrodictyon is changed again!).<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows users ===<br />
<br />
If you use Windows, you will probably want to use either Samba (if on campus) or FileZilla/CyberDuck (from off campus) to move files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Using Samba ====<br />
<br />
Hydrodictyon runs [http://www.samba.org/ Samba], which makes it possible for a Windows user to mount their home directory on hydrodictyon as if it were a network share on a Windows machine. Each person given an account on hydrodictyon is automatically set up to use this method, but be aware that UConn prevents the use of Windows file sharing from off-campus sites unless you log into the [http://security.uconn.edu/guides/vpn.html VPN (Virtual Private Network)]. <br />
<br />
To mount your home directory on hydrodictyon as (for example) drive Z: on your Windows XP machine, follow these steps (I will use the user name <nowiki>userid</nowiki> here, but you should of course '''substitute your own user name''' wherever <nowiki>userid</nowiki> appears):<br />
<br />
# Open My Computer<br />
# Choose Tools from the main menu, then Map Network Drive... <br />
# Choose Z: (or some other letter) as Drive<br />
# Specify <nowiki>\\hydrodictyon\userid</nowiki> for Folder (remember to replace <nowiki>plewis</nowiki> with your own user name (given to you when your account on hydrodictyon was created)<br />
# Check Reconnect at logon if you want your Windows machine to try to map this drive every time you start it up<br />
# Press the Finish button<br />
# In the dialog box that appears, type <nowiki>hydrodictyon\userid</nowiki> for the user name (note: no leading double backslash this time) and enter your password.<br />
# If all goes well, you should be able to access files on hydrodictyon using drive Z: on your Windows PC. If things don't go well, please feel free to ask for help from the [mailto:eebwebmaster@uconn.edu EEB Webmaster]<br />
<br />
Another approach is to simply open your Start menu, choose Run..., and type <nowiki>\\hydrodictyon\userid</nowiki> into the edit box labeled Open. You can also set up a network neighborhood shortcut to hydrodictyon. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== FileZilla for Windows ====<br />
<br />
[http://filezilla.sourceforge.net/ FileZilla] provides a free secure file transfer solution for Windows computers. FileZilla is a bit bewildering at first, but it is free. It is only for transferring files. It will not help you create or edit web pages. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#filezilla_setup "How do I connect to the web server using FileZilla?"] for help in setting up FileZilla.<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Cyberduck for Windows ====<br />
<br />
[http://cyberduck.ch/ Cyberduck] provides a free secure file transfer solution for Windows computers. Information about connecting to hydrodictyon using Cyberduck is forthcoming...<br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using FileZilla? ====<br />
<br />
To set up file transfer using FileZilla (I'm using version 2.2.18), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# Choose File, Site Manager... from the main menu (or press Ctrl-S)<br />
# Click the New Site button. You can change the name of the site now from "New FTP site" to something more appropriate, such as "Hydrodictyon" or "EEB Web Server "<br />
# For Host, enter hydrodictyon.eeb.uconn.edu<br />
# For Port, enter 22 (FileZilla defaults to using the old, insecure FTP port 21, but hydodictyon will not grant you an audience if you arrive at port 21; you want to dock at the Secure Shell SSH port 22 instead)<br />
# For Servertype, enter SFTP using SSH2<br />
# For Logontype, click Normal<br />
# For User, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# For Password, enter beaker (your password should be more secure than this one!)<br />
# I would prefer that you check Don't save password, but I know better than to ask<br />
# Now press the Connect button. If you have never connected to hydrodictyon before, you will see a warning starting "The server's host key is not cached in the registry." You can ignore this warning and just press the Yes button.<br />
# At this point, you should see an alias (shortcut) named html in the window labeled "Remote Site". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local Site window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, choose File, Disconnect from the main menu (or use the key combination Ctrl-D)<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows or Mac users ===<br />
<br />
==== Dreamweaver ====<br />
The [http://www.adobe.com/products/dreamweaver/ Adobe (formerly Macromedia) Dreamweaver] software is installed on many of the [http://hydrodictyon.eeb.uconn.edu/department/computerroom/installed%20software.pdf computers] in the McCarthy room computer lab. Dreamweaver allows you to edit web pages and upload them at any time to the web server with the click of a button. It is available for Windows or MacIntosh computers. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#dreamweaver_setup "How do I connect to the web server using Dreamweaver"] for help setting up Dreamweaver. You can also purchase Dreamweaver 8 from the Co-op. Note: do not just go to the Co-op and buy it off the shelf; you will pay way too much this way! Take a BO46 form (see Stephanie Balough in the Bio Central Services) to the bookstore after figuring out the price at the UConn Co-op's [http://www.bookstore.uconn.edu/howto.html Adobe and Macromedia Licensing] web page. As of this writing (30-Aug-2006), the Dreamweaver 8 software itself costs $100, with a media fee of $7.95.<br />
<br />
==== How do I connect to the web server using Dreamweaver? ====<br />
<br />
To set up file transfer using Dreamweaver MX 2004, follow the steps below:<br />
<br />
# Click Start, then navigate to Dreamweaver 2004 (you might need to go through a link named Macromedia to get there) to start Dreamweaver<br />
# If you have never used Dreamweaver before, you will be asked to choose which workspace setup you want (just choose one or the other).<br />
# Once the program is started, choose Site (from the main menu at the top), then Manage Sites...<br />
# Click the New... button, then choose Site, and finally click the Advanced tab (you will end up providing the same information whether you choose Basic or Advanced, but Advanced is faster given that you have these instructions)<br />
# For category (see left side) Local Info:<br />
#* For Site name, just make something up (e.g. mysite)<br />
#* For Local root folder, choose the folder where your web site files will be stored on the computer you are now sitting at. In my case, I chose \\dentata\faculty\plewis\My Documents\mysite\. The \\dentata part means that my files are actually stored on the server named dentata, which manages the new EEB domain. (Your folder path may start with \\matrix if you are still in the older EEB-NET domain, which is managed by the file server named matrix.)<br />
#* For HTTP address, I entered http://hydrodictyon.eeb.uconn.edu/people/plewis/. You should enter the same thing, except change the final plewis part to your own login name. If you do not yet have an account on hydrodictyon, you will need to send an email request to the EEB Webmaster to get one.<br />
# For category Remote Info:<br />
#* For Access, enter FTP<br />
#* For FTP Host, enter hydrodictyon.eeb.uconn.edu<br />
#* For Host directory, I entered /var/www/html/people/plewis/, but you would of course replace the plewis with the user name you use to login to hydrodictyon<br />
#* Now skip ahead and check the box beside Use Secure FTP (SFTP)<br />
#* Fill in your user name and password (these were assigned when you obtained your hydrodictyon account from the EEB Webmaster) and press the Test button. You may get a Windows Security Alert popping up. I was able to dismiss this, but if this turns out to be an insurmountable roadblock, please contact the computer room administrator to help you punch a hole in the firewall. Dreamweaver should indicate that it was able to log in to your site successfully. The EEB webmaster can help if something goes wrong at this point.<br />
# The defaults should work well for the remaining options. Once you close the dialog box, you can view your files on hydrodictyon by choosing Remote view in the Files window (if the Files window is not obvious, hit the F8 button to open it). Choosing Local view lets you see the files currently on your local computer. The up and down arrow buttons in the Files window allow you to upload selected files to (or download selected files from) hydrodictyon.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Miscellany ==<br />
<br />
==== How do I create a web page that will redirect users to my new site? ====<br />
<br />
Here is how to create a very basic redirect page using an HTML meta tag. This assumes your name is Jonathan and your new web site URL is <nowiki>http://www.uconn.edu/</nowiki>. Just create a file named <tt>index.html</tt> in your old web folder (and remove all other files), then add the following text to <tt>index.html</tt><pre><br />
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><br />
<html><br />
<head><br />
<title>Redirecting to Jonathan's new home page</title><br />
<META http-equiv="refresh" content="5;URL=http://www.uconn.edu/"><br />
</head><br />
<body><br />
<center><br />
You will be redirected to Jonathan's new home page automatically in 5 seconds.<br/> <br />
Please update any bookmarks to point to the new address, which is<br/><br />
<a href="http://www.uconn.edu/">http://www.uconn.edu/</a><br />
</center><br />
</body><br />
</html> <br />
</pre><br />
<br />
[[#top|Back to top]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Web_site_FAQ&diff=19724Web site FAQ2011-11-11T21:38:48Z<p>PaulLewis: /* CyberDuck for Windows */</p>
<hr />
<div>This page contains frequently asked questions (and answers!) about the EEB department's web server.<br />
<br />
== The web server (hydrodictyon) ==<br />
<br />
=== What is hydrodictyon? ===<br />
<br />
Hydrodictyon is the name of the computer that serves up all the web pages that together constitute the [http://hydrodictyon.eeb.uconn.edu/ EEB web site]. The term ''web server'' can refer to either the ''software'' that serves web pages ([http://httpd.apache.org/ Apache] in our case) or the computer that runs that software (a Dell Optiplex 755 in our case). Hydrodictyon runs the [http://fedoraproject.org/ Red Hat Fedora 9] Linux operating system.<br />
<br />
=== Do I need an account on hydrodictyon? ===<br />
<br />
You need an account on hydrodictyon if you want to create a traditional HTML-based web page for yourself or a course. Many find it much easier to create and maintain web pages using EEBedia than the traditional approach. This FAQ page, for example, was created in EEBedia. If you would like to try using EEBedia, click on the [[Help:Contents|Help]] link to your left to get started.<br />
<br />
=== How do I get an account on hydrodictyon? ===<br />
<br />
Just send an email request to the [mailto:eebwebmaster@uconn.edu EEB Webmaster]. Ordinarily, you must be a current member of the EEB department to obtain an account, but exceptions will be made under some circumstances.<br />
<br />
=== What is the difference between my home directory and my web folder on hydrodictyon? ===<br />
<br />
When your account is created, you automatically get a '''home directory'''. Your home directory is located within the <tt>/home</tt> directory on hydrodictyon. (For those unfamiliar with Linux, the root of the file system is "/", which is akin to "C:/" in Windows, so <tt>/home</tt> is one level up from the root of the file system.) Items you upload or create in your home directory will not be visible on the internet. Inside your home directory, you should find an an item named "html". While "html" looks and acts like a directory, it is actually an alias (or symbolic link, in Linux terminology) to a completely separate directory on the hard drive, your '''web folder'''. For example, my (Paul Lewis) home directory is <tt>/home/plewis</tt>, whereas my web folder is <tt>/var/www/html/people/plewis</tt>. Items placed in your web folder will be immediately visible on the internet at an address (URL) that looks like this:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
or, equivalently, <br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
Note that you should replace the "yourusername" part of the URL with your own username. <br />
<br />
The "html" alias makes it easy for you to transfer files to your web folder. No matter how you connect to hydrodictyon, you will be dumped first in your home directory, where you should see the "html" alias staring you in the face. Just double-click that alias and you will be transported across the hard drive to your web folder.<br />
<br />
Before you begin uploading files, read the next section entitled "Why you should name your home page index.html"<br />
<br />
=== Why you should name your home page index.html ===<br />
<br />
Suppose you name your home page <tt>MyHomePage.html</tt>. In order for someone to see your homepage, they must know the exact name of your home page file and append it to your base URL, as follows:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/MyHomePage.html<br />
If someone does not know the name of the file serving as your home page, they may try typing this URL into their browser instead:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
[[Image:Dirlisting.png|thumb|right]]If they were to do that, they would not see your home page. Instead, they would see a directory listing like the one shown on the right (click the thumbnail image to see the full size image if you want). Now they have to wade through all your web files and try to figure out which one is your home page. In the meantime, they might happen on some files you didn't plan on anyone viewing (e.g. <tt>junk_I_home_noone_ever_sees.html</tt>), perhaps because they represent works in progress or obsolete content that you just can't bring yourself to delete.<br />
<br />
If you name your home page index.html, however, then users will always get your home page when they enter your base URL, i.e.<br />
<nowiki>http://hydrodictyon.eeb.uconn.edu/people/yourusername/</nowiki><br />
and they will never get an index showing all your files. This gives you a lot of control over what people see: they can only see the files you have linked to your home page or to other pages linked to your home page. It also gives you control over what will appear in searches conducted on Google (and other search sites) because the webbots used by the search engines also cannot get a listing of all your files.<br />
<br />
=== Who is the EEB Webmaster? ===<br />
<br />
The current EEB webmaster is [mailto:eebwebmaster@uconn.edu Paul Lewis].<br />
<br />
=== What can the EEB Webmaster do for me? ===<br />
<br />
The EEB Webmaster's duties include:<br />
* maintaining the web server (both hardward and software)<br />
* backing up the web content daily<br />
* creating accounts and providing edit access to EEBedia<br />
* creating and maintaining software for editing course, event and people information<br />
* maintaining and creating department-wide content, such as the flash display on the EEB home page<br />
* helping with problems involving access to the web server<br />
<br />
The EEB Webmaster's duties do not, however, include helping you write web pages. You must create your own content, either as a traditional HTML web page or using EEBedia.<br />
<br />
=== How do I change my password on hydrodictyon? ===<br />
<br />
Use the [https://hydrodictyon.eeb.uconn.edu/password.php web form] to create your first password, or change your password. <br />
<br />
'''<span style="color: red">Important!</span>''' If an account has '''just been created''' for you, or if your password has '''just been reset''' by the [[EEB Webmaster]], you should '''leave the field labeled ''Old password'' blank'''. <br />
<br />
[[#top|Back to top]]<br />
<br />
== The EEB home page ==<br />
<br />
=== How do I get an image into the Flash display on the home page? ===<br />
Send the [mailto:eebwebmaster@uconn.edu webmaster] these three things:<br />
# A landscape-style image (e.g. jpeg format) at least 500 pixels wide and 350 pixels tall<br />
# An appropriate caption about 10 words long<br />
# The URL of an existing web page that can be linked to the image<br />
Keep in mind that the caption inside the purple rectangle will obscure part of the image, so try to compose your photo so that important parts are not hidden by the caption.<br />
<br />
=== Why do I sometimes not see a particular image in the Flash presentation when I view the home page? ===<br />
To keep the file size of the Flash presentation low enough so that there is no noticeable delay when the home page is loaded, photos are grouped into casettes of about 4-5 images. The casette that will be shown is chosen randomly when the home page is loaded. If you want to see other casettes, simply refresh your browser to load another randomly-chosen group of photos.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Transferring files ==<br />
<br />
Hydrodictyon does not support FTP for security reasons (the old FTP protocol sends passwords across the network in plain text), but it does allow file transfers via the Secure Shell protocol (Secure FTP, or SFTP for short) or Samba-mediated Windows network shares. What means you use to move files back and forth depends on what operating system you use.<br />
<br />
=== Mac users ===<br />
<br />
If you use a MacIntosh running Mac OS 10.x, Fugu is probably the easiest means of transferring files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Fugu for MacOS 10.x ====<br />
[http://rsug.itd.umich.edu/software/fugu/ Fugu] provides a free secure file transfer solution for MacIntosh computers running MacOS X. Fugu is only for transferring files. It will not help you create or edit web pages. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using Fugu? ====<br />
<br />
To set up file transfer using Fugu (I'm using version 1.1), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# In the Connect to field, enter hydrodictyon.eeb.uconn.edu<br />
# In the Username field, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# In the Port field, enter 22 (this is the standard Secure Shell, or SSH, port)<br />
# Click the Add to Favorites button to make it easier to connect to hydrodictyon the next time<br />
# Click the Connect button to login to hydrodictyon. If you have never connected to hydrodictyon before, you will see a warning stating "The authenticity of host 'hydrodictyon.eeb.uconn.edu (137.99.88.31)' can't be established. Unable to get host key. Something is odd. Are you sure you want to continue connecting? " You can ignore this warning (the first time you see it, at least) and just press the Continue button.<br />
# You should now be asked for a password. Here is where Dr. Bunsen Honeydew would type his password, beaker (your password should be more secure than his!). After entering your password, click the button Authenticate.<br />
# At this point, you should see an alias (shortcut) named html in the righthand window labeled "hydrodictyon.eeb.uconn.edu". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, click the Disconnect button on the menu bar at the top<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Why does Fugu say <tt>@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @</tt>? ====<br />
<br />
You will get this warning whenever the machine serving as hydrodictyon is changed, which will happen once or twice per year. Fugu's warning is designed to make you think twice about connecting to hydrodictyon because the identity of hydrodictyon has changed. To stop this warning, choose Fugu &gt; Preferences... from the main menu, then click the Known Hosts tab. You should see an entry that looks like this<pre>hydrodictyon.eeb.uconn.edu.137.99.88.31</pre> Select this entry, then press the Delete button, and finally press the Save button before closing the Preferences dialog box. Now when you attempt to connect to hydrodictyon, it will present a different warning (''The authenticity of host...Something is odd. Are you sure you want to continue connecting?''), but it will at least let you continue connecting if you press the Continue button. Your Fugu client will now download a new host key from hydrodictyon, which it will use each time you connect to verify that you are indeed connecting to hydrodictyon (at least until hydrodictyon is changed again!).<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows users ===<br />
<br />
If you use Windows, you will probably want to use either Samba (if on campus) or FileZilla/CyberDuck (from off campus) to move files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Using Samba ====<br />
<br />
Hydrodictyon runs [http://www.samba.org/ Samba], which makes it possible for a Windows user to mount their home directory on hydrodictyon as if it were a network share on a Windows machine. Each person given an account on hydrodictyon is automatically set up to use this method, but be aware that UConn prevents the use of Windows file sharing from off-campus sites unless you log into the [http://security.uconn.edu/guides/vpn.html VPN (Virtual Private Network)]. <br />
<br />
To mount your home directory on hydrodictyon as (for example) drive Z: on your Windows XP machine, follow these steps (I will use the user name <nowiki>userid</nowiki> here, but you should of course '''substitute your own user name''' wherever <nowiki>userid</nowiki> appears):<br />
<br />
# Open My Computer<br />
# Choose Tools from the main menu, then Map Network Drive... <br />
# Choose Z: (or some other letter) as Drive<br />
# Specify <nowiki>\\hydrodictyon\userid</nowiki> for Folder (remember to replace <nowiki>plewis</nowiki> with your own user name (given to you when your account on hydrodictyon was created)<br />
# Check Reconnect at logon if you want your Windows machine to try to map this drive every time you start it up<br />
# Press the Finish button<br />
# In the dialog box that appears, type <nowiki>hydrodictyon\userid</nowiki> for the user name (note: no leading double backslash this time) and enter your password.<br />
# If all goes well, you should be able to access files on hydrodictyon using drive Z: on your Windows PC. If things don't go well, please feel free to ask for help from the [mailto:eebwebmaster@uconn.edu EEB Webmaster]<br />
<br />
Another approach is to simply open your Start menu, choose Run..., and type <nowiki>\\hydrodictyon\userid</nowiki> into the edit box labeled Open. You can also set up a network neighborhood shortcut to hydrodictyon. <br />
<br />
[[#top|Back to top]]<br />
<br />
==== FileZilla for Windows ====<br />
<br />
[http://filezilla.sourceforge.net/ FileZilla] provides a free secure file transfer solution for Windows computers. FileZilla is a bit bewildering at first, but it is free. It is only for transferring files. It will not help you create or edit web pages. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#filezilla_setup "How do I connect to the web server using FileZilla?"] for help in setting up FileZilla.<br />
<br />
[[#top|Back to top]]<br />
<br />
==== Cyberduck for Windows ====<br />
<br />
[http://cyberduck.ch/ cyberduck] provides a free secure file transfer solution for Windows computers. Information about connecting to hydrodictyon using Cyberduck is forthcoming...<br />
<br />
[[#top|Back to top]]<br />
<br />
==== How do I connect to the web server using FileZilla? ====<br />
<br />
To set up file transfer using FileZilla (I'm using version 2.2.18), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# Choose File, Site Manager... from the main menu (or press Ctrl-S)<br />
# Click the New Site button. You can change the name of the site now from "New FTP site" to something more appropriate, such as "Hydrodictyon" or "EEB Web Server "<br />
# For Host, enter hydrodictyon.eeb.uconn.edu<br />
# For Port, enter 22 (FileZilla defaults to using the old, insecure FTP port 21, but hydodictyon will not grant you an audience if you arrive at port 21; you want to dock at the Secure Shell SSH port 22 instead)<br />
# For Servertype, enter SFTP using SSH2<br />
# For Logontype, click Normal<br />
# For User, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# For Password, enter beaker (your password should be more secure than this one!)<br />
# I would prefer that you check Don't save password, but I know better than to ask<br />
# Now press the Connect button. If you have never connected to hydrodictyon before, you will see a warning starting "The server's host key is not cached in the registry." You can ignore this warning and just press the Yes button.<br />
# At this point, you should see an alias (shortcut) named html in the window labeled "Remote Site". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local Site window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, choose File, Disconnect from the main menu (or use the key combination Ctrl-D)<br />
<br />
[[#top|Back to top]]<br />
<br />
=== Windows or Mac users ===<br />
<br />
==== Dreamweaver ====<br />
The [http://www.adobe.com/products/dreamweaver/ Adobe (formerly Macromedia) Dreamweaver] software is installed on many of the [http://hydrodictyon.eeb.uconn.edu/department/computerroom/installed%20software.pdf computers] in the McCarthy room computer lab. Dreamweaver allows you to edit web pages and upload them at any time to the web server with the click of a button. It is available for Windows or MacIntosh computers. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#dreamweaver_setup "How do I connect to the web server using Dreamweaver"] for help setting up Dreamweaver. You can also purchase Dreamweaver 8 from the Co-op. Note: do not just go to the Co-op and buy it off the shelf; you will pay way too much this way! Take a BO46 form (see Stephanie Balough in the Bio Central Services) to the bookstore after figuring out the price at the UConn Co-op's [http://www.bookstore.uconn.edu/howto.html Adobe and Macromedia Licensing] web page. As of this writing (30-Aug-2006), the Dreamweaver 8 software itself costs $100, with a media fee of $7.95.<br />
<br />
==== How do I connect to the web server using Dreamweaver? ====<br />
<br />
To set up file transfer using Dreamweaver MX 2004, follow the steps below:<br />
<br />
# Click Start, then navigate to Dreamweaver 2004 (you might need to go through a link named Macromedia to get there) to start Dreamweaver<br />
# If you have never used Dreamweaver before, you will be asked to choose which workspace setup you want (just choose one or the other).<br />
# Once the program is started, choose Site (from the main menu at the top), then Manage Sites...<br />
# Click the New... button, then choose Site, and finally click the Advanced tab (you will end up providing the same information whether you choose Basic or Advanced, but Advanced is faster given that you have these instructions)<br />
# For category (see left side) Local Info:<br />
#* For Site name, just make something up (e.g. mysite)<br />
#* For Local root folder, choose the folder where your web site files will be stored on the computer you are now sitting at. In my case, I chose \\dentata\faculty\plewis\My Documents\mysite\. The \\dentata part means that my files are actually stored on the server named dentata, which manages the new EEB domain. (Your folder path may start with \\matrix if you are still in the older EEB-NET domain, which is managed by the file server named matrix.)<br />
#* For HTTP address, I entered http://hydrodictyon.eeb.uconn.edu/people/plewis/. You should enter the same thing, except change the final plewis part to your own login name. If you do not yet have an account on hydrodictyon, you will need to send an email request to the EEB Webmaster to get one.<br />
# For category Remote Info:<br />
#* For Access, enter FTP<br />
#* For FTP Host, enter hydrodictyon.eeb.uconn.edu<br />
#* For Host directory, I entered /var/www/html/people/plewis/, but you would of course replace the plewis with the user name you use to login to hydrodictyon<br />
#* Now skip ahead and check the box beside Use Secure FTP (SFTP)<br />
#* Fill in your user name and password (these were assigned when you obtained your hydrodictyon account from the EEB Webmaster) and press the Test button. You may get a Windows Security Alert popping up. I was able to dismiss this, but if this turns out to be an insurmountable roadblock, please contact the computer room administrator to help you punch a hole in the firewall. Dreamweaver should indicate that it was able to log in to your site successfully. The EEB webmaster can help if something goes wrong at this point.<br />
# The defaults should work well for the remaining options. Once you close the dialog box, you can view your files on hydrodictyon by choosing Remote view in the Files window (if the Files window is not obvious, hit the F8 button to open it). Choosing Local view lets you see the files currently on your local computer. The up and down arrow buttons in the Files window allow you to upload selected files to (or download selected files from) hydrodictyon.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Miscellany ==<br />
<br />
==== How do I create a web page that will redirect users to my new site? ====<br />
<br />
Here is how to create a very basic redirect page using an HTML meta tag. This assumes your name is Jonathan and your new web site URL is <nowiki>http://www.uconn.edu/</nowiki>. Just create a file named <tt>index.html</tt> in your old web folder (and remove all other files), then add the following text to <tt>index.html</tt><pre><br />
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><br />
<html><br />
<head><br />
<title>Redirecting to Jonathan's new home page</title><br />
<META http-equiv="refresh" content="5;URL=http://www.uconn.edu/"><br />
</head><br />
<body><br />
<center><br />
You will be redirected to Jonathan's new home page automatically in 5 seconds.<br/> <br />
Please update any bookmarks to point to the new address, which is<br/><br />
<a href="http://www.uconn.edu/">http://www.uconn.edu/</a><br />
</center><br />
</body><br />
</html> <br />
</pre><br />
<br />
[[#top|Back to top]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Web_site_FAQ&diff=19723Web site FAQ2011-11-11T21:38:27Z<p>PaulLewis: /* Windows users */</p>
<hr />
<div>This page contains frequently asked questions (and answers!) about the EEB department's web server.<br />
<br />
== The web server (hydrodictyon) ==<br />
<br />
=== What is hydrodictyon? ===<br />
<br />
Hydrodictyon is the name of the computer that serves up all the web pages that together constitute the [http://hydrodictyon.eeb.uconn.edu/ EEB web site]. The term ''web server'' can refer to either the ''software'' that serves web pages ([http://httpd.apache.org/ Apache] in our case) or the computer that runs that software (a Dell Optiplex 755 in our case). Hydrodictyon runs the [http://fedoraproject.org/ Red Hat Fedora 9] Linux operating system.<br />
<br />
=== Do I need an account on hydrodictyon? ===<br />
<br />
You need an account on hydrodictyon if you want to create a traditional HTML-based web page for yourself or a course. Many find it much easier to create and maintain web pages using EEBedia than the traditional approach. This FAQ page, for example, was created in EEBedia. If you would like to try using EEBedia, click on the [[Help:Contents|Help]] link to your left to get started.<br />
<br />
=== How do I get an account on hydrodictyon? ===<br />
<br />
Just send an email request to the [mailto:eebwebmaster@uconn.edu EEB Webmaster]. Ordinarily, you must be a current member of the EEB department to obtain an account, but exceptions will be made under some circumstances.<br />
<br />
=== What is the difference between my home directory and my web folder on hydrodictyon? ===<br />
<br />
When your account is created, you automatically get a '''home directory'''. Your home directory is located within the <tt>/home</tt> directory on hydrodictyon. (For those unfamiliar with Linux, the root of the file system is "/", which is akin to "C:/" in Windows, so <tt>/home</tt> is one level up from the root of the file system.) Items you upload or create in your home directory will not be visible on the internet. Inside your home directory, you should find an an item named "html". While "html" looks and acts like a directory, it is actually an alias (or symbolic link, in Linux terminology) to a completely separate directory on the hard drive, your '''web folder'''. For example, my (Paul Lewis) home directory is <tt>/home/plewis</tt>, whereas my web folder is <tt>/var/www/html/people/plewis</tt>. Items placed in your web folder will be immediately visible on the internet at an address (URL) that looks like this:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
or, equivalently, <br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
Note that you should replace the "yourusername" part of the URL with your own username. <br />
<br />
The "html" alias makes it easy for you to transfer files to your web folder. No matter how you connect to hydrodictyon, you will be dumped first in your home directory, where you should see the "html" alias staring you in the face. Just double-click that alias and you will be transported across the hard drive to your web folder.<br />
<br />
Before you begin uploading files, read the next section entitled "Why you should name your home page index.html"<br />
<br />
=== Why you should name your home page index.html ===<br />
<br />
Suppose you name your home page <tt>MyHomePage.html</tt>. In order for someone to see your homepage, they must know the exact name of your home page file and append it to your base URL, as follows:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/MyHomePage.html<br />
If someone does not know the name of the file serving as your home page, they may try typing this URL into their browser instead:<br />
http://hydrodictyon.eeb.uconn.edu/people/yourusername/<br />
[[Image:Dirlisting.png|thumb|right]]If they were to do that, they would not see your home page. Instead, they would see a directory listing like the one shown on the right (click the thumbnail image to see the full size image if you want). Now they have to wade through all your web files and try to figure out which one is your home page. In the meantime, they might happen on some files you didn't plan on anyone viewing (e.g. <tt>junk_I_home_noone_ever_sees.html</tt>), perhaps because they represent works in progress or obsolete content that you just can't bring yourself to delete.<br />
<br />
If you name your home page index.html, however, then users will always get your home page when they enter your base URL, i.e.<br />
<nowiki>http://hydrodictyon.eeb.uconn.edu/people/yourusername/</nowiki><br />
and they will never get an index showing all your files. This gives you a lot of control over what people see: they can only see the files you have linked to your home page or to other pages linked to your home page. It also gives you control over what will appear in searches conducted on Google (and other search sites) because the webbots used by the search engines also cannot get a listing of all your files.<br />
<br />
=== Who is the EEB Webmaster? ===<br />
<br />
The current EEB webmaster is [mailto:eebwebmaster@uconn.edu Paul Lewis].<br />
<br />
=== What can the EEB Webmaster do for me? ===<br />
<br />
The EEB Webmaster's duties include:<br />
* maintaining the web server (both hardward and software)<br />
* backing up the web content daily<br />
* creating accounts and providing edit access to EEBedia<br />
* creating and maintaining software for editing course, event and people information<br />
* maintaining and creating department-wide content, such as the flash display on the EEB home page<br />
* helping with problems involving access to the web server<br />
<br />
The EEB Webmaster's duties do not, however, include helping you write web pages. You must create your own content, either as a traditional HTML web page or using EEBedia.<br />
<br />
=== How do I change my password on hydrodictyon? ===<br />
<br />
Use the [https://hydrodictyon.eeb.uconn.edu/password.php web form] to create your first password, or change your password. <br />
<br />
'''<span style="color: red">Important!</span>''' If an account has '''just been created''' for you, or if your password has '''just been reset''' by the [[EEB Webmaster]], you should '''leave the field labeled ''Old password'' blank'''. <br />
<br />
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<br />
== The EEB home page ==<br />
<br />
=== How do I get an image into the Flash display on the home page? ===<br />
Send the [mailto:eebwebmaster@uconn.edu webmaster] these three things:<br />
# A landscape-style image (e.g. jpeg format) at least 500 pixels wide and 350 pixels tall<br />
# An appropriate caption about 10 words long<br />
# The URL of an existing web page that can be linked to the image<br />
Keep in mind that the caption inside the purple rectangle will obscure part of the image, so try to compose your photo so that important parts are not hidden by the caption.<br />
<br />
=== Why do I sometimes not see a particular image in the Flash presentation when I view the home page? ===<br />
To keep the file size of the Flash presentation low enough so that there is no noticeable delay when the home page is loaded, photos are grouped into casettes of about 4-5 images. The casette that will be shown is chosen randomly when the home page is loaded. If you want to see other casettes, simply refresh your browser to load another randomly-chosen group of photos.<br />
<br />
[[#top|Back to top]]<br />
<br />
== Transferring files ==<br />
<br />
Hydrodictyon does not support FTP for security reasons (the old FTP protocol sends passwords across the network in plain text), but it does allow file transfers via the Secure Shell protocol (Secure FTP, or SFTP for short) or Samba-mediated Windows network shares. What means you use to move files back and forth depends on what operating system you use.<br />
<br />
=== Mac users ===<br />
<br />
If you use a MacIntosh running Mac OS 10.x, Fugu is probably the easiest means of transferring files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Fugu for MacOS 10.x ====<br />
[http://rsug.itd.umich.edu/software/fugu/ Fugu] provides a free secure file transfer solution for MacIntosh computers running MacOS X. Fugu is only for transferring files. It will not help you create or edit web pages. <br />
<br />
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<br />
==== How do I connect to the web server using Fugu? ====<br />
<br />
To set up file transfer using Fugu (I'm using version 1.1), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# In the Connect to field, enter hydrodictyon.eeb.uconn.edu<br />
# In the Username field, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# In the Port field, enter 22 (this is the standard Secure Shell, or SSH, port)<br />
# Click the Add to Favorites button to make it easier to connect to hydrodictyon the next time<br />
# Click the Connect button to login to hydrodictyon. If you have never connected to hydrodictyon before, you will see a warning stating "The authenticity of host 'hydrodictyon.eeb.uconn.edu (137.99.88.31)' can't be established. Unable to get host key. Something is odd. Are you sure you want to continue connecting? " You can ignore this warning (the first time you see it, at least) and just press the Continue button.<br />
# You should now be asked for a password. Here is where Dr. Bunsen Honeydew would type his password, beaker (your password should be more secure than his!). After entering your password, click the button Authenticate.<br />
# At this point, you should see an alias (shortcut) named html in the righthand window labeled "hydrodictyon.eeb.uconn.edu". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, click the Disconnect button on the menu bar at the top<br />
<br />
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<br />
==== Why does Fugu say <tt>@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @</tt>? ====<br />
<br />
You will get this warning whenever the machine serving as hydrodictyon is changed, which will happen once or twice per year. Fugu's warning is designed to make you think twice about connecting to hydrodictyon because the identity of hydrodictyon has changed. To stop this warning, choose Fugu &gt; Preferences... from the main menu, then click the Known Hosts tab. You should see an entry that looks like this<pre>hydrodictyon.eeb.uconn.edu.137.99.88.31</pre> Select this entry, then press the Delete button, and finally press the Save button before closing the Preferences dialog box. Now when you attempt to connect to hydrodictyon, it will present a different warning (''The authenticity of host...Something is odd. Are you sure you want to continue connecting?''), but it will at least let you continue connecting if you press the Continue button. Your Fugu client will now download a new host key from hydrodictyon, which it will use each time you connect to verify that you are indeed connecting to hydrodictyon (at least until hydrodictyon is changed again!).<br />
<br />
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<br />
=== Windows users ===<br />
<br />
If you use Windows, you will probably want to use either Samba (if on campus) or FileZilla/CyberDuck (from off campus) to move files back and forth from your own computer to hydrodictyon.<br />
<br />
==== Using Samba ====<br />
<br />
Hydrodictyon runs [http://www.samba.org/ Samba], which makes it possible for a Windows user to mount their home directory on hydrodictyon as if it were a network share on a Windows machine. Each person given an account on hydrodictyon is automatically set up to use this method, but be aware that UConn prevents the use of Windows file sharing from off-campus sites unless you log into the [http://security.uconn.edu/guides/vpn.html VPN (Virtual Private Network)]. <br />
<br />
To mount your home directory on hydrodictyon as (for example) drive Z: on your Windows XP machine, follow these steps (I will use the user name <nowiki>userid</nowiki> here, but you should of course '''substitute your own user name''' wherever <nowiki>userid</nowiki> appears):<br />
<br />
# Open My Computer<br />
# Choose Tools from the main menu, then Map Network Drive... <br />
# Choose Z: (or some other letter) as Drive<br />
# Specify <nowiki>\\hydrodictyon\userid</nowiki> for Folder (remember to replace <nowiki>plewis</nowiki> with your own user name (given to you when your account on hydrodictyon was created)<br />
# Check Reconnect at logon if you want your Windows machine to try to map this drive every time you start it up<br />
# Press the Finish button<br />
# In the dialog box that appears, type <nowiki>hydrodictyon\userid</nowiki> for the user name (note: no leading double backslash this time) and enter your password.<br />
# If all goes well, you should be able to access files on hydrodictyon using drive Z: on your Windows PC. If things don't go well, please feel free to ask for help from the [mailto:eebwebmaster@uconn.edu EEB Webmaster]<br />
<br />
Another approach is to simply open your Start menu, choose Run..., and type <nowiki>\\hydrodictyon\userid</nowiki> into the edit box labeled Open. You can also set up a network neighborhood shortcut to hydrodictyon. <br />
<br />
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<br />
==== FileZilla for Windows ====<br />
<br />
[http://filezilla.sourceforge.net/ FileZilla] provides a free secure file transfer solution for Windows computers. FileZilla is a bit bewildering at first, but it is free. It is only for transferring files. It will not help you create or edit web pages. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#filezilla_setup "How do I connect to the web server using FileZilla?"] for help in setting up FileZilla.<br />
<br />
[[#top|Back to top]]<br />
<br />
==== CyberDuck for Windows ====<br />
<br />
[http://cyberduck.ch/] provides a free secure file transfer solution for Windows computers. Information about connecting to hydrodictyon using Cyberduck is forthcoming...<br />
<br />
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<br />
==== How do I connect to the web server using FileZilla? ====<br />
<br />
To set up file transfer using FileZilla (I'm using version 2.2.18), follow the steps below (I will assume your user name on hydrodictyon is honeydew and your password is beaker)<br />
<br />
# Choose File, Site Manager... from the main menu (or press Ctrl-S)<br />
# Click the New Site button. You can change the name of the site now from "New FTP site" to something more appropriate, such as "Hydrodictyon" or "EEB Web Server "<br />
# For Host, enter hydrodictyon.eeb.uconn.edu<br />
# For Port, enter 22 (FileZilla defaults to using the old, insecure FTP port 21, but hydodictyon will not grant you an audience if you arrive at port 21; you want to dock at the Secure Shell SSH port 22 instead)<br />
# For Servertype, enter SFTP using SSH2<br />
# For Logontype, click Normal<br />
# For User, enter honeydew (remember, this is just an example, I doubt that honeydew is really your username)<br />
# For Password, enter beaker (your password should be more secure than this one!)<br />
# I would prefer that you check Don't save password, but I know better than to ask<br />
# Now press the Connect button. If you have never connected to hydrodictyon before, you will see a warning starting "The server's host key is not cached in the registry." You can ignore this warning and just press the Yes button.<br />
# At this point, you should see an alias (shortcut) named html in the window labeled "Remote Site". If you don't, write to me. This alias (when double-clicked) takes you to your web folder on hydrodictyon. Anything you transfer from your computer to the web folder will be immediately visible on the web at http://hydrodictyon.eeb.uconn.edu/people/honeydew/ (once again, remember that you are not Bunsen Honeydew, so you will use your user name instead of honeydew when typing in the URL).<br />
# To upload a file, find it in the Local Site window, then simply double-click the name of the file to move it over to hydodictyon<br />
# To disconnect from hydodictyon, choose File, Disconnect from the main menu (or use the key combination Ctrl-D)<br />
<br />
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<br />
=== Windows or Mac users ===<br />
<br />
==== Dreamweaver ====<br />
The [http://www.adobe.com/products/dreamweaver/ Adobe (formerly Macromedia) Dreamweaver] software is installed on many of the [http://hydrodictyon.eeb.uconn.edu/department/computerroom/installed%20software.pdf computers] in the McCarthy room computer lab. Dreamweaver allows you to edit web pages and upload them at any time to the web server with the click of a button. It is available for Windows or MacIntosh computers. Go to [http://hydrodictyon.eeb.uconn.edu/eebwww/FAQ/#dreamweaver_setup "How do I connect to the web server using Dreamweaver"] for help setting up Dreamweaver. You can also purchase Dreamweaver 8 from the Co-op. Note: do not just go to the Co-op and buy it off the shelf; you will pay way too much this way! Take a BO46 form (see Stephanie Balough in the Bio Central Services) to the bookstore after figuring out the price at the UConn Co-op's [http://www.bookstore.uconn.edu/howto.html Adobe and Macromedia Licensing] web page. As of this writing (30-Aug-2006), the Dreamweaver 8 software itself costs $100, with a media fee of $7.95.<br />
<br />
==== How do I connect to the web server using Dreamweaver? ====<br />
<br />
To set up file transfer using Dreamweaver MX 2004, follow the steps below:<br />
<br />
# Click Start, then navigate to Dreamweaver 2004 (you might need to go through a link named Macromedia to get there) to start Dreamweaver<br />
# If you have never used Dreamweaver before, you will be asked to choose which workspace setup you want (just choose one or the other).<br />
# Once the program is started, choose Site (from the main menu at the top), then Manage Sites...<br />
# Click the New... button, then choose Site, and finally click the Advanced tab (you will end up providing the same information whether you choose Basic or Advanced, but Advanced is faster given that you have these instructions)<br />
# For category (see left side) Local Info:<br />
#* For Site name, just make something up (e.g. mysite)<br />
#* For Local root folder, choose the folder where your web site files will be stored on the computer you are now sitting at. In my case, I chose \\dentata\faculty\plewis\My Documents\mysite\. The \\dentata part means that my files are actually stored on the server named dentata, which manages the new EEB domain. (Your folder path may start with \\matrix if you are still in the older EEB-NET domain, which is managed by the file server named matrix.)<br />
#* For HTTP address, I entered http://hydrodictyon.eeb.uconn.edu/people/plewis/. You should enter the same thing, except change the final plewis part to your own login name. If you do not yet have an account on hydrodictyon, you will need to send an email request to the EEB Webmaster to get one.<br />
# For category Remote Info:<br />
#* For Access, enter FTP<br />
#* For FTP Host, enter hydrodictyon.eeb.uconn.edu<br />
#* For Host directory, I entered /var/www/html/people/plewis/, but you would of course replace the plewis with the user name you use to login to hydrodictyon<br />
#* Now skip ahead and check the box beside Use Secure FTP (SFTP)<br />
#* Fill in your user name and password (these were assigned when you obtained your hydrodictyon account from the EEB Webmaster) and press the Test button. You may get a Windows Security Alert popping up. I was able to dismiss this, but if this turns out to be an insurmountable roadblock, please contact the computer room administrator to help you punch a hole in the firewall. Dreamweaver should indicate that it was able to log in to your site successfully. The EEB webmaster can help if something goes wrong at this point.<br />
# The defaults should work well for the remaining options. Once you close the dialog box, you can view your files on hydrodictyon by choosing Remote view in the Files window (if the Files window is not obvious, hit the F8 button to open it). Choosing Local view lets you see the files currently on your local computer. The up and down arrow buttons in the Files window allow you to upload selected files to (or download selected files from) hydrodictyon.<br />
<br />
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<br />
== Miscellany ==<br />
<br />
==== How do I create a web page that will redirect users to my new site? ====<br />
<br />
Here is how to create a very basic redirect page using an HTML meta tag. This assumes your name is Jonathan and your new web site URL is <nowiki>http://www.uconn.edu/</nowiki>. Just create a file named <tt>index.html</tt> in your old web folder (and remove all other files), then add the following text to <tt>index.html</tt><pre><br />
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><br />
<html><br />
<head><br />
<title>Redirecting to Jonathan's new home page</title><br />
<META http-equiv="refresh" content="5;URL=http://www.uconn.edu/"><br />
</head><br />
<body><br />
<center><br />
You will be redirected to Jonathan's new home page automatically in 5 seconds.<br/> <br />
Please update any bookmarks to point to the new address, which is<br/><br />
<a href="http://www.uconn.edu/">http://www.uconn.edu/</a><br />
</center><br />
</body><br />
</html> <br />
</pre><br />
<br />
[[#top|Back to top]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Principles_and_Methods_of_Systematic_Biology_(EEB_5347)&diff=19637Principles and Methods of Systematic Biology (EEB 5347)2011-11-04T15:06:53Z<p>PaulLewis: </p>
<hr />
<div>[[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]<br />
<span style="font-size: large">Fall 2011<br/><br />
<br />
<span style="font-size: large">Lecture MW 9:00-10:30, Lab F 9:00-10:30<br/><br />
<br/><br />
<span style="font-size: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/><br />
Phone: 486-2139<br/> <br />
office hours as available<br/><br />
email: [mailto:david.wagner'at'uconn.edu david.wagner'at'uconn.edu]<br/><br />
<br/><br />
'''Graduate Teaching Assistant''': Chris Owen<br/><br />
Office hours: BioPharm 325 Wednesdays 10:30-11:30 or by appointment<br/><br />
Phone: 486-6650<br/><br />
email: [mailto:christopher.l.owen'at'uconn.edu christopher.l.owen'at'uconn.edu]<br/><br />
<br/><br />
== '''Textbook and readings''' ==<br />
There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Many readings will be available as pdfs, downloadable from the course website. Others, available in hard copy only, will be on reserve in the departmental office (TLS 312) in the filing cabinet next to the window. You are free to check out copy #2 for 3 hours; copy #1 should stay in the office, i.e., so one is always there for others to photocopy.<br />
<br/><br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|- <br />
| Aug 29 ||Class canceled due to Hurricane Irene<br/><!--{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Introduction%202009%20class%20notes.pdf}}Introduction 2009 class notes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Syllabus%202009.pdf}}Syllabus.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Rules%20of%20Pronunciation%20Sci.%20Name.PDF}}Rules of Pronunciation Sci.Name.pdf--><br />
|| || rowspan="3"| Lecture instead of lab this week<br />
|-<br />
| Aug 31 ||Organizational meeting, an introduction to biological systematics||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs1-18.pdf}}Mayr&Ashlock1991_pgs1-18.pdf (optional)<br />
|-<br />
| Sept 2 ||The many roles of biological systematics & collections tour <!--Species definitions & species intermediacy<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}De Queiroz 2007.pdf<br/>http://en.wikipedia.org/wiki/Species#Definitions_of_species<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445-451.pdf}}Futuyma_spconcepts_445-451.pdf<br />
|-<br />
| Sept 5 ||Labor Day No class || || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 '''<br />
|-<br />
|Sept 7 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf ||<br />
|-<br />
|Sept 9 || Meet in library || Meet in library <br />
|-<br />
|Sept 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II%202011.pdf}}Species II 2011.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf || rowspan="3"| Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Sept 14 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.pdf ||<br />
<!--Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18) --><br />
|-<br />
|Sept 16 || lab || lab<br />
|-<br />
|Sept 19 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202011.pdf}}Subspecies 2011.pdf || || rowspan="3"| Intro to Mesquite and Morphological Matrices '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Sept 21 || Infrapopulation variation (lecture sent via email) ||<br />
|-<br />
|Sept 23 || lab || lab<br />
|-<br />
|Sept 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202011.pdf}}Higher Categories 2011.pdf || || rowspan="3"| Keys, species descriptions, and cybertaxonomy '''(Meet in McCarthy Room, 4th floor TLS)''' <br />
|-<br />
|Sept 28 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inferencev2_2011.pdf}}Intro to phylogenetic inference ||<br />
|-<br />
|Sept 30 || lab || lab<br />
|-<br />
|Oct 3 || ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf<br/>(only read chapter 2)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf || rowspan="3"| Manipulating molecular characters with Mesquite<br/>and a BLAST tutorial '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Oct 5 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters_1%202011.pdf}}Characters_1 2011.pdf ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf<br />
|-<br />
|Oct 7 || lab || lab<br />
|-<br />
|Oct 10 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202011.pdf}}Multivariate Methods 2011.pdf || || rowspan="3"| Parsimony and distant methods with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Oct 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf<br />
|-<br />
|Oct 14 || lab || lab<br />
|-<br />
|Oct 17 || ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PageHolmesChptr5.pdf}}PageHolmesChptr5.pdf|| rowspan="3"| Parsimony with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Oct 19 || ||<br />
|-<br />
|Oct 21 || lab || lab<br />
|-<br />
|Oct 24 || |||| rowspan="3"| AMNH and Bronx Zoo Trip<br />
|-<br />
|Oct 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202011.pdf}}Reliability 2011.pdf||<br />
|-<br />
|Oct 28 || No Lab || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lewis_2001-TREE-16-1.30-37.pdf}}Lewis_2001_TREE.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Holder%26Lewis2003NatRevGen.pdf}}Holder&Lewis2003_NatRevGen.pdf<br />
|-<br />
|Oct 31 ||lab ||lab || rowspan="3"| Model comparison with Modeltest '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Nov 2 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Guest Lecture Paul Lewis || <br />
|-<br />
|Nov 4 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_4Nov2011.pdf}}Guest Lecture Paul Lewis ||<br />
|-<br />
<!--|Sept 21 ||Variation within a genotype: ontogeny & phenotypic plasticity{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Infrasubspecific%20Variation%202009.pdf}}Infrasubspecific Variation 2009.pdf || || rowspan="3"| Alpha Taxonomy<br/>Tiger Beetle Exercise<br/>Mesquite Morphological Matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%201999.pdf}}Winston 1999.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20morphological%20matrices.pdf}}Mesquite morphological tutorial.pdf<br />
|-<br />
|Sept 23 ||Supraspecfic taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)<br />
|-<br />
|Sept 25 ||Lab {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf ||<br />
|-<br />
|Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Chart%20the%20evol%20history%20of%20life.pdf}}Chart the evol history of life.pdf(For 09/30)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools<br />
|-<br />
|Sept 30 ||Trees and characters: types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf ||<br />
|-<br />
|Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)<br />
|-<br />
|Oct 5 ||Taxonomic characters: polarity, outgroups, order, weighting, and step matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters%20II.pdf}}Characters II.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CompleatCladist.pdf}}Cladistics Review I.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Collin%26Miglietta%202008%20Dollo%20Law.pdf}}Collin&Miglietta 2008 Dollo's Law.pdf|| rowspan="3"| Mesquite II: manipulating DNA/amino acid sequences<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20Lab%20II}}Mesquite Lab II<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/GenBank%20Tutorial%202009}}GenBank Tutorial<br />
|-<br />
|Oct 7 ||More on trees<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/More%20on%20Trees.pdf}}Trees.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Cladistics.pdf}}Cladistics Review II.pdf<br />
|-<br />
|Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16)<br />
|-<br />
|Oct 12 ||Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate techniques<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202009.pdf}}Multivariate Methods 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202009.pdf}}Distance Methods 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf (For 10/14&16)|| rowspan="3"|Intro to PAUP*:<br/>neighbor-joining<br/>corrected distances<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab%205_PAUP%20Intro%20revised-1.doc}}Lab 5 PAUP Intro.doc<br />
|-<br />
|Oct 14 ||Molecular systematics in animals (Simon guest lecture)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Guest%20Lecture%20Wagner%27s%20Systematics-%20How%20Molecules%20Evolve.%20Fall%2009.pdf}}How Molecules Evolve.pdf||<br />
|-<br />
|Oct 16 ||Lab ||<br />
|-<br />
|Oct 19 ||Exam||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Sample%20Questions%202009.pdf}}Midterm Sample Questions 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Neighbor-joining%20Exercise.pdf}}Neighbor-joining Exercise.pdf||rowspan="3"|American Museum of Natural History<br />
|-<br />
|Oct 21 ||Midterm Review<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Post-Exam%20Review.pdf}}Midterm Post-Exam Review.pdf||<br />
|-<br />
|Oct 23 ||AMNH Trip ||<br />
|-<br />
|Oct 26 ||Parsimony; search algorithms;<br/>algorithmic power, accuracy, and inconsistency<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony.pdf}}Parsimony.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Part2_1.pdf}}Page&Holmes_Rest_of_Ch6.pdf||rowspan="3"|Parsimony Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab6_parsimony_2009.doc}}Lab6 Parsimony.doc<br />
|-<br />
|Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf||<br />
|-<br />
|Oct 30 ||Lab ||<br />
|-<br />
|Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab7_2009_corrected.doc}}Lab7.doc<br />
|-<br />
|Nov 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf||<br />
|-<br />
|Nov 6 ||Lab ||<br />
|-<br />
|Nov 9 ||Molecular systematics in plants (Don Les)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Systematics_2009_Les.pdf}}Plant Systematics Les.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes280_285.pdf}}Page&Holmes280-285.pdf||rowspan="3"|Garli and MrBayes Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab8_2009.doc}}Lab8.doc<br />
|-<br />
|Nov 11 ||Reliability and measures of tree support: c.i., r.i.,<br/>decay indices, bootstraps ; jackknifes; and sensitivity analyses;<br/>bootstraps, randomization tests<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202009.pdf}}Reliability 2009.pdf||<br />
|-<br />
|Nov 13 ||Lab ||<br />
|-<br />
|Nov 16 ||Data partitions; consensus; ILD<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ILD%202009.doc}}ILD 2009.doc||rowspan="3"|COI data set analysis<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_barcoding_2009_corrected.doc}}Lab9 COI Barcodes.doc<br />
|-<br />
|Nov 18 ||DNA Barcodes<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes.pdf}}DNA Barcodes.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/FunkOmlandARev.pdf}}Funk & Omland.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Astraptes%20fulgerator.pdf}}Hebert et al. 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meyer%20and%20Paulaypdf%20copy.pdf}}Meyer and Paulay.pdf<br />
|-<br />
|Nov 20 ||Lab ||<br />
|-<br />
|Nov 23-28 ||No class-Thanksgiving Break||<br />
|-<br />
|Nov 30 ||Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202009.pdf}}Nomenclature 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Berenbaum%20Article.pdf}}Berenbaum Article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conniff%20article.pdf}}Conniff article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Gould_Bully%20for%20Bront.pdf}}Gould_Bully for Bront.pdf||rowspan="3"|Mesquite: Ancestral States Reconstruction<br />
|-<br />
|Dec 2 ||Nomenclature; Phylocode||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mares2009.pdf}}Mares2009.pdf<br />
|-<br />
|Dec 4 ||Lab ||<br />
|-<br />
|Dec 7 ||Special topic: Taxonomic Collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab<br />
|-<br />
|Dec 9 ||Special topic: Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202009%20Class%20Version.pdf}}Patterns and Processes.pdf||<br />
|-<br />
|Dec 11 ||Conservation, Systematics, and looking ahead<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}Looking Ahead 2009.pdf||<br />
|}--><br />
<br/><br />
=='''Supplementary Reading'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#2A52BE;" width="275"|Topics<br />
!style="background:#008080;" width="975"|Additional Reading<br />
|- <br />
| Species as ranked taxa and species concepts || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Application%20of%20Evol%20Spp%20concept.pdf}}Application of Evolutionary Species concept.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20concept%20for%20prokaryotes%202001.pdf}}Species concept for prokaryotes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Noor%202002%20BSC%20showing%20age%3F.pdf}}Is the BSC showing its age?.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Sites%20and%20Crandall%20Con.Bio%201997.pdf}}Importance of stating species concept for conservation purposes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/AgapowSpeciesQRB04.pdf}}Impact of species concepts on biodiversity studies.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Urge%20to%20state%20species%20concept.pdf}}The need for specifying species concepts.pdf{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hey%202007.pdf}}On the failure of modern species concepts.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20as%20Ranked%20Taxa%20Baum%202009.pdf}}Species as ranked taxa.pdf<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Increase%20in%20bird%20species.pdf}}Does the choice of species concept result in an increase in bird species?.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bond%20and%20Stockman%202008.pdf}}Method for delimiting Cohesion speceis.pdf<br />
|-<br />
|DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Barcoding%20Leps%20of%20Costa%20Rica%20Guanacaste%20red.%20Janzen%20et%20al.pdf}}Janzen et al 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/TenReasonsBarcoding.pdf}}Ten Reasons For Barcoding.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Will%20%26%20Rubinoff%202004.pdf}}Will & Rubinoff 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert%20and%20Gregory%202005.pdf}}Hebert and Gregory 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_PromisesAndPitfalls.pdf}}Moritz and Cicero 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2003_DNABarcodes.pdf}}Hebert et al.2003.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_Birds_Hebert_et_al_2004.pdf}}PLoS_Birds_Hebert et al. 2004.pdf<br />
|}<br />
=='''Grading'''==<br />
{| border="1" cellpadding="1"<br />
| Lab and take home exercises || 20% || 200 pts<br />
|-<br />
| Midterm || 20% || 200 pts<br />
|-<br />
| Term paper || 22% || 220 pts<br />
|-<br />
| Nomenclature exercise || 1% || 10 pts<br />
|-<br />
| Participation || 2% || 20 pts<br />
|-<br />
| Final || 35% || 350 pts<br />
|-<br />
| '''Total''' || '''100%''' || '''1000 pts'''<br />
|}<br />
<br/><br />
=='''Term paper'''==<br />
Each student will be required to prepare a paper that will be due on December 4th. Styles that have been adopted in the past include (1) a literature review<br />
that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on 20 November. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm<br />
<br/><br />
=='''Funding sources for taxonomy and biodiversity'''==<br />
Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies. It was created in 2010, so most sources are up to date.<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Funding%20for%20biodiversity%20and%20taxonomy%202010.pdf}}Funding for biodiversity and taxonomy 2010.pdf<br />
<br/><br />
=='''Important dates'''==<br />
<span style="font-size: large"><br />
7 October, 2011: conference; topic selection<br/><br />
17 October, 2011: midterm<br/><br />
21 October, 2011: outline with 5+ references<br/><br />
18 November, 2011: first draft due<br/><br />
2 December, 2011: paper due<br/><br />
[[Category:EEB Courses]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Principles_and_Methods_of_Systematic_Biology_(EEB_5347)&diff=19606Principles and Methods of Systematic Biology (EEB 5347)2011-11-03T13:17:12Z<p>PaulLewis: </p>
<hr />
<div>[[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]<br />
<span style="font-size: large">Fall 2011<br/><br />
<br />
<span style="font-size: large">Lecture MW 9:00-10:30, Lab F 9:00-10:30<br/><br />
<br/><br />
<span style="font-size: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/><br />
Phone: 486-2139<br/> <br />
office hours as available<br/><br />
email: [mailto:david.wagner'at'uconn.edu david.wagner'at'uconn.edu]<br/><br />
<br/><br />
'''Graduate Teaching Assistant''': Chris Owen<br/><br />
Office hours: BioPharm 325 Wednesdays 10:30-11:30 or by appointment<br/><br />
Phone: 486-6650<br/><br />
email: [mailto:christopher.l.owen'at'uconn.edu christopher.l.owen'at'uconn.edu]<br/><br />
<br/><br />
== '''Textbook and readings''' ==<br />
There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Many readings will be available as pdfs, downloadable from the course website. Others, available in hard copy only, will be on reserve in the departmental office (TLS 312) in the filing cabinet next to the window. You are free to check out copy #2 for 3 hours; copy #1 should stay in the office, i.e., so one is always there for others to photocopy.<br />
<br/><br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|- <br />
| Aug 29 ||Class canceled due to Hurricane Irene<br/><!--{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Introduction%202009%20class%20notes.pdf}}Introduction 2009 class notes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Syllabus%202009.pdf}}Syllabus.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Rules%20of%20Pronunciation%20Sci.%20Name.PDF}}Rules of Pronunciation Sci.Name.pdf--><br />
|| || rowspan="3"| Lecture instead of lab this week<br />
|-<br />
| Aug 31 ||Organizational meeting, an introduction to biological systematics||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs1-18.pdf}}Mayr&Ashlock1991_pgs1-18.pdf (optional)<br />
|-<br />
| Sept 2 ||The many roles of biological systematics & collections tour <!--Species definitions & species intermediacy<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}De Queiroz 2007.pdf<br/>http://en.wikipedia.org/wiki/Species#Definitions_of_species<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445-451.pdf}}Futuyma_spconcepts_445-451.pdf<br />
|-<br />
| Sept 5 ||Labor Day No class || || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 '''<br />
|-<br />
|Sept 7 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf ||<br />
|-<br />
|Sept 9 || Meet in library || Meet in library <br />
|-<br />
|Sept 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II%202011.pdf}}Species II 2011.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf || rowspan="3"| Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Sept 14 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.pdf ||<br />
<!--Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18) --><br />
|-<br />
|Sept 16 || lab || lab<br />
|-<br />
|Sept 19 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202011.pdf}}Subspecies 2011.pdf || || rowspan="3"| Intro to Mesquite and Morphological Matrices '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Sept 21 || Infrapopulation variation (lecture sent via email) ||<br />
|-<br />
|Sept 23 || lab || lab<br />
|-<br />
|Sept 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202011.pdf}}Higher Categories 2011.pdf || || rowspan="3"| Keys, species descriptions, and cybertaxonomy '''(Meet in McCarthy Room, 4th floor TLS)''' <br />
|-<br />
|Sept 28 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inferencev2_2011.pdf}}Intro to phylogenetic inference ||<br />
|-<br />
|Sept 30 || lab || lab<br />
|-<br />
|Oct 3 || ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf<br/>(only read chapter 2)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf || rowspan="3"| Manipulating molecular characters with Mesquite<br/>and a BLAST tutorial '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Oct 5 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters_1%202011.pdf}}Characters_1 2011.pdf ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf<br />
|-<br />
|Oct 7 || lab || lab<br />
|-<br />
|Oct 10 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202011.pdf}}Multivariate Methods 2011.pdf || || rowspan="3"| Parsimony and distant methods with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Oct 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf<br />
|-<br />
|Oct 14 || lab || lab<br />
|-<br />
|Oct 17 || ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PageHolmesChptr5.pdf}}PageHolmesChptr5.pdf|| rowspan="3"| Parsimony with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Oct 19 || ||<br />
|-<br />
|Oct 21 || lab || lab<br />
|-<br />
|Oct 24 || |||| rowspan="3"| AMNH and Bronx Zoo Trip<br />
|-<br />
|Oct 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202011.pdf}}Reliability 2011.pdf||<br />
|-<br />
|Oct 28 || No Lab || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lewis_2001-TREE-16-1.30-37.pdf}}Lewis_2001_TREE.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Holder%26Lewis2003NatRevGen.pdf}}Holder&Lewis2003_NatRevGen.pdf<br />
|-<br />
|Oct 31 ||lab ||lab || rowspan="3"| Model comparison with Modeltest '''(Meet in McCarthy Room, 4th floor TLS)'''<br />
|-<br />
|Nov 2 || Guest Lecture Paul Lewis|| {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Likelihood_2Nov2011.pdf<br />
|-<br />
|Nov 4 || Guest Lecture Paul Lewis ||<br />
|-<br />
<!--|Sept 21 ||Variation within a genotype: ontogeny & phenotypic plasticity{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Infrasubspecific%20Variation%202009.pdf}}Infrasubspecific Variation 2009.pdf || || rowspan="3"| Alpha Taxonomy<br/>Tiger Beetle Exercise<br/>Mesquite Morphological Matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%201999.pdf}}Winston 1999.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20morphological%20matrices.pdf}}Mesquite morphological tutorial.pdf<br />
|-<br />
|Sept 23 ||Supraspecfic taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)<br />
|-<br />
|Sept 25 ||Lab {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf ||<br />
|-<br />
|Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Chart%20the%20evol%20history%20of%20life.pdf}}Chart the evol history of life.pdf(For 09/30)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools<br />
|-<br />
|Sept 30 ||Trees and characters: types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf ||<br />
|-<br />
|Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)<br />
|-<br />
|Oct 5 ||Taxonomic characters: polarity, outgroups, order, weighting, and step matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters%20II.pdf}}Characters II.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CompleatCladist.pdf}}Cladistics Review I.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Collin%26Miglietta%202008%20Dollo%20Law.pdf}}Collin&Miglietta 2008 Dollo's Law.pdf|| rowspan="3"| Mesquite II: manipulating DNA/amino acid sequences<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20Lab%20II}}Mesquite Lab II<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/GenBank%20Tutorial%202009}}GenBank Tutorial<br />
|-<br />
|Oct 7 ||More on trees<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/More%20on%20Trees.pdf}}Trees.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Cladistics.pdf}}Cladistics Review II.pdf<br />
|-<br />
|Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16)<br />
|-<br />
|Oct 12 ||Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate techniques<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202009.pdf}}Multivariate Methods 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202009.pdf}}Distance Methods 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf (For 10/14&16)|| rowspan="3"|Intro to PAUP*:<br/>neighbor-joining<br/>corrected distances<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab%205_PAUP%20Intro%20revised-1.doc}}Lab 5 PAUP Intro.doc<br />
|-<br />
|Oct 14 ||Molecular systematics in animals (Simon guest lecture)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Guest%20Lecture%20Wagner%27s%20Systematics-%20How%20Molecules%20Evolve.%20Fall%2009.pdf}}How Molecules Evolve.pdf||<br />
|-<br />
|Oct 16 ||Lab ||<br />
|-<br />
|Oct 19 ||Exam||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Sample%20Questions%202009.pdf}}Midterm Sample Questions 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Neighbor-joining%20Exercise.pdf}}Neighbor-joining Exercise.pdf||rowspan="3"|American Museum of Natural History<br />
|-<br />
|Oct 21 ||Midterm Review<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Post-Exam%20Review.pdf}}Midterm Post-Exam Review.pdf||<br />
|-<br />
|Oct 23 ||AMNH Trip ||<br />
|-<br />
|Oct 26 ||Parsimony; search algorithms;<br/>algorithmic power, accuracy, and inconsistency<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony.pdf}}Parsimony.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Part2_1.pdf}}Page&Holmes_Rest_of_Ch6.pdf||rowspan="3"|Parsimony Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab6_parsimony_2009.doc}}Lab6 Parsimony.doc<br />
|-<br />
|Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf||<br />
|-<br />
|Oct 30 ||Lab ||<br />
|-<br />
|Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab7_2009_corrected.doc}}Lab7.doc<br />
|-<br />
|Nov 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf||<br />
|-<br />
|Nov 6 ||Lab ||<br />
|-<br />
|Nov 9 ||Molecular systematics in plants (Don Les)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Systematics_2009_Les.pdf}}Plant Systematics Les.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes280_285.pdf}}Page&Holmes280-285.pdf||rowspan="3"|Garli and MrBayes Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab8_2009.doc}}Lab8.doc<br />
|-<br />
|Nov 11 ||Reliability and measures of tree support: c.i., r.i.,<br/>decay indices, bootstraps ; jackknifes; and sensitivity analyses;<br/>bootstraps, randomization tests<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202009.pdf}}Reliability 2009.pdf||<br />
|-<br />
|Nov 13 ||Lab ||<br />
|-<br />
|Nov 16 ||Data partitions; consensus; ILD<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ILD%202009.doc}}ILD 2009.doc||rowspan="3"|COI data set analysis<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_barcoding_2009_corrected.doc}}Lab9 COI Barcodes.doc<br />
|-<br />
|Nov 18 ||DNA Barcodes<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes.pdf}}DNA Barcodes.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/FunkOmlandARev.pdf}}Funk & Omland.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Astraptes%20fulgerator.pdf}}Hebert et al. 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meyer%20and%20Paulaypdf%20copy.pdf}}Meyer and Paulay.pdf<br />
|-<br />
|Nov 20 ||Lab ||<br />
|-<br />
|Nov 23-28 ||No class-Thanksgiving Break||<br />
|-<br />
|Nov 30 ||Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202009.pdf}}Nomenclature 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Berenbaum%20Article.pdf}}Berenbaum Article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conniff%20article.pdf}}Conniff article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Gould_Bully%20for%20Bront.pdf}}Gould_Bully for Bront.pdf||rowspan="3"|Mesquite: Ancestral States Reconstruction<br />
|-<br />
|Dec 2 ||Nomenclature; Phylocode||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mares2009.pdf}}Mares2009.pdf<br />
|-<br />
|Dec 4 ||Lab ||<br />
|-<br />
|Dec 7 ||Special topic: Taxonomic Collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab<br />
|-<br />
|Dec 9 ||Special topic: Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202009%20Class%20Version.pdf}}Patterns and Processes.pdf||<br />
|-<br />
|Dec 11 ||Conservation, Systematics, and looking ahead<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}Looking Ahead 2009.pdf||<br />
|}--><br />
<br/><br />
=='''Supplementary Reading'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#2A52BE;" width="275"|Topics<br />
!style="background:#008080;" width="975"|Additional Reading<br />
|- <br />
| Species as ranked taxa and species concepts || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Application%20of%20Evol%20Spp%20concept.pdf}}Application of Evolutionary Species concept.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20concept%20for%20prokaryotes%202001.pdf}}Species concept for prokaryotes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Noor%202002%20BSC%20showing%20age%3F.pdf}}Is the BSC showing its age?.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Sites%20and%20Crandall%20Con.Bio%201997.pdf}}Importance of stating species concept for conservation purposes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/AgapowSpeciesQRB04.pdf}}Impact of species concepts on biodiversity studies.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Urge%20to%20state%20species%20concept.pdf}}The need for specifying species concepts.pdf{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hey%202007.pdf}}On the failure of modern species concepts.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20as%20Ranked%20Taxa%20Baum%202009.pdf}}Species as ranked taxa.pdf<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Increase%20in%20bird%20species.pdf}}Does the choice of species concept result in an increase in bird species?.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bond%20and%20Stockman%202008.pdf}}Method for delimiting Cohesion speceis.pdf<br />
|-<br />
|DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Barcoding%20Leps%20of%20Costa%20Rica%20Guanacaste%20red.%20Janzen%20et%20al.pdf}}Janzen et al 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/TenReasonsBarcoding.pdf}}Ten Reasons For Barcoding.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Will%20%26%20Rubinoff%202004.pdf}}Will & Rubinoff 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert%20and%20Gregory%202005.pdf}}Hebert and Gregory 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_PromisesAndPitfalls.pdf}}Moritz and Cicero 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2003_DNABarcodes.pdf}}Hebert et al.2003.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_Birds_Hebert_et_al_2004.pdf}}PLoS_Birds_Hebert et al. 2004.pdf<br />
|}<br />
=='''Grading'''==<br />
{| border="1" cellpadding="1"<br />
| Lab and take home exercises || 20% || 200 pts<br />
|-<br />
| Midterm || 20% || 200 pts<br />
|-<br />
| Term paper || 22% || 220 pts<br />
|-<br />
| Nomenclature exercise || 1% || 10 pts<br />
|-<br />
| Participation || 2% || 20 pts<br />
|-<br />
| Final || 35% || 350 pts<br />
|-<br />
| '''Total''' || '''100%''' || '''1000 pts'''<br />
|}<br />
<br/><br />
=='''Term paper'''==<br />
Each student will be required to prepare a paper that will be due on December 4th. Styles that have been adopted in the past include (1) a literature review<br />
that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on 20 November. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm<br />
<br/><br />
=='''Funding sources for taxonomy and biodiversity'''==<br />
Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies. It was created in 2010, so most sources are up to date.<br/><br />
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Funding%20for%20biodiversity%20and%20taxonomy%202010.pdf}}Funding for biodiversity and taxonomy 2010.pdf<br />
<br/><br />
=='''Important dates'''==<br />
<span style="font-size: large"><br />
7 October, 2011: conference; topic selection<br/><br />
17 October, 2011: midterm<br/><br />
21 October, 2011: outline with 5+ references<br/><br />
18 November, 2011: first draft due<br/><br />
2 December, 2011: paper due<br/><br />
[[Category:EEB Courses]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Seminar_speaker_sign-up&diff=19337Seminar speaker sign-up2011-10-18T14:47:42Z<p>PaulLewis: </p>
<hr />
<div>'''Seminar Speaker:''' Chris Eckert<br><br />
'''Institution:''' Department of Biology, Queens University<br><br />
'''Web site:''' http://post.queensu.ca/~eckertc/Eckert_Lab/Welcome.html <br><br />
'''Seminar Title:''' Ecology and evolution of geographic range limits <br><br />
'''Faculty or Student Contact:''' Carl Schlichting<br />
==Thursday, October 18==<br />
{|border=1 cellpadding=8<br />
| '''Time''' || '''Name''' || '''Room''' <br />
<br />
<br />
|-<br />
| 7:45 a.m. ||Katherine Theiss|| Breakfast Tolland Inn <br />
|-<br />
| 9:00 a.m. || || <br />
|-<br />
| 9:30 a.m. || ||<br />
|-<br />
| 10:00 a.m. || || <br />
|-<br />
| 10:30 a.m. || || <br />
|-<br />
| 11:00 a.m. || || <br />
|-<br />
| 11:30 a.m. || ||<br />
|-<br />
| 12:00 p.m. || Lunch with Graduate Students|| Bamford<br />
|-<br />
| 1:00 p.m. || || <br />
|-<br />
| 1:30 p.m. || ||<br />
|-<br />
| 2:00 p.m. || || <br />
|-<br />
| 2:30 p.m. || ||<br />
|-<br />
| 3:00 p.m. || Prep for seminar || TLS 363<br />
|-<br />
| 3:30 p.m. || coffee & cookies || Bamford Room <br />
Reminder: pick up laser pointer and seminar speaker form from Kathy Tebo <br />
|-<br />
| 4:00 p.m. || Seminar || BPB 130<br />
|-<br />
| Dinner 6:00 p.m. ||Dinner ||David <br />
|-<br />
<br />
<br />
|-<br />
|}<br />
==Friday, October 19==<br />
{|border=1 cellpadding=8<br />
| '''Time''' || '''Name''' || '''Room''' <br />
<br />
<br />
|-<br />
| 7:45 a.m. |||| Breakfast Tolland Inn<br />
|-<br />
| 9:00 a.m. || || <br />
|-<br />
| 9:30 a.m. || ||<br />
|-<br />
| 10:00 a.m. || Paul Lewis || TLS 166a <br />
|-<br />
| 10:30 a.m. || || <br />
|-<br />
| 11:00 a.m. || || <br />
|-<br />
| 11:30 a.m. || ||</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=19073Systematics Seminar2011-09-16T17:40:05Z<p>PaulLewis: /* Tuesday, September 20, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=19072Systematics Seminar2011-09-16T17:39:51Z<p>PaulLewis: /* Tuesday, September 20, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae<br />
(Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=19071Systematics Seminar2011-09-16T17:38:15Z<p>PaulLewis: /* Tuesday, September 20, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Laszlo et al 2010 - shrooms.pdf<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=19070Systematics Seminar2011-09-16T17:36:37Z<p>PaulLewis: /* Tuesday, September 13, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
=== Tuesday, September 20, 2011 ===<br />
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18921Systematics Seminar2011-09-06T17:32:06Z<p>PaulLewis: /* Tuesday, September 6, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18920Systematics Seminar2011-09-06T17:31:47Z<p>PaulLewis: /* Meeting time and place */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)<br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at 4 pm today in TLS 154, and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18919Systematics Seminar2011-09-06T17:30:59Z<p>PaulLewis: </p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''. <br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at 4 pm today in TLS 154, and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18918Systematics Seminar2011-09-06T17:30:22Z<p>PaulLewis: /* Tuesday, September 13, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar. This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''. <br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at 4 pm today in TLS 154, and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18917Systematics Seminar2011-09-06T17:27:35Z<p>PaulLewis: /* Tuesday, September 13, 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar. This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''. <br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at 4 pm today in TLS 154, and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18916Systematics Seminar2011-09-06T17:14:37Z<p>PaulLewis: /* Theme for Fall Semester 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar. This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''. <br />
<br />
== Schedule for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
=== Tuesday, September 6, 2011 ===<br />
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at 4 pm today in TLS 154, and is entitled “Sympatric Speciation on the Seashore.”<br />
<br />
=== Tuesday, September 13, 2011 ===<br />
Eric Schultz will lead a discussion of the following paper:<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18915Systematics Seminar2011-09-06T17:10:49Z<p>PaulLewis: /* Theme for Fall Semester 2011 */</p>
<hr />
<div>This is the home page of the UConn EEB department's Systematics Seminar. This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
<br />
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
<br />
== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''. <br />
<br />
== Theme for Fall Semester 2011 ==<br />
<br />
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.<br />
* Ancestral state reconstruction<br />
* Use of niche modeling in delimiting species<br />
* Informativeness of genes <br />
* Cryptic species<br />
<br />
== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
<br />
[[Category:EEB Seminars]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Help:Contents&diff=18895Help:Contents2011-09-06T14:45:00Z<p>PaulLewis: </p>
<hr />
<div>EEBedia uses the same software that runs [http://en.wikipedia.org/wiki/Main_Page Wikipedia], so that means it is easy to contribute information. Here are some basic instructions, but a '''much more in depth tutorial''' is available at http://meta.wikimedia.org/wiki/Help:Contents.<br />
<br />
== How to find information in EEBedia ==<br />
* Use the '''search box''' on the left (you might need to scroll up to see it) to find pages that have certain keywords<br />
* If you just want to browse, start by clicking on the [[Special:Specialpages|Special Pages]] link (in the navigation bar on your left), then on one of the special summary page links provided. The two I find most useful are [[Special:Categories|Categories]] and [[Special:Allpages|All pages]]<br />
* If you want to see what people have been working on recently, check out [[Special:Recentchanges|Recent changes]]<br />
<br />
== Who can add to EEBedia ==<br />
EEBedia is open to everyone for reading, but only current members of the [http://hydrodictyon.eeb.uconn.edu/ EEB Department] can add content. The specific requirements for authoring content are:<br />
# You must have a UConn NetID<br />
# You must be on a list of allowed UConn NetIDs <br />
<br />
For information about UConn NetIDs (getting one if you are new to UConn, or finding out your NetID and password if you have forgotten it), go to the main [http://netid.uconn.edu UConn NetID web page].<br />
<br />
To get added to the list of allowed NetIDs, send your NetID (but '''not''' your NetID ''password''!) to the [[EEB Webmaster]].<br />
<br />
==Info for new users==<br />
=== For all users... ===<br />
* After you login for the first time, you should '''click my preferences''' at the top and at least '''enter your real name and email address.''' Do not be tempted to change your password here; the normal password system has been routed through the university's NetID system, so changing your password in EEBedia will have no effect (or at least not a positive effect).<br />
* '''Please do not edit the main page.''' The main page is special because it is the first thing everyone sees when they enter the EEBedia. It would be confusing if it were always changing, so please add your 2 cents elsewhere. The same goes for the navigation bar; yes, it is possible to change it, but please resist the temptation. You are welcome to send me (the [[EEB Webmaster]]) suggestions, however, if you think something should be added or subtracted to the main page.<br />
* Visit [[How to add to EEBedia]] (always available under the Help link on the navigation bar to your left) to learn how to get started creating and editing articles.<br />
<br />
=== For graduate students... ===<br />
If you want your research to show up in the EEB Spotlight area of the main page, create a ''short'' intro with a single image and a title like this "Dissertation Research: Your Name". See [[Dissertation Research: Jon Richmond]] for an example. By starting your title with "Dissertation Research:", it makes it easy to find all of these research synopses by typing "Dissertation Research" into the search tool.<br />
<br />
At the end of this page, put in a "More..." link to a page with a more extensive description of your research, and a few more photos (including one of yourself if possible). See Jon's page for an example (i.e. click on his More... link).<br />
<br />
== Troubleshooting ==<br />
Here are some tips if you are having trouble logging into EEBedia:<br />
* Note that in order to edit EEBedia pages you must enable [http://en.wikipedia.org/wiki/HTTP_cookie cookies] in your browser. EEBedia uses cookies to remember that you are logged in (so that you don't have to re-enter your NetID and password each time you move from one article to another. In the FireFox browser, at least, you can search your cookies for the word <tt>hydrodictyon</tt> to see what information is being stored on your computer (you will find it is pretty innocuous). <br />
* Although www.eeb.uconn.edu is an alias for hydrodictyon.eeb.uconn.edu in general, don't use www.eeb.uconn.edu when accessing EEBedia pages (at least not if you need to login to create or edit pages). Thus, if you are having trouble logging in (and you know your browser is accepting cookies), look at the address bar and make sure the address of the page you are editing begins with <tt>http://hydrodictyon.eeb.uconn.edu/eebedia/...</tt> and not <tt>http://hydrodictyon.eeb.uconn.edu/eebedia/...</tt>.<br />
<br />
==Starting a new page==<br />
There are two easy ways to create a brand new page:<br />
<br />
* Type the title of your new page in the search box, then press go. The search will fail, but you will be given the option of creating a new page with that title (click on the red link text "create this page")<br />
* Edit an existing page, putting in a link to the non-existant new page. When you save the page you edited, the link will show up in red, meaning it does not yet exist. Click the new link and you will be given the option to create the page.<br />
<br />
Avoid the temptation to edit the main page (say for the purpose of adding a link to your new page). If your page represents a news item or an upcoming event, you might want to make a link to it on the [[Current events]] page. This page can be found by clicking the Current events link on the navigation bar to your left, and its contents are dumped into the Main Page. Just remember to date your entry (formatted like the other news items) and ''keep your announcement short''. You can link to a page with more information, for example by placing wikitext like the following in your advertisement: <tt><nowiki>[[MyPage|More...]]</nowiki></tt>, where MyPage is the title of your more extensive page.<br />
<br />
==Text==<br />
Just type text in the window that appears upon clicking the edit tab of any existing page. You can use the toolbar at the top of the window to learn how to ''italicize'' or '''bold''' words. <br />
<br />
===Subsections===<br />
Creating a new section can be done by surrounding the title with equals signs. Two equals signs flanking a title produces a subheading. For example, the heading of this subsection looks like this: <tt><nowiki>==Title==</nowiki></tt>. Three equals signs flanking some text produces a subsubsection heading. For example, this subsubsection was created using this syntax: <tt><nowiki>===Subsections===</nowiki></tt><br />
<br />
===Lists===<br />
To create a bulleted list, just precede each item in the list by an asterisk (*), like this:<br />
* first item<br />
* second item<br />
* third item<br />
This will generate a list that looks like this:<br />
* first item<br />
* second item<br />
* third item<br />
To create an enumerated (numbered) list, use hash marks (#) instead of asterisks:<br />
# first item<br />
# second item<br />
# third item<br />
Here's what this kind of list looks like:<br />
# first item<br />
# second item<br />
# third item<br />
<br />
===Preformatted text===<br />
Preformatted text is text that appears exactly as typed, in a fixed-width typewriter font such as Courier. You can create preformatted text by simply placing a space at the beginning of each line. For example,<br />
This line begins with a space and is treated as preformatted text<br />
<br />
===Centering text===<br />
Use an HTML div tag to center text<br />
<nowiki><div style="text-align: center">text you want to have centered</div></nowiki><br />
<br />
===Changing the font size===<br />
Use an HTML span tag to make text larger<br />
<nowiki><span style="font-size: larger">To be shown in large font</span></nowiki><br />
<br />
===Line breaks===<br />
You may have noticed that pressing the enter key in the editor does not insert a line break, and pressing the enter key twice inserts two line breaks! There are many situations where you would like to insert just one line break (say, to separate the lines in your address). To insert just one line break, use a <nowiki><br/></nowiki> HTML tag. Here is an example of what is typed into the editor: <br />
<pre><br />
Department of Ecology and Evolutionary Biology<br/><br />
University of Connecticut<br/><br />
75 N. Eagleville Road<br/><br />
Storrs, CT 06269<br />
</pre><br />
And here is what it looks like when formatted:<br />
<br />
University of Connecticut<br/><br />
75 N. Eagleville Road<br/><br />
Storrs, CT 06269<br />
<br />
===More information about text formatting===<br />
More information about what to include in style attributes can be found at the [http://www.w3schools.com/css/css_howto.asp CSS HowTo]<br />
<br />
Much more information about organizing and formatting wiki pages is available at the [http://meta.wikimedia.org/wiki/Help:Wikitext Wikitext] site.<br />
<br />
==Hyperlinks==<br />
To add a hyperlink to a page external to EEBedia, just type in the URL (including the initial <tt><nowiki>http://</nowiki></tt>): For example, here is a link to the EEB home page: http://hydrodictyon.eeb.uconn.edu/ that is created by simply adding the text <tt><nowiki>http://hydrodictyon.eeb.uconn.edu/</nowiki></tt> to the sentence. <br />
<br />
Most of the time, you will not want long URLs to clutter up your page. It is easy to create a short hyperlink by enclosing the URL in square brackets and, after a space, typing in the name you wish to use: For example, here is a link to [http://hydrodictyon.eeb.uconn.edu/ EEB] that is done like this: <tt><nowiki>[http://hydrodictyon.eeb.uconn.edu/ EEB]</nowiki></tt>.<br />
<br />
See http://meta.wikimedia.org/wiki/Help:Link for information about creating more complicated hyperlinks.<br />
<br />
==Footnotes and citations==<br />
To add a footnote or citation to a page, insert the text of the footnote at the spot where you want the footnote symbol to appear, surrounded by a <nowiki><ref></nowiki> tag. For example, here is a a reference to a work familiar to biologists<ref>Darwin, C. R. 1859. ''On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life.'' London: John Murray.</ref>. Here is what I inserted at this point in the document:<pre><br />
...work familiar to biologists<ref>Darwin, C. R. 1859. ''Darwin, C. R. 1859. ''On the origin <br />
of species by means of natural selection, or the preservation of favoured races in the struggle for<br />
life.'' London: John Murray.</ref>. At this point...</pre><br />
Note that the body of the footnote does not appear here. Instead, it appears at the bottom bottom of this page in a "References cited" section, at a point where I inserted the following tag:<pre><references/></pre><br />
This is an example of a very simple use of footnotes/citations. If you want to get more elaborate, see http://meta.wikimedia.org/wiki/Cite/Cite.php<br />
<br />
==Uploading files (e.g. images)==<br />
[[Image:Slime_mold_2777.jpg|thumb|left|Slime mold at Goodwin Conservation Center]][[Image:Pediastrum_duplex.jpg|thumb|right|''Pediastrum duplex''.]] You can upload an image file at [[Special:Upload]]. Please refrain from uploading an image that is excessively large. If you click the image of ''Pediastrum duplex'' at right, you are shown its actual size, which is about 60 KB. This is a reasonable size. The image of slime mold fruiting bodies at left is about as large as an image on EEBedia should be (150 KB). Images larger than this must be reduced in size to fit on a typical computer screen, so such files take up more space on the server than is necessary.<br/><br/>Below is the wiki text that was used to create the two images shown here. Note that including the keyword thumb causes the photo to be shown as a thumbnail (reduced size) image. The larger image can be obtained by clicking on the thumbnail. You can use the keywords left, right, or center to position the image horizontally on the page. Finally, the last entry in the image tag is the caption text. See the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax extended image syntax] page for more information about inserting images in to wiki pages.<pre><br />
[[Image:Pediastrum_duplex.jpg|thumb|right|''Pediastrum duplex'']]<br />
[[Image:Slime_mold_2777.jpg|thumb|left|Slime mold at Goodwin Conservation Center]]</pre><br />
<br />
==Linking to PDF files==<br />
To create a little PDF icon that links to an actual pdf file somewhere on the internet, you can do this:<br />
<br />
<nowiki>{{pdf|http://hydrodictyon.eeb.uconn.edu/test.pdf}} A test PDF file.</nowiki> <br />
<br />
The double-squiggly brackets are essential, as is the word pdf followed by the vertical bar. The rest of the template should be filled with an actual URL starting with <tt>http://</tt> and ending with the name of the pdf document. Here is how it will look in your EEBedia page:<br />
<br />
:{{pdf|http://hydrodictyon.eeb.uconn.edu/test.pdf}} A test PDF file.<br />
<br />
== Templates ==<br />
<br />
Templates are small articles that can be embedded within other articles. To see an example of a template, click [[Template:Under Construction|this link]]. This template can be inserted in an article using the following syntax:<br />
<nowiki>{{Under Construction}}</nowiki><br />
Here is what the template looks like when it is embedded:<br />
<br />
{{Under Construction}}<br />
<br />
To create a template, create a page in which the title begins with prefix <tt>Template:</tt>. The part following the colon becomes the label used when embedding the template in a page. The "Under Construction" template referenced above was created by creating an article entitled <br />
<nowiki>Template:Under Construction</nowiki><br />
<br />
== Categories ==<br />
<br />
You can assign your article to a category named "EEB courses" by placing something like this at the bottom<br />
<nowiki>[[Category:EEB Courses]]</nowiki><br />
This would create the category if it does not yet exist. This will place a link to the category at the bottom of your article that enables users to find other articles in the category. You can get a listing of all existing categories by clicking on the "Special pages" link in the toolbox at left.<br />
<br />
== Tweaks ==<br />
<br />
; <nowiki>__NOEDITSECTION__</nowiki><br />
Putting this command anywhere in an article inhibits [edit] links from appearing on the righthand side of each section of your article. (Note that there are '''two''' leading and '''two''' trailing underscores in the name of the command.)<br />
<br />
== References cited ==<br />
<references/></div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Ph.D._Ontogeny&diff=18811Ph.D. Ontogeny2011-08-31T15:40:01Z<p>PaulLewis: </p>
<hr />
<div>This page is for graduate students pursuing a Doctor of Philosphy (Ph.D.) degree in EEB and their advisor(s). This document is provided as a convenience, but please consult the [http://catalog.grad.uconn.edu/grad_catalog.html Graduate Catalog] for authoritative information, or for clarification and elaboration of information found here. If you would like this information in the form of a table that can be printed, filled in and kept on file, Eric Schultz's original Ph.D. Ontogeny documents can be downloaded in either [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/PhD_Student_Ontogeny_Table.doc Word] or [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/PhD_Student_Ontogeny_Table.pdf PDF] format. There is a corresponding [[M.S. Ontogeny|ontogeny for M.S. students]].<br />
<br />
== Advisory committee ==<br />
Formation of the advisory committee is recommended by the beginning of the second semester. The committee should include at least 3 faculty members: the major advisor, a second advisor (normally from EEB), and a third advisor, who must be a member of the graduate faculty at UConn.<br />
<br />
== Plan of Study ==<br />
EEB recommends that the Plan of Study be filed with the Graduate School by the (end of the?) third semester.<br />
<br />
== Foreign Language/Related Area requirement==<br />
The Ecology and Evolutionary Biology graduate field of study has no foreign language/related area requirement<br />
<br />
== General examination ==<br />
Within 5 years of commencing doctoral study (4 years if entry with a related Master's). No later than 8 months prior to completion. EEB recommendation is by the end of the second year. Attended and conducted by the advisory committee, and others (no fewer than five faculty members).<br />
<br />
== Dissertation proposal submitted ==<br />
Should occur no later than 6 months prior to degree completion. EEB recommendation is by end of third year. Advisory committee (major advisor and more than 2 members of committee) reviews proposal and recommends additional reviewers, which may include faculty in other departments and may be outside the university.<br />
<br />
== Candidacy status ==<br />
Candidacy status is conferred after the dissertation proposal is approved by all reviewers, is signed by the Head, and finally is approved by the Executive Committee of the Graduate Faculty Council.<br />
<br />
== &quot;Working copy&quot; dissertation filed ==<br />
Degree must be completed after at least 3 years of study beyond baccalaureate (2 years beyond Master's in related subject) and within 8 years of commencing doctoral study (7 years if entry with a related Master's). The Tentative Approval Page must be filed at least 7 days prior to examination. Please see the [http://grad.uconn.edu/dissert.html Graduate School Dissertation Information] web page for details.<br />
<br />
== Examination ==<br />
<br />
Final dissertation approval pages must be received by August 31, December 31 or 13 days prior to commencement. Not fewer than 5 faculty members must participate, including advisory committee. Notice of the examination must be submitted to the UConn Events Calendar at least 2 weeks prior to the event; Lectures, Meetings and Conferences section and at the campus where the defense/presentation is taking place.<br />
<br />
[[Category:Graduate Student Resources]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Ph.D._Ontogeny&diff=18810Ph.D. Ontogeny2011-08-31T15:39:10Z<p>PaulLewis: /* &quot;Working copy&quot; dissertation filed */</p>
<hr />
<div>This page is for graduate students pursuing a Doctor of Philosphy (Ph.D.) degree in EEB and their advisor(s). This document is provided as a convenience, but please consult the Graduate Catalog for authoritative information, or for clarification and elaboration of information found here. If you would like this information in the form of a table that can be printed, filled in and kept on file, Eric Schultz's original Ph.D. Ontogeny documents can be downloaded in either [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/PhD_Student_Ontogeny_Table.doc Word] or [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/PhD_Student_Ontogeny_Table.pdf PDF] format. There is a corresponding [[M.S. Ontogeny|ontogeny for M.S. students]].<br />
<br />
== Advisory committee ==<br />
Formation of the advisory committee is recommended by the beginning of the second semester. The committee should include at least 3 faculty members: the major advisor, a second advisor (normally from EEB), and a third advisor, who must be a member of the graduate faculty at UConn.<br />
<br />
== Plan of Study ==<br />
EEB recommends that the Plan of Study be filed with the Graduate School by the (end of the?) third semester.<br />
<br />
== Foreign Language/Related Area requirement==<br />
The Ecology and Evolutionary Biology graduate field of study has no foreign language/related area requirement<br />
<br />
== General examination ==<br />
Within 5 years of commencing doctoral study (4 years if entry with a related Master's). No later than 8 months prior to completion. EEB recommendation is by the end of the second year. Attended and conducted by the advisory committee, and others (no fewer than five faculty members).<br />
<br />
== Dissertation proposal submitted ==<br />
Should occur no later than 6 months prior to degree completion. EEB recommendation is by end of third year. Advisory committee (major advisor and more than 2 members of committee) reviews proposal and recommends additional reviewers, which may include faculty in other departments and may be outside the university.<br />
<br />
== Candidacy status ==<br />
Candidacy status is conferred after the dissertation proposal is approved by all reviewers, is signed by the Head, and finally is approved by the Executive Committee of the Graduate Faculty Council.<br />
<br />
== &quot;Working copy&quot; dissertation filed ==<br />
Degree must be completed after at least 3 years of study beyond baccalaureate (2 years beyond Master's in related subject) and within 8 years of commencing doctoral study (7 years if entry with a related Master's). The Tentative Approval Page must be filed at least 7 days prior to examination. Please see the [http://grad.uconn.edu/dissert.html Graduate School Dissertation Information] web page for details.<br />
<br />
== Examination ==<br />
<br />
Final dissertation approval pages must be received by August 31, December 31 or 13 days prior to commencement. Not fewer than 5 faculty members must participate, including advisory committee. Notice of the examination must be submitted to the UConn Events Calendar at least 2 weeks prior to the event; Lectures, Meetings and Conferences section and at the campus where the defense/presentation is taking place.<br />
<br />
[[Category:Graduate Student Resources]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Ph.D._Ontogeny&diff=18809Ph.D. Ontogeny2011-08-31T14:51:51Z<p>PaulLewis: </p>
<hr />
<div>This page is for graduate students pursuing a Doctor of Philosphy (Ph.D.) degree in EEB and their advisor(s). This document is provided as a convenience, but please consult the Graduate Catalog for authoritative information, or for clarification and elaboration of information found here. If you would like this information in the form of a table that can be printed, filled in and kept on file, Eric Schultz's original Ph.D. Ontogeny documents can be downloaded in either [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/PhD_Student_Ontogeny_Table.doc Word] or [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/PhD_Student_Ontogeny_Table.pdf PDF] format. There is a corresponding [[M.S. Ontogeny|ontogeny for M.S. students]].<br />
<br />
== Advisory committee ==<br />
Formation of the advisory committee is recommended by the beginning of the second semester. The committee should include at least 3 faculty members: the major advisor, a second advisor (normally from EEB), and a third advisor, who must be a member of the graduate faculty at UConn.<br />
<br />
== Plan of Study ==<br />
EEB recommends that the Plan of Study be filed with the Graduate School by the (end of the?) third semester.<br />
<br />
== Foreign Language/Related Area requirement==<br />
The Ecology and Evolutionary Biology graduate field of study has no foreign language/related area requirement<br />
<br />
== General examination ==<br />
Within 5 years of commencing doctoral study (4 years if entry with a related Master's). No later than 8 months prior to completion. EEB recommendation is by the end of the second year. Attended and conducted by the advisory committee, and others (no fewer than five faculty members).<br />
<br />
== Dissertation proposal submitted ==<br />
Should occur no later than 6 months prior to degree completion. EEB recommendation is by end of third year. Advisory committee (major advisor and more than 2 members of committee) reviews proposal and recommends additional reviewers, which may include faculty in other departments and may be outside the university.<br />
<br />
== Candidacy status ==<br />
Candidacy status is conferred after the dissertation proposal is approved by all reviewers, is signed by the Head, and finally is approved by the Executive Committee of the Graduate Faculty Council.<br />
<br />
== &quot;Working copy&quot; dissertation filed ==<br />
Degree must be completed after at least 3 years of study beyond baccalaureate (2 years beyond Master's in related subject) and within 8 years of commencing doctoral study (7 years if entry with a related Master's). Working copy of dissertation is filed at least 7 days prior to examination.<br />
<br />
== Examination ==<br />
<br />
Final dissertation approval pages must be received by August 31, December 31 or 13 days prior to commencement. Not fewer than 5 faculty members must participate, including advisory committee. Notice of the examination must be submitted to the UConn Events Calendar at least 2 weeks prior to the event; Lectures, Meetings and Conferences section and at the campus where the defense/presentation is taking place.<br />
<br />
[[Category:Graduate Student Resources]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=M.S._Ontogeny&diff=18808M.S. Ontogeny2011-08-31T14:51:33Z<p>PaulLewis: </p>
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<div>This page is for graduate students pursuing a Master of Science (M.S.) degree in EEB and their advisor(s). This document is provided as a convenience, but please consult the Graduate Catalog for authoritative information, or for clarification and elaboration of information found here. If you would like this information in the form of a table that can be printed, filled in and kept on file, Eric Schultz's original M.S. Ontogeny documents can be downloaded in either [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/MS_Student_Ontogeny_Table.doc Word] or [http://hydrodictyon.eeb.uconn.edu/department/grads/ontogeny/MS_Student_Ontogeny_Table.pdf PDF] format. There is a corresponding [[Ph.D. Ontogeny|ontogeny for Ph.D. students]].<br />
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== Advisory committee ==<br />
Formation of the advisory committee is recommended prior to completion of 12 credit hours of course work. The committee should include at least 3 faculty members: the major advisor, a second advisor (normally from EEB), and a third advisor, who must be a member of the graduate faculty at UConn.<br />
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== Plan of Study ==<br />
It is recommended that the Plan of Study be filed with the Graduate School prior to completion of 12 credit hours of course work.<br />
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== Thesis plan approved ==<br />
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== Thesis filed ==<br />
Completion of degree is expected &quot;within two years or so.&quot; Thesis should be filed by August 31, December 31 or 13 days prior to commencement.<br />
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== Defense ==<br />
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[[Category:Graduate Student Resources]]</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Main_Page&diff=18807Main Page2011-08-31T14:38:19Z<p>PaulLewis: </p>
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<div>Welcome to EEBedia. This is a supplementary web resource for the Ecology and Evolutionary Biology Department of the University of Connecticut, whose main page exists [http://hydrodictyon.eeb.uconn.edu/eebwww/ here]. Faculty, staff, and students of the department are encouraged to contribute content. To activate your account, contact the [[EEB Webmaster]]. Because EEBedia only supplements the main department page, please note that the lists of people and courses may be incomplete. Comments and suggestions are welcome.<br />
{|style="border-spacing:8px;margin:0px -8px"<br />
|class="MainPageBG" style="width:55%;border:1px solid #cef2e0;background-color:#f5fffa;vertical-align:top;color:#000"|<br />
{|width="100%" cellpadding="2" cellspacing="5" style="vertical-align:top;background-color:#f5fffa"<br />
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| <h2 style="margin:0;background-color:#cedff2;font-size:120%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">COURSES</h2><br />
'''[[:Category:EEB Courses|Lecture Format]]'''<br><br />
'''[[:Category:EEB Seminars|Seminars]]'''<br />
| <h2 style="margin:0;background-color:#cef2e0;font-size:120%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">[[:Category:EEB People|PEOPLE]]</h2><br />
'''[[:Category:EEB Faculty|Faculty]]'''<br><br />
'''[[:Category:EEB Postdoctoral Associates|Postdoctoral Associates]]'''<br><br />
'''[[:Category:EEB Graduate Students|Graduate Students]]'''<br><br />
'''[[:Category:EEB BS/MS Students|BS/MS Students]]'''<br><br />
'''[[:Category:EEB and BCS Staff|EEB and BCS Staff]]<br><br />
'''[[:Biology Club|Biology Club]]<br />
| <h2 style="margin:0;background-color:#cedff2;font-size:120%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">RESOURCES</h2><br />
'''[[EEB Department Seminar]]'''<br><br />
'''[[:Category:Graduate Student Resources|Graduate Student Resources]]'''<br><br />
'''[[:Category:Undergraduate Resources|Undergraduate Resources]]'''<br><br />
'''[[Help:Contents|EEBedia Help]]'''<br />
| <h2 style="margin:0;background-color:#cef2e0;font-size:120%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">EXTERNAL LINKS</h2><br />
'''[http://hydrodictyon.eeb.uconn.edu/eebwww/ EEB Home]'''<br><br />
'''[http://www.biodiversity.uconn.edu/BRC.html Collections]'''<br><br />
'''[http://www.cese.uconn.edu/env_commons.html CESE Newsletter]'''<br><br />
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__NOTOC__ __NOEDITSECTION__</div>PaulLewishttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_Seminar&diff=18610Systematics Seminar2011-08-23T14:51:41Z<p>PaulLewis: /* Past Systematics Seminars */</p>
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<div>This is the home page of the UConn EEB department's Systematics Seminar. This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the systematics program at the University of Connecticut. <br />
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]<br />
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== Meeting time and place ==<br />
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''. <br />
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== Theme for Fall Semester 2011 ==<br />
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No theme has yet been established. Please attend the organizational meeting 4-5pm on Tueseday, 30 Aug 2011, in the Bamford Room (Torrey Life Science Room 171b) to help us decide the topic(s) discussed this semester.<br />
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== Past Systematics Seminars ==<br />
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)<br />
* [[Systematics Seminar Fall 2010|Fall 2010]]<br />
* [[Systematics Seminar Spring 2010|Spring 2010]]<br />
* [[Systematics Seminar Fall 2009|Fall 2009]]<br />
* [[Systematics Seminar Fall 2008|Fall 2008]]<br />
* [[Systematics Seminar Spring 2008|Spring 2008]]<br />
* [[Systematics Seminar Fall 2007|Fall 2007]]<br />
* [[Systematics Seminar Spring 2007|Spring 2007]]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]<br />
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]<br />
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[[Category:EEB Seminars]]</div>PaulLewis