Difference between revisions of "Systematics Seminar"

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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.  
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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.
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<br><br>
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.  
  
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
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The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector. 
  
== Meeting time and place ==
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'''Readings:''' In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources.  The readings should be posted to EEBedia at least 5 days in advance.
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''.  
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== Theme for Fall Semester 2009 ==
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'''Announcing the reading:''' The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:
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This semester we will focus on speciation and hybridization, then transition into phylogeography/ historical biogeography. Random papers/ themes, however, are welcomed.
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== Schedule for Fall Semester 2009 ==
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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
'''Note: the papers linked here require a user name and password to access.''' If you have forgotten the user name and/or password, contact [mailto:paul.lewis@uconn.edu Paul Lewis]. If you want to upload a PDF file for an upcoming discussion, use the [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html Systematics Seminar PDF upload form]. Uploading PDFs requires the same user name and password as viewing PDFs.
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<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
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In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with <code><nowiki>http://dx.doi.org/</nowiki></code>. Here is how the above link looks embedded in this EEBedia page:
 +
:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
  
=== Tuesday, September 8th, 2009: ===
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2. If the paper is not available through the library, upload a PDF of the paper to [http://dropbox.uconn.edu the UConn dropbox], being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the [[Dropbox Test]] page for other examples):
Discussion leader: [[Elizabeth Wade]]
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<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
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In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bossu_Near_2009_SysBio.pdf}}Bossu_Near_2009_SysBio.pdf
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:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.] Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041
  
=== Tuesday, September 15th, 2009 ===
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If you have ancillary papers, upload those to the dropbox individually and create separate links.
  
Discussion Leader: Elizabeth Timpe
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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bonett%20and%20Chippindale%202004.pdf}}Bonett and Chippindale 2004.pdf
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'''Introductory PowerPoint/KeyNote Presentation:''' Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation.  Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes. (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.).  Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging.  Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated). You may also want to provide more detail and background about ancillary readings which likely have not been read by all.  
  
=== Tuesday, September 22nd, 2009 ===
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'''Discussion:''' You are responsible for driving the discussion.  Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site.  See section under expectations. 
  
Discussion leaders: Nic Tippery and Dave Wagner
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Prepare 3-5 questions that you expect will spur discussion.  Ideally, you would distribute questions a day or two before our class meeting.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield-etal-2006_Apis-biogeog.pdf}}Whitfield et al. 2006. Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, ''Apis mellifera''. ''Science'' 314: 642-645.
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'''Projector:'''  
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The presenter will be responsible for setting up the projector for each class session—you will need to get it from the EEB office, make sure you have appropriate adaptors and have it set up so that class can begin on schedule. Kathy has reserved the pink projector for our class. If you do not have a laptop, let Wagner know and he will bring his. (Nick McIntosh may also be able to provide a loaner.)
  
http://www.sciencemag.org/cgi/content/abstract/314/5799/642
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
 
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Albrecht-etal-2007_Dreissena-native.pdf}}Albrecht et al. 2007. Invaders or endemics? Molecular phylogenetics, biogeography and systematics of ''Dreissena'' in the Balkans. ''Freshwater Biology'' 52: 1525-1536.
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http://www3.interscience.wiley.com/journal/117962459/abstract
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=== Tuesday, September 29th, 2009 ===
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Discussion leader: Chris Owen
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Clark_et_al-2008-SystBio.pdf}}Clark_et_al-2008-SystBio.pdf
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=== Tuesday, October 6th, 2009 ===
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Discussion leader: Daniel Fan
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We will continue talking about Dispersal-Extinction-Cladogesis (DEC) model this week. In 2005, Ree et al. proposed the initial version of DEC although this approach was not named at that time. In 2008, Ree and Smith developed it and published a paper in Sys. Bio., which might be thought as the second version. The paper we will read is about the third version of DEC, likelihood with fossil, and they call it DEC*.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moore_2009_.pdf}}Moore et al. 2009. Incorporating Fossil Data in Biogeographic Inference: A Likelihood Approach.
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=== Tuesday, October 13th, 2009 ===
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Juan Carlos Villarreal
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Santos.etal.2009.Plosbiolo.pdf}}Santos.etal.2009.Plosbiolo.pdf
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I would recommend to check Figure S6 (supplements are available online).
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http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.1000056;jsessionid=697A5A8835708B33E83085CE4729FB59
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The next paper is optional. It talks about priors for molecular dating analyses. Simon Ho has published a more recent paper on the topic, this is shorter/simpler.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/ho.2007.j.avianbiol..pdf}}ho.2007.j.avianbiol..pdf
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=== Tuesday, October 20th, 2009 ===
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Discussion Leader: Roberta
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{{pdf|http://www.bioone.org/doi/abs/10.1111/j.1558-5646.2008.00566.x}}
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Hurt et al. 2009 A MULTILOCUS TEST OF SIMULTANEOUS DIVERGENCE ACROSS THE ISTHMUS OF PANAMA USING SNAPPING SHRIMP IN THE GENUS ALPHEUS
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=== Tuesday, October 27th, 2009 ===
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Discussion leader: Geert Goemans
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Himes%20et%20al%202008.pdf}}Himes et al 2008.pdf
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=== Tuesday, November 3rd, 2009 ===
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Discussion leader: Nic Tippery
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nielsen-Beaumont-2009_phylogeog.pdf}}Nielsen, R. and M. A. Beaumont. 2009. Statistical inferences in phylogeography. Molecular Ecology 18: 1034-1047.
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http://www3.interscience.wiley.com/journal/121681049/abstract?CRETRY=1&SRETRY=0
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=== Tuesday, November 10th, 2009 ===
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=== Tuesday, November 17th, 2009 ===
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=== Tuesday, December 1st, 2009 ===
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=== Tuesday, December 8th, 2009 ===
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== Meeting time and place ==
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For the Fall 2015 semester, we are meeting in the '''Bamford Room (TLS 171B), Tuesdays 2:30-3:30pm'''
  
[[#top|Back to top]]
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=== Tuesday, 1 September 2015, 3pm, Bamford Room (TLS 171b) ===
 +
At this meeting we discussed possible themes for this semester's seminar, and determined the meeting time. For starters, we will explore how to use RevBayes, and afterwards explore current topics such as new developments in comparative methods.
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
 +
* [[Systematics Seminar Spring 2015|Spring 2015]]
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 +
* [[Systematics Seminar Spring 2012|Spring 2012]]
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* [[Systematics Seminar Fall 2011|Fall 2011]]
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* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
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* [[Systematics Seminar Fall 2010|Fall 2010]]
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* [[Systematics Seminar Spring 2010|Spring 2010]]
 +
* [[Systematics Seminar Fall 2009|Fall 2009]]
 
* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]

Revision as of 19:45, 1 September 2015

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.

Seminar Format: Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.

The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector.

Readings: In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources. The readings should be posted to EEBedia at least 5 days in advance.

Announcing the reading: The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:

1. If the paper is available online through our library, it is sufficient to create a link to the DOI:

:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]

In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with http://dx.doi.org/. Here is how the above link looks embedded in this EEBedia page:

Doyle et al. 2015. Syst. Biol. 64:824-837.

2. If the paper is not available through the library, upload a PDF of the paper to the UConn dropbox, being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the Dropbox Test page for other examples):

:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]

In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:

Doyle et al. 2015. Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041

If you have ancillary papers, upload those to the dropbox individually and create separate links.

Finally, send a note to the Systematics Listserv letting everyone know that a paper is available.

Introductory PowerPoint/KeyNote Presentation: Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation. Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes. (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.). Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging. Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated). You may also want to provide more detail and background about ancillary readings which likely have not been read by all.

Discussion: You are responsible for driving the discussion. Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site. See section under expectations.

Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.

Projector: The presenter will be responsible for setting up the projector for each class session—you will need to get it from the EEB office, make sure you have appropriate adaptors and have it set up so that class can begin on schedule. Kathy has reserved the pink projector for our class. If you do not have a laptop, let Wagner know and he will bring his. (Nick McIntosh may also be able to provide a loaner.)

Click here for information about joining and using the Systematics email list

Meeting time and place

For the Fall 2015 semester, we are meeting in the Bamford Room (TLS 171B), Tuesdays 2:30-3:30pm

Tuesday, 1 September 2015, 3pm, Bamford Room (TLS 171b)

At this meeting we discussed possible themes for this semester's seminar, and determined the meeting time. For starters, we will explore how to use RevBayes, and afterwards explore current topics such as new developments in comparative methods.

Past Systematics Seminars