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.  
  
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
 
== Meeting time and place ==
 
== Meeting time and place ==
We are meeting this semester in the '''Bamford Room (TLS 171) Tuesdays 4-5pm'''.  
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Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
  
== Theme for Fall Semester 2008 ==
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== Schedule for Fall 2017 ==
We've agreed to start the semester with some articles on molecular dating, then spend a couple of weeks on taxonomy papers, and possibly read a revised version of David Baum's tree thinking book. If you are interested in leading a particular week's discussion, please sign up below.
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=== Sep. 4 ===
 +
Labor day holiday (no meeting)
  
== Schedule for Fall Semester 2008 ==
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=== Sep. 11 ===
'''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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Paul and Suman will lead the discussion of the paper:
  
=== Tuesday, September 2nd, 2008: ===
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Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. [https://doi.org/10.1093/sysbio/syw101 doi:10.1093/sysbio/syw101]
Discussion leader: [[Elizabeth Wade]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Drummond%20%26%20Rambaut%202007.pdf}}Drummond & Rambaut 2007.pdf
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Molecular%20Dating%20Review.pdf}}Molecular Dating Review (for more background info)
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=== Sep. 18  (next meeting) ===
 +
Noah Reid will lead discussion on this paper today:
  
=== Tuesday, September 9th, 2008 ===
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Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.
Discussion leader: [[Christopher Owen]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lepage%20et%20al.%202007%20MBE%20Relaxed%20Molec%20Clock%20Models.pdf}}Lepage et al. 2007
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=== Tuesday, September 16th, 2008 ===
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https://www.nature.com/articles/s41559-017-0126
Discussion leader: [[Karolina Fučíková]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/BumbleBees2008.pdf}}Hines, H. 2008.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cameron2007BumbleBees.pdf}}Cameron 2007 (for more info on the original phylogeny)
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=== Tuesday, September 23rd, 2008 ===
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We’ll be particularly interested in comparing it to this past Monday’s paper:
Discussion leader: [[Nic Tippery]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rabosky-Lovette-2008_extinction.pdf}}Rabosky, D. L. and I. J. Lovette. 2008. Explosive evolutionary radiations: Decreasing speciation or increasing extinction through time? ''Evolution'' 62-8: 1866-1875.
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=== Tuesday, September 30th, 2008 ===
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Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Luthey-Schulten%20et%20al%2C%20PNAS%202008%20%20vol.%20105%20%20no.%2037%20%2013953-13958.pdf}}Luthey-Schulten et al. 2008. Molecular signatures of ribosomal evolution. PNAS vol.105 no.37 13953-13958.
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=== Tuesday, October 7th, 2008 ===
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Discussion leader: Chris Owen
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bond%20and%20Stockman%202008%283%29.pdf}}Bond and Stockman 2008
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=== Tuesday, October 14th, 2008 ===
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https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Luke%20Harmon%20et%20al.%202008.pdf}}Luke Harmon et al. 2008
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=== Tuesday, October 21st, 2008 ===
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=== Sep. 25 ===
Seminar postponed due to conflict with a popular Paleo Seminar.
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=== Tuesday, October 28th, 2008 ===
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=== Oct. 2 ===
Discussion leader:
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[[Karolina Fucikova]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/DNADiatoms.pdf}} Amato et al. 2007, a paper on cryptic species in Diatoms
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=== Tuesday, November 4th, 2008 ===
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=== Oct. 9 ===
Discussion leader: Geert Goemans
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Damgaard%20et%20al.%2C%202008%20Phylogeny%20Heelwalkers.pdf}}Damgaard et al., 2008
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=== Oct. 16 ===
  
=== Tuesday, November 11th, 2008 ===
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=== Oct. 23 ===
Discussion leader: [[Nic Tippery]]
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Please forgive the bulk of papers I have selected for discussion. The large phylogeny papers are simply examples of implementing Phylogenetic Nomeclature, so focus only on the taxonomy and not the phylogenetics. There are two short papers that present two sides of a relatively recent PhyloCode debate, which may form the bulk of our discussion, so please focus on them. I have uploaded the bundle of pdfs to the Drop Box, in a zip file:
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=== Oct. 30 ===
  
:{{pdf|http://dropbox.uconn.edu/dropbox?n=Systematics_08-1111.zip&p=WC9a4kJVW5dLCUnYz}} <- Click on icon to download.
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=== Nov. 6 ===
  
====Summary of papers:====
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=== Nov. 13 ===
  
Read these papers in their entirety:
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=== Nov. 20 ===
* Pickett, K. M. 2005. The new and improved PhyloCode, now with types, ranks, and even polyphyly: a conference report from the First International Phylogenetic Nomenclature Meeting. ''Cladistics'' 21: 79-82.
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* Laurin, M., K. de Queiroz, P. Cantino, N. Cellinese, and R. Olmstead. 2005. The PhyloCode, types, ranks and monophyly: a response to Pickett. ''Cladistics'' 21: 605-607.
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Example of higher-level taxa (unranked, of course) in plants [the first paper is the phylogenetic taxonomy, and the second gives the complete phylogeny]:
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* Stefanovic, S., D. F. Austin, and R. G. Olmstead. 2003. Classification of Convolvulaceae: A phylogenetic approach. ''Systematic Botany'' 28: 791-806.
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* Stefanovic, S., L. Krueger, and R. G. Olmstead. 2002. Monophyly of the Convolvulaceae and circumscription of their major lineages based on DNA sequences of multiple chloroplast loci. ''American Journal of Botany'' 89: 1510-1522.
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Example of an "''incertae sedis''" animal species:
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* Dayrat, B. 2005. Advantages of naming species under the PhyloCode : An example of how a new species of Discodorididae (Mollusca , Gastropoda , Euthyneura , Nudibranchia , Doridina ) may be named. ''Marine Biology Research'' 1: 216-232.
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In the interest of conservation, please avoid printing the phylogenetics papers unless you'll want them later; we'll have enough laptops to share phylogeny images at the meeting.
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=== Nov. 27 ===
  
=== Tuesday, November 18th, 2008 ===
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=== Dec. 4 ===
Discussion leader:
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=== Tuesday, December 2nd, 2008 ===
 
Discussion leader:
 
  
=== Tuesday, December 9th, 2008 ===
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== Information for discussion leaders ==
Discussion leader:  
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.
  
=== Some papers to pick from ===
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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.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/DivergenceTimesLargeTrees2007.pdf}} Britton et al. 2007 <br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SkewDivergenceTimes2008.pdf}}Burbrink & Pyron 2008
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<br>
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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.
  
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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:
  
[[#top|Back to top]]
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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
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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:
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:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
  
== Past Systematics Seminars ==
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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):
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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:
 +
 
 +
:[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
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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.)
 +
 
 +
== Past Seminars ==
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
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* [[Systematics Seminar Fall 2013|Fall 2013]]
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* [[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]]
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* [[Systematics Seminar Fall 2009|Fall 2009]]
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* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]

Revision as of 17:41, 18 September 2017

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.

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

Meeting time and place

Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).

Schedule for Fall 2017

Sep. 4

Labor day holiday (no meeting)

Sep. 11

Paul and Suman will lead the discussion of the paper:

Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. doi:10.1093/sysbio/syw101

Sep. 18 (next meeting)

Noah Reid will lead discussion on this paper today:

Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.

https://www.nature.com/articles/s41559-017-0126

We’ll be particularly interested in comparing it to this past Monday’s paper:

Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.

https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896

Sep. 25

Oct. 2

Oct. 9

Oct. 16

Oct. 23

Oct. 30

Nov. 6

Nov. 13

Nov. 20

Nov. 27

Dec. 4

Information for discussion leaders

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.)

Past Seminars