Difference between revisions of "Systematics Seminar"

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(Tuesday, December 2nd, 2008)
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== 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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We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm'''.  
  
 
== Theme for Fall Semester 2008 ==
 
== Theme for Fall Semester 2008 ==
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.
 
  
 
== Schedule for Fall Semester 2008 ==
 
== Schedule for Fall Semester 2008 ==
 
'''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.
 
'''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.
  
=== Tuesday, September 2nd, 2008: ===
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=== Tuesday, September 8th, 2009: ===
 
Discussion leader: [[Elizabeth Wade]]
 
Discussion leader: [[Elizabeth Wade]]
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<!-- THE LINE BELOW IS FOR REFERENCE TO MAKE A LINK WITH PDF ICON. YOU CAN DELETE IT (AND THIS COMMENT) AFTER YOU POST THE FIRST ACTUAL LINK
 
:{{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/Drummond%20%26%20Rambaut%202007.pdf}}Drummond & Rambaut 2007.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Molecular%20Dating%20Review.pdf}}Molecular Dating Review (for more background info)
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=== Tuesday, September 15th, 2008 ===
 
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=== Tuesday, September 9th, 2008 ===
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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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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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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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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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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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Seminar postponed due to conflict with a popular Paleo Seminar.
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=== Tuesday, October 28th, 2008 ===
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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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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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=== Tuesday, November 11th, 2008 ===
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=== Tuesday, September 22nd, 2008 ===
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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=== Tuesday, September 29th, 2008 ===
  
:[[Image:Pdficon_small.gif|left]] [http://dropbox.uconn.edu/dropbox?n=Systematics_08-1111.zip&p=WC9a4kJVW5dLCUnYz Click here to download.]
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=== Tuesday, October 6th, 2008 ===
  
====Summary of papers====
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=== Tuesday, October 13th, 2008 ===
  
Read these papers in their entirety:
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=== Tuesday, October 20th, 2008 ===
* 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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=== Tuesday, October 27th, 2008 ===
  
=== Tuesday, November 18th, 2008 ===
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=== Tuesday, November 3rd, 2008 ===
Discussion leader: Beth Wade
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hoskin%202007%20.pdf}}Hoskin 2007 .pdf
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=== Tuesday, December 2nd, 2008 ===
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=== Tuesday, November 10th, 2008 ===
Discussion leader: Geert Goemans
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Tsukamoto%20et%20al.%2C%202003%20Anguillid%20eels.pdf}}Tsukamoto et al., 2003 Anguillid eels.pdf
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=== Some papers to pick from ===
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=== Tuesday, November 17th, 2008 ===
:{{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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=== Tuesday, December 1st, 2008 ===
  
  
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== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
 +
* [[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 20:38, 1 September 2009

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.

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

Meeting time and place

We are meeting this semester in the Bamford Room (TLS 171B) Tuesdays 4-5pm.

Theme for Fall Semester 2008

Schedule for Fall Semester 2008

Note: the papers linked here require a user name and password to access. If you have forgotten the user name and/or password, contact Paul Lewis. If you want to upload a PDF file for an upcoming discussion, use the Systematics Seminar PDF upload form. Uploading PDFs requires the same user name and password as viewing PDFs.

Tuesday, September 8th, 2009:

Discussion leader: Elizabeth Wade


Tuesday, September 15th, 2008

Tuesday, September 22nd, 2008

Tuesday, September 29th, 2008

Tuesday, October 6th, 2008

Tuesday, October 13th, 2008

Tuesday, October 20th, 2008

Tuesday, October 27th, 2008

Tuesday, November 3rd, 2008

Tuesday, November 10th, 2008

Tuesday, November 17th, 2008

Tuesday, December 1st, 2008

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Past Systematics Seminars