Systematics Seminar

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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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This is the home page of the UConn EEB department's Co-evolution Seminar, taking the place of the Systematics Seminar this semester (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 ==
For the Fall 2013 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm'''
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For the Spring 2015 semester, we are meeting in the '''Bamford Room (TLS 171B) Day/time TBD'''
  
=== Monday, 26 August 2013 ===
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=== Topics ===
At this meeting we will discuss possible themes for this semester's seminar:
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This seminar will be split between class meetings that emphasize phylogenetic underpinnings, tree comparisons, and reconciliation methods, with those focused on the evolutionary processes underlying co-evolutionary phenomena (as well as the forces and circumstances that, more often than not, prevent it from occurring). And while parasites will figure large in our readings and discussions, we will also explore insect-plant co-evolution, endosymbionts and other mutualisms, mimicry, and others.
  
=== Monday, 2 September 2013 ===
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=== Tuesday, 20 January 2015 ===
Labor Day, no meeting
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At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time
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<br>
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=== Tuesday, 27 January 2015 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Futuyma%20and%20Slatkin%201983.pdf}}Futuyma and Slatkin, 1983. Coevolution.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Janzen%201980.pdf}}Janzen, 1980. What is coevolution?
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ehrlich%20and%20Raven%201964.pdf}}Ehrlich and Raven, 1964. Butterflies and Plants: A Study in Coevolution.
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=== Monday, 9 September 2013 ===
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=== Monday, 8 September 2014 ===
Elizabeth Jockusch will lead the discussion this week.
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We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. 
 
<ul>
 
<li>Lemmon AR, Emme SA, Lemmon EM. 2012.  Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. [http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/61/5/727.long link]</li>
 
</ul>
 
  
=== Monday, 16 September 2013 ===
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=== Monday, 15 September 2014 ===
Lily Lewis will lead the discussion this week
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Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
 
:Wagner et al. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology 22(3):787-798 [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/mec.12023/full link]
 
Here is a link to a supplementary paper folks may be interested in for an overview of the applications of RAD-sequencing (or at least those conceived of thus far):
 
:Davey, J. W., and M. L. Blaxter. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9(5-6):416-423 [http://ezproxy.lib.uconn.edu/login?url=http://bfg.oxfordjournals.org/content/9/5-6/416 link]
 
Here is a link to a protocol for RAD-seq library prep, just in case anyone is interested:
 
:Etter, P. Sequenced RAD markers for rapid SNP disovery and genetic mapping. [http://ezproxy.lib.uconn.edu/login?url=https://www.wiki.ed.ac.uk/download/attachments/68630442/sequenced+RAD-Tag+protocol-version+2.doc?version=1 link]
 
Finally, here is a PowerPoint concatenation of a few figures from various papers laying out how the RAD-seq process works. This may be a helpful supplement for understanding the methods in the cichlid paper [http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/RAD-seq_Compiled-Figues.ppt link]
 
  
=== Monday, 23 September 2013 ===
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=== Monday, 22 September 2014 ===
Paul Lewis will lead the discussion this week.
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:Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. [http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/SalichosRokas2013.pdf link]
 
  
:Paul's handout on calculating internode certainty measure [http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
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=== Monday, 29 September 2014 ===
  
=== Monday, 30 September 2013 ===
 
Brigette Zacharczenko will lead the discussion this week.<br>
 
:Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2013-Adams-181-92.pdf}}Link
 
  
=== Monday, 07 October 2013 ===
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=== Monday, 6 October 2014 ===
Veronica Bueno will lead the discussion this week.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Fujisawa%2C%20Barraclough_2013_Delimiting%20Species%20Using%20Single-Locus%20Data%20and%20the%20Generalized%20Mixed%20Yule%20Coalescent%20Approach%20A%20Revised%20Metho.pdf}}Fujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf
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=== Monday, 14 October 2013 ===
 
Paul Lewis will lead the discussion.
 
  
Main paper for discussion:
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=== Monday, 13 October 2014 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Proceedings%20of%20the%20National%20Academy%20of%20Sciences%202010%20Yang.pdf}} Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269.
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Optional followup paper describing improvements in technical details:
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Genetics%202013%20Rannala.pdf}} Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253.
 
  
=== Monday, 21 October 2013 ===
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=== Monday, 20 October 2014 ===
Simona Augyte will lead the discussion this week.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2012-Moalic-127-37.pdf}}Syst Biol-2012-Moalic-127-37.pdf
 
  
=== Monday, 28 October 2013 ===
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=== Monday, 27 October 2014 ===
Paul Lewis will lead the discussion this week.
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:[http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/62/1/50.full.pdf link] Goremykin et al. 2013. The evolutionary root of flowering plants. Systematic Biology 62(1): 50-61
 
  
:{{pdf|http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/gorymykin_etal_2013_systbiol_62_50-61.key.pdf}} Paul's handout
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=== Monday, 3 November 2014 ===
  
=== Monday, 4 November 2013 ===
 
There are two things to do to prepare for this week:
 
<ul>
 
<li> Come up with an example of speciation that does not follow the classic bifurcating tree structure.</li>
 
<li>Read this article <br>
 
[http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/62/3/479.long link] Mindell, D. 2013. The Tree of Life: Metaphor, Model, and Heuristic Device. Syst. Biol. 62:479-489.</li>
 
</ul>
 
  
=== Monday, 11 November 2013 ===
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=== Monday, 10 November 2014 ===
Paper for this week:
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:{{pdf|http://www.eeb.uconn.edu/courses/systematicsseminar/restricted/SystematicBiology2013-Leache.pdf}} Leaché A.D., Harris R.B., Rannala B., Yang Z. 2013. The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology. doi:10.1093/sysbio/syt049 (Advance Access, August 13, 2013)
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=== Monday, 18 November 2013 ===
 
Veronica Bueno will lead the discussion this week. Zhang et al., 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. doi:10.1093/bioinformatics/btt499
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bioinformatics-2013-Zhang-2869-76.pdf}}Bioinformatics-2013-Zhang-2869-76.pdf
 
  
=== Monday, 2 December 2013===
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=== Monday, 17 November 2014 ===
Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading. <br>
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/BIN%20paper.pdf}}A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System <br>
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/geography_barcoding.pdf}}The Effect of Geographical Scale of Sampling on DNA Barcoding
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=== Monday, 1 December 2014===
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== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
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* [[Systematics Seminar Fall 2014|Fall 2014]]
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* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]

Latest revision as of 14:25, 23 January 2015

This is the home page of the UConn EEB department's Co-evolution Seminar, taking the place of the Systematics Seminar this semester (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

Contents

Meeting time and place

For the Spring 2015 semester, we are meeting in the Bamford Room (TLS 171B) Day/time TBD

Topics

This seminar will be split between class meetings that emphasize phylogenetic underpinnings, tree comparisons, and reconciliation methods, with those focused on the evolutionary processes underlying co-evolutionary phenomena (as well as the forces and circumstances that, more often than not, prevent it from occurring). And while parasites will figure large in our readings and discussions, we will also explore insect-plant co-evolution, endosymbionts and other mutualisms, mimicry, and others.

Tuesday, 20 January 2015

At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time

Tuesday, 27 January 2015

Pdficon small.gifFutuyma and Slatkin, 1983. Coevolution.
Pdficon small.gifJanzen, 1980. What is coevolution?
Pdficon small.gifEhrlich and Raven, 1964. Butterflies and Plants: A Study in Coevolution.

Past Systematics Seminars

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