Systematics Seminar

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== 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 Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm'''
  
=== Monday, 26 August 2013 ===
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=== Monday, 25 August 2014 ===
 
At this meeting we will discuss possible themes for this semester's seminar:
 
At this meeting we will discuss possible themes for this semester's seminar:
  
=== Monday, 2 September 2013 ===
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=== Monday, 1 September 2014 ===
 
Labor Day, no meeting
 
Labor Day, no meeting
  
=== Monday, 9 September 2013 ===
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=== Monday, 8 September 2014 ===
Elizabeth Jockusch will lead the discussion this week.
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For this meeting, please come with an example (or examples) of a source of systematic error in datasets, and a paper that attempts to address this source of systematic error. We will use these examples and papers as a basis for discussions in upcoming weeks.
  
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. 
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=== Monday, 15 September 2014 ===
<ul>
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<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>
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</ul>
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=== Monday, 16 September 2013 ===
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=== Monday, 22 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:
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=== Monday, 29 September 2014 ===
: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]
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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):
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: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]
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Here is a link to a protocol for RAD-seq library prep, just in case anyone is interested:
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: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]
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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]
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=== Monday, 23 September 2013 ===
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=== Monday, 6 October 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]
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=== Monday, 13 October 2014 ===
  
: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, 20 October 2014 ===
  
=== Monday, 30 September 2013 ===
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=== Monday, 27 October 2014 ===
Brigette Zacharczenko will lead the discussion this week.<br>
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: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
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=== Monday, 07 October 2013 ===
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=== Monday, 3 November 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 ===
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=== Monday, 10 November 2014 ===
Paul Lewis will lead the discussion.
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Main paper for discussion:
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=== Monday, 17 November 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:
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:{{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.
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=== Monday, 21 October 2013 ===
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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
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=== Monday, 1 December 2014===
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
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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 18:50, 26 August 2014

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

Contents

Meeting time and place

For the Fall 2014 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2-3pm

Monday, 25 August 2014

At this meeting we will discuss possible themes for this semester's seminar:

Monday, 1 September 2014

Labor Day, no meeting

Monday, 8 September 2014

For this meeting, please come with an example (or examples) of a source of systematic error in datasets, and a paper that attempts to address this source of systematic error. We will use these examples and papers as a basis for discussions in upcoming weeks.

Monday, 15 September 2014

Monday, 22 September 2014

Monday, 29 September 2014

Monday, 6 October 2014

Monday, 13 October 2014

Monday, 20 October 2014

Monday, 27 October 2014

Monday, 3 November 2014

Monday, 10 November 2014

Monday, 17 November 2014

Monday, 1 December 2014

Past Systematics Seminars

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