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 171B) Tuesdays 4-5pm'''.
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For the Fall 2013 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm'''
  
== Theme for Spring Semester 2010 ==
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=== Monday, 26 August 2013 ===
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At this meeting we will discuss possible themes for this semester's seminar:
This semester we will focus on random papers/themes.
+
  
== Schedule for Spring Semester 2010 ==
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=== Monday, 2 September 2013 ===
'''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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Labor Day, no meeting
  
=== Tuesday, January 26th, 2010: ===
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=== Monday, 9 September 2013 ===
Discussion leader: [[Chris Owen]]<br/>
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Elizabeth Jockusch will lead the discussion this week.
This week we will look at two new methods (nonparametric and parametric) that aim to find the correct species tree in the forest of gene trees.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/O%27Meara%202009%20SystBiol.pdf}}O'Meara 2009 SystBiol.pdf
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=== Tuesday, February 2nd, 2010: ===
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We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. 
Discussion leader: [[Geert Goemans the 15th]]<br/>
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<ul>
This week we will look at biogeography and evolution in the West Indies.
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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>
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ricklefs%20%26%20Birmingham%2C%202008%20West%20Indies.pdf}}Ricklefs & Birmingham, 2008 West Indies.pdf
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</ul>
  
===Tuesday, February 10th, 2010: ===
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=== Monday, 16 September 2013 ===
Discussion leader: [[Lily Lewis]]<br/>
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Lily Lewis will lead the discussion this week
This week we will discuss dating of bryophyte phylogenies.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Vanderpoorten%20leptoscyphus.pdf}}Vanderpoorten leptoscyphus.pdf
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===Tuesday, February 16th, 2010: ===
+
Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
Discussion leader: [[Elizabeth Timpe]]<br/>
+
: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]
This week we will discuss the estimation of species trees based on multilocus nuclear data.
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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):
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Leache_2009.pdf}}Leache_2009.pdf
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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]
 +
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]
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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://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/RAD-seq_Compiled-Figues.ppt link]
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Leache_2009_supplementary_material.pdf}}Leache_2009_supplementary_material.pdf
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=== Monday, 23 September 2013 ===
 +
Paul Lewis will lead the discussion this week.
  
===Tuesday, February 23rd, 2010: ===
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:Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SalichosRokas2013.pdf link]
Discussion leader: [[Dave Wagner]]<br/>
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This week we will discuss the most recent reconstruction of the arthropod phylogeny.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Regier%20et%20al%202010.pdf}}Regier et al 2010.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Supp.%20Material%20Regier%20et%20al%202010.pdf}}Supp. Material Regier et al 2010.pdf
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:Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
  
===Tuesday, March 2nd, 2010: ===
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=== Monday, 30 September 2013 ===
Discussion leader: [[Chris Owen]]<br/>
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Brigette Zacharczenko will lead the discussion this week.<br>
This week we will discuss the limits of estimating extinction rates from phylogenies.
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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
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rabosky_2010_Extinction.pdf}}Rabosky_2010_Extinction.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Supporting%20info.pdf}}Supporting info.pdf
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===Tuesday, March 16th, 2010: ===
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=== Monday, 07 October 2013 ===
Discussion leader: [[Molly Letsch]]<br/>
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Veronica Bueno will lead the discussion this week.  
This week we will continue the discussion Lily started about dating and distribution patterns, this time in lichens.
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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
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ot%C3%A1lora_2010.pdf}}Otálora_2010.pdf
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===Tuesday, March 23rd, 2010: ===
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=== Monday, 14 October 2013 ===
Discussion leader: [[Karolina Fucikova]]<br/>
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Paul Lewis will lead the discussion.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Dobes%20%26%20Paule%202010%20MPE.pdf}}Dobes & Paule 2010 MPE.pdf
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===Tuesday, March 30th, 2010: ===
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Main paper for discussion:
Discussion leader: [[Beth Wade]]<br/>
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:{{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.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ross%20et%20al%202010%20fire%20ant%20species.pdf}}Ross et al 2010 fire ant species.pdf
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===Tuesday, April 6th, 2010: ===
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Optional followup paper describing improvements in technical details:
Discussion leader: [[Daniel Fan]]<br/>
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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.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Venditti_2010_Nature.pdf}}Venditti_2010_Nature.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Venditti_2010_Nature_Supplement.pdf}}Venditti_2010_Nature_Supplement.pdf
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===Tuesday, April 13th, 2010: ===
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=== Monday, 21 October 2013 ===
Discussion leader: [[Molly Letscj]]<br/>
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Simona Augyte will lead the discussion this week.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Detwiler%20etal%202010.pdf}}Detwiler et al 2010 cryptic species.pdf
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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, 28 October 2013 ===
 +
Paul Lewis will lead the discussion this week.
 +
 
 +
:[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://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/gorymykin_etal_2013_systbiol_62_50-61.key.pdf}} Paul's handout
 +
 
 +
=== 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>
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</ul>
 +
 
 +
=== Monday, 11 November 2013 ===
 +
Paper for this week:
 +
:{{pdf|http://hydrodictyon.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)
 +
 
 +
=== 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===
 +
Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading. <br>
 +
{{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>
 +
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/geography_barcoding.pdf}}The Effect of Geographical Scale of Sampling on DNA Barcoding
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
 +
* [[Systematics Seminar Spring 2012|Spring 2012]]
 +
* [[Systematics Seminar Fall 2011|Fall 2011]]
 +
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
 +
* [[Systematics Seminar Fall 2010|Fall 2010]]
 +
* [[Systematics Seminar Spring 2010|Spring 2010]]
 
* [[Systematics Seminar Fall 2009|Fall 2009]]
 
* [[Systematics Seminar Fall 2009|Fall 2009]]
 
* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Fall 2008|Fall 2008]]

Revision as of 18:37, 28 November 2013

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

For the Fall 2013 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2-3pm

Monday, 26 August 2013

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

Monday, 2 September 2013

Labor Day, no meeting

Monday, 9 September 2013

Elizabeth Jockusch will lead the discussion this week.

We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment.

  • Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. link

Monday, 16 September 2013

Lily Lewis will lead the discussion this week

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 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 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. 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 link

Monday, 23 September 2013

Paul Lewis will lead the discussion this week.

Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. link
Paul's handout on calculating internode certainty measure link

Monday, 30 September 2013

Brigette Zacharczenko will lead the discussion this week.

Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using LikelihoodPdficon small.gifLink

Monday, 07 October 2013

Veronica Bueno will lead the discussion this week.

Pdficon small.gifFujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf

Monday, 14 October 2013

Paul Lewis will lead the discussion.

Main paper for discussion:

Pdficon small.gif Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269.

Optional followup paper describing improvements in technical details:

Pdficon small.gif Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253.

Monday, 21 October 2013

Simona Augyte will lead the discussion this week.

Pdficon small.gifSyst Biol-2012-Moalic-127-37.pdf

Monday, 28 October 2013

Paul Lewis will lead the discussion this week.

link Goremykin et al. 2013. The evolutionary root of flowering plants. Systematic Biology 62(1): 50-61
Pdficon small.gif Paul's handout

Monday, 4 November 2013

There are two things to do to prepare for this week:

  • Come up with an example of speciation that does not follow the classic bifurcating tree structure.
  • Read this article
    link Mindell, D. 2013. The Tree of Life: Metaphor, Model, and Heuristic Device. Syst. Biol. 62:479-489.

Monday, 11 November 2013

Paper for this week:

Pdficon small.gif 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)

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

Pdficon small.gifBioinformatics-2013-Zhang-2869-76.pdf

Monday, 2 December 2013

Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading.
Pdficon small.gifA DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
Pdficon small.gifThe Effect of Geographical Scale of Sampling on DNA Barcoding

Past Systematics Seminars