Systematics Seminar

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=== Monday, 9 September 2013 ===
 
=== Monday, 9 September 2013 ===
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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.   
 
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment.   
 
<ul>
 
<ul>
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=== Monday, 16 September 2013 ===
 
=== Monday, 16 September 2013 ===
 +
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:
 
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]
 
: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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: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]
 
: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]
 
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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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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 +
: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, 30 September 2013 ===
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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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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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Paul Lewis will lead the discussion.
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 +
Main paper for discussion:
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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.
 +
 +
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.
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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, 28 October 2013 ===
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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
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:{{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, 4 November 2013 ===
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There are two things to do to prepare for this week:
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<ul>
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<li> Come up with an example of speciation that does not follow the classic bifurcating tree structure.</li>
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<li>Read this article <br>
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[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>
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=== Monday, 11 November 2013 ===
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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
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=== Monday, 2 December 2013===
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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 ==

Revision as of 13:37, 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

Contents

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

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