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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''' | + | For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm''' |
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− | === Monday, 26 August 2013 === | + | === 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: |
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− | === Monday, 2 September 2013 === | + | === Monday, 1 September 2014 === |
| Labor Day, no meeting | | Labor Day, no meeting |
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− | === Monday, 9 September 2013 === | + | === 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.
| + | === 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 === | + | === 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:
| + | === 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://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/RAD-seq_Compiled-Figues.ppt link]
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− | === Monday, 23 September 2013 === | + | === 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://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SalichosRokas2013.pdf link]
| + | === Monday, 13 October 2014 === |
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− | :Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
| + | === Monday, 20 October 2014 === |
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− | === Monday, 30 September 2013 === | + | === 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 === | + | === 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 === | + | === Monday, 10 November 2014 === |
− | Paul Lewis will lead the discussion.
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− | Main paper for discussion:
| + | === 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:
| + | === Monday, 1 December 2014=== |
− | :{{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 === | + | |
− | 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://hydrodictyon.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 === | + | |
− | 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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− | :[http://sysbio.oxfordjournals.org/content/early/2013/09/18/sysbio.syt049.full.pdf+html link] 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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| == Past Systematics Seminars == | | == Past Systematics Seminars == |
| + | * [[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]] |
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.