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 171) 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 Fall Semester 2008 ==
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=== Monday, 26 August 2013 ===
We've agreed to start the semester with some articles on molecular dating, then spend a couple of weeks on taxonomy papers, and possibly read a revised version of David Baum's tree thinking book. If you are interested in leading a particular week's discussion, please sign up below.
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At this meeting we will discuss possible themes for this semester's seminar:
  
== Schedule for Fall Semester 2008 ==
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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, September 2nd, 2008: ===
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=== Monday, 9 September 2013 ===
Discussion leader: [[Elizabeth Wade]]
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Elizabeth Jockusch will lead the discussion this week.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Drummond%20%26%20Rambaut%202007.pdf}}Drummond & Rambaut 2007.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Molecular%20Dating%20Review.pdf}}Molecular Dating Review (for more background info)
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We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. 
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<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>
  
=== Tuesday, September 9th, 2008 ===
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=== Monday, 16 September 2013 ===
Discussion leader: [[Christopher Owen]]
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Lily Lewis will lead the discussion this week
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lepage%20et%20al.%202007%20MBE%20Relaxed%20Molec%20Clock%20Models.pdf}}Lepage et al. 2007
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=== Tuesday, September 16th, 2008 ===
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Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
Discussion leader: [[Karolina Fučíková]]
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: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]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/BumbleBees2008.pdf}}Hines, H. 2008.
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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/Cameron2007BumbleBees.pdf}}Cameron 2007 (for more info on the original phylogeny)
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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]
  
=== Tuesday, September 23rd, 2008 ===
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=== Monday, 23 September 2013 ===
Discussion leader: [[Nic Tippery]]
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Paul Lewis will lead the discussion this week.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rabosky-Lovette-2008_extinction.pdf}}Rabosky, D. L. and I. J. Lovette. 2008. Explosive evolutionary radiations: Decreasing speciation or increasing extinction through time? ''Evolution'' 62-8: 1866-1875.
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=== Tuesday, September 30th, 2008 ===
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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: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Luthey-Schulten%20et%20al%2C%20PNAS%202008%20%20vol.%20105%20%20no.%2037%20%2013953-13958.pdf}}Luthey-Schulten et al. 2008. Molecular signatures of ribosomal evolution. PNAS vol.105 no.37 13953-13958.
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=== Tuesday, October 7th, 2008 ===
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Discussion leader: Chris Owen
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bond%20and%20Stockman%202008%283%29.pdf}}Bond and Stockman 2008
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=== Tuesday, October 14th, 2008 ===
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:Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Luke%20Harmon%20et%20al.%202008.pdf}}Luke Harmon et al. 2008
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=== Tuesday, October 21st, 2008 ===
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=== Monday, 30 September 2013 ===
Seminar postponed due to conflict with a popular Paleo Seminar.
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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
  
=== Tuesday, October 28th, 2008 ===
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=== Monday, 07 October 2013 ===
Discussion leader:
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Veronica Bueno will lead the discussion this week.
[[Karolina Fucikova]]
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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/DNADiatoms.pdf}} Amato et al. 2007, a paper on cryptic species in Diatoms
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=== Tuesday, November 4th, 2008 ===
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=== Monday, 14 October 2013 ===
Discussion leader: Geert Goemans
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Paul Lewis will lead the discussion.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Damgaard%20et%20al.%2C%202008%20Phylogeny%20Heelwalkers.pdf}}Damgaard et al., 2008
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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.
  
=== Tuesday, November 11th, 2008 ===
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Optional followup paper describing improvements in technical details:
Discussion leader: [[Nic Tippery]]
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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.
  
Please forgive the bulk of papers I have selected for discussion. The large phylogeny papers are simply examples of implementing Phylogenetic Nomeclature, so focus only on the taxonomy and not the phylogenetics. There are two short papers that present two sides of a relatively recent PhyloCode debate, which may form the bulk of our discussion, so please focus on them. I have uploaded the bundle of pdfs to the Drop Box, in a zip file:
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=== Monday, 21 October 2013 ===
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Simona Augyte will lead the discussion this week.
  
:[[Image:Pdficon_small.gif|left]] [http://dropbox.uconn.edu/dropbox?n=Systematics_08-1111.zip&p=WC9a4kJVW5dLCUnYz Click here to download.]
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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
  
====Summary of papers====
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=== Monday, 28 October 2013 ===
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Paul Lewis will lead the discussion this week.
  
Read these papers in their entirety:
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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
* Pickett, K. M. 2005. The new and improved PhyloCode, now with types, ranks, and even polyphyly: a conference report from the First International Phylogenetic Nomenclature Meeting. ''Cladistics'' 21: 79-82.
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* Laurin, M., K. de Queiroz, P. Cantino, N. Cellinese, and R. Olmstead. 2005. The PhyloCode, types, ranks and monophyly: a response to Pickett. ''Cladistics'' 21: 605-607.
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Example of higher-level taxa (unranked, of course) in plants [the first paper is the phylogenetic taxonomy, and the second gives the complete phylogeny]:
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* Stefanovic, S., D. F. Austin, and R. G. Olmstead. 2003. Classification of Convolvulaceae: A phylogenetic approach. ''Systematic Botany'' 28: 791-806.
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* Stefanovic, S., L. Krueger, and R. G. Olmstead. 2002. Monophyly of the Convolvulaceae and circumscription of their major lineages based on DNA sequences of multiple chloroplast loci. ''American Journal of Botany'' 89: 1510-1522.
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Example of an "''incertae sedis''" animal species:
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* Dayrat, B. 2005. Advantages of naming species under the PhyloCode : An example of how a new species of Discodorididae (Mollusca , Gastropoda , Euthyneura , Nudibranchia , Doridina ) may be named. ''Marine Biology Research'' 1: 216-232.
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In the interest of conservation, please avoid printing the phylogenetics papers unless you'll want them later; we'll have enough laptops to share phylogeny images at the meeting.
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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
  
=== Tuesday, November 18th, 2008 ===
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=== Monday, 4 November 2013 ===
Discussion leader: Beth Wade
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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>
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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>
  
=== Tuesday, December 2nd, 2008 ===
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=== Monday, 11 November 2013 ===
Discussion leader:  
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Paper for this week:
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:{{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)
  
=== Tuesday, December 9th, 2008 ===
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=== Monday, 18 November 2013 ===
Discussion leader:  
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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
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bioinformatics-2013-Zhang-2869-76.pdf}}Bioinformatics-2013-Zhang-2869-76.pdf
  
=== Some papers to pick from ===
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=== Monday, 2 December 2013===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/DivergenceTimesLargeTrees2007.pdf}} Britton et al. 2007 <br>
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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/SkewDivergenceTimes2008.pdf}}Burbrink & Pyron 2008
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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>
<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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[[#top|Back to top]]
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== 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]]
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* [[Systematics Seminar Spring 2010|Spring 2010]]
 +
* [[Systematics Seminar Fall 2009|Fall 2009]]
 +
* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]

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