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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.  
+
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 ==
Except for the first meeting, we will meet in the Bamford Room (TLS 171) '''Tuesdays at 4pm'''. The '''first meeting''' will be held in the '''BioPharm 3rd. floor fishbowl''' (Bamford room reserved at this time by ecology search committee).
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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 2008 ==
+
=== Monday, 26 August 2013 ===
Unless there is loud objection, the theme this semester will be '''Tree Thinking'''. David Baum (Univ. Wisconsin, Madison) is writing a book on Tree Thinking and has agreed to let us read the chapters he has written in return for some constructive criticism. Baum's book will be supplemented with some thought-provoking and heated-debate-generating papers on subjects such as these:
+
At this meeting we will discuss possible themes for this semester's seminar:
* can you ever say that a clade is basal?
+
* do non-uniform clade priors make sense?
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* what can and can't fossils say about node age
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* when gene trees and species trees are both right, but different
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* the signature of an adaptive radiation
+
Some suggested papers are listed below the schedule in the section entitled [[#Some possibilities|Some possibilities]].
+
  
== Schedule for Spring Semester 2008 ==
+
=== 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].
+
Labor Day, no meeting
  
=== Tuesday, January 22, 2008: Basal clades ===
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=== Monday, 9 September 2013 ===
Discussion leader: Paul Lewis
+
Elizabeth Jockusch will lead the discussion this week.
  
Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word ''basal''.
+
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment.
:'''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}}
+
<ul>
:'''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}}
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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>
 +
</ul>
  
=== Tuesday, January 29, 2008 ===
+
=== Monday, 16 September 2013 ===
Discussion leader:
+
Lily Lewis will lead the discussion this week
  
=== Tuesday, February 5, 2008 ===
+
Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
Discussion leader:
+
: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]
Change meeting time (EEB Dept. Seminar conflicts)?
+
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 [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]
 +
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, February 12, 2008 ===
+
=== Monday, 23 September 2013 ===
Discussion leader:
+
Paul Lewis will lead the discussion this week.
Change meeting time (EEB Dept. Seminar conflicts)?
+
  
=== Tuesday, February 19, 2008 ===
+
: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:
+
  
=== Tuesday, February 26, 2008 ===
+
:Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
Discussion leader:
+
  
=== Tuesday, March 4, 2008 ===
+
=== Monday, 30 September 2013 ===
Discussion leader:
+
Brigette Zacharczenko will lead the discussion this week.<br>
 +
: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, March 11, 2008 ===
+
=== Monday, 07 October 2013 ===
No meeting (Spring Break)
+
Veronica Bueno will lead the discussion this week.
 +
:{{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
  
=== Tuesday, March 18, 2008 ===
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=== Monday, 14 October 2013 ===
Discussion leader:
+
Paul Lewis will lead the discussion.
  
=== Tuesday, March 25, 2008 ===
+
Main paper for discussion:
Discussion leader:
+
:{{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, April 1, 2008 ===
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Optional followup paper describing improvements in technical details:
Watch out! (April Fool's Day)
+
:{{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.
  
Discussion leader:
+
=== Monday, 21 October 2013 ===
 +
Simona Augyte will lead the discussion this week.
  
=== Tuesday, April 8, 2008 ===
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2012-Moalic-127-37.pdf}}Syst Biol-2012-Moalic-127-37.pdf
Discussion leader:
+
  
=== Tuesday, April 15, 2008 ===
+
=== Monday, 28 October 2013 ===
Discussion leader:
+
Paul Lewis will lead the discussion this week.
  
=== Tuesday, April 22, 2008 ===
+
:[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
Discussion leader:
+
  
=== Tuesday, April 29, 2008 ===
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/gorymykin_etal_2013_systbiol_62_50-61.key.pdf}} Paul's handout
Discussion leader:
+
  
== Some possibilities ==
+
=== Monday, 4 November 2013 ===
Feel free to expand this list, and there is of course no requirement that papers for discussion be chosen from this list. To upload a PDF (and receive a free email describing how to make a link to it here), click [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html this link to the upload form]. You will need to know the username and password to upload a PDF (same combination needed to download PDFs from this web site).
+
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>
 +
</ul>
  
=== Tree terms ===
+
=== 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)
  
Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE 22114-115
+
=== Monday, 18 November 2013 ===
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}}
+
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
  
=== Necessity of unequal split priors: undesirable? ===
+
=== Monday, 2 December 2013===
 
+
Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading. <br>
The Velasco response in combination with one of the other two would make for an interesting discussion.
+
{{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
:'''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}}
+
 
+
:'''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}}
+
 
+
:'''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}}
+
 
+
=== Phylocode: how to name a clade ===
+
 
+
Discusses tree terms such as ''crown group'', ''stem lineage'', etc.
+
 
+
:'''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}}
+
 
+
=== Using fossils in dating lineages ===
+
 
+
Among other things, this paper explains why fossils cannot indicate actual branching dates.
+
 
+
:Donoghue, P. C. J., and M. J. Benton. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}}
+
 
+
=== Signature of adaptive radiations ===
+
 
+
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
+
 
+
:Whitfield, J. B., and P. J. Lockhart. 2007. Deciphering ancient rapid radiations. TREE 22:258-265 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}}
+
 
+
[[#top|Back to top]]
+
  
 
== 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 2008|Fall 2008]]
 +
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
Line 116: Line 103:
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 
__NOTOC__
 
  
 
[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

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