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) Fridays from 2-3pm'''. Let's try to get started on time, as another group is meeting in the Bamford Room starting at 3pm on Fridays.
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For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm'''
  
== Theme for Spring Semester 2008 ==
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=== Monday, 25 August 2014 ===
The theme this semester is '''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:
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At this meeting we will discuss possible themes for this semester's seminar:
* can you ever say that a clade is basal?
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* 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
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Some suggested papers are listed below the schedule in the section entitled [[#Some possibilities|Some possibilities]].
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== Schedule for Spring Semester 2008 ==
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=== Monday, 1 September 2014 ===
'''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 22, 2008: Basal clades ===
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=== Monday, 8 September 2014 ===
Discussion leader: Paul Lewis
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For this meeting, please come with an example (or examples) of a source of systematic error in datasets, and a paper that attempts to address this source of systematic error. We will use these examples and papers as a basis for discussions in upcoming weeks.
  
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''.
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=== Monday, 15 September 2014 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}} '''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}} '''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281.
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=== Friday, February 1, 2008 ===
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=== Monday, 22 September 2014 ===
Discussion leader: Frank Smith
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}} '''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974.
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=== Monday, 29 September 2014 ===
  
In this paper, Kevin de Queiroz considers how to define names for clades, and discusses tree terms such as ''crown group'', ''stem lineage'', etc.
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=== Monday, 6 October 2014 ===
  
=== Friday, February 8, 2008 ===
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=== Monday, 13 October 2014 ===
Discussion leader: Karolina Fucikova
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''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.
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=== Friday, February 15, 2008 ===
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=== Monday, 20 October 2014 ===
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
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Suggested reading
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=== Monday, 27 October 2014 ===
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
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=== Monday, 3 November 2014 ===
  
=== Friday, February 22, 2008 ===
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=== Monday, 10 November 2014 ===
''Cancelled due to snow storm''
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=== Friday, February 26, 2008 ===
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=== Monday, 17 November 2014 ===
Discussion leader: Juan Carlos Villarreal Aguilar
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pagel_etal_2006_science.pdf}} '''Pagel et al.''' 2006. Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level. Science 314: 119-121.
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=== Monday, 1 December 2014===
 
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pagel-1.etal.20006.science.suppl.pdf}} '''Supporting online material'''
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=== Friday, February 29, 2008 ===
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Discussion leader:
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=== Friday, March 7, 2008 ===
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Discussion leader: [[Nic Tippery]]
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ricklefs-2007_diversification.pdf}} '''Ricklefs, R. E.''' 2007. Estimating diversification rates from phylogenetic information. ''Trends in Ecology and Evolution'' 22: 601-610.
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=== Friday, March 14, 2008 ===
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No meeting (Spring Break)
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=== Friday, March 21, 2008 (next meeting) ===
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Discussion leader: Roberta Engel
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Introduction.pdf}} Introduction of David Baum's book on Tree Thinking
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%201.pdf}} Chapter 1 of David Baum's book on Tree Thinking
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=== Friday, March 28, 2008 ===
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Discussion leader:
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=== Friday, April 4, 2008 ===
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Discussion leader:
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=== Friday, April 11, 2008 ===
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Discussion leader:
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=== Friday, April 18, 2008 ===
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Discussion leader:
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=== Friday, April 25, 2008 ===
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Discussion leader:
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== Some possibilities ==
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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).
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=== Paraphyly vs. Polyphyly ===
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Farris' paper is not recent, but would almost certainly be cited by more recent treatments of this subject.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Farris_1974_SystZool_23_548-554.pdf}} '''Farris, J. S.''' 1974. Formal definitions of paraphyly and polyphyly. Systematic Zoology 23: 548-554.
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=== Tree terms ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}} '''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 22:114-115.
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=== Necessity of unequal split priors: undesirable? ===
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The Velasco response in combination with one of the other two would make for an interesting discussion.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}} '''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
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=== Using fossils in dating lineages ===
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Among other things, this paper explains why fossils cannot indicate actual branching dates.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''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.
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=== Signature of adaptive radiations ===
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Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}} '''Whitfield, J. B., and P. J. Lockhart'''. 2007. Deciphering ancient rapid radiations. TREE 22:258-265.
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[[#top|Back to top]]
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== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
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* [[Systematics Seminar Fall 2013|Fall 2013]]
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* [[Systematics Seminar Spring 2012|Spring 2012]]
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* [[Systematics Seminar Fall 2011|Fall 2011]]
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* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
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* [[Systematics Seminar Fall 2010|Fall 2010]]
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* [[Systematics Seminar Spring 2010|Spring 2010]]
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* [[Systematics Seminar Fall 2009|Fall 2009]]
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* [[Systematics Seminar Fall 2008|Fall 2008]]
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* [[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]]

Revision as of 22:50, 26 August 2014

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 2014 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2-3pm

Monday, 25 August 2014

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

Monday, 1 September 2014

Labor Day, no meeting

Monday, 8 September 2014

For this meeting, please come with an example (or examples) of a source of systematic error in datasets, and a paper that attempts to address this source of systematic error. We will use these examples and papers as a basis for discussions in upcoming weeks.

Monday, 15 September 2014

Monday, 22 September 2014

Monday, 29 September 2014

Monday, 6 October 2014

Monday, 13 October 2014

Monday, 20 October 2014

Monday, 27 October 2014

Monday, 3 November 2014

Monday, 10 November 2014

Monday, 17 November 2014

Monday, 1 December 2014

Past Systematics Seminars