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| | == 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. | + | We are meeting this semester in the '''Bamford Room (TLS 171) Tuesdays 4-5pm'''. |
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| − | == Theme for Spring Semester 2008 == | + | == Theme for Fall Semester 2008 == |
| − | 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:
| + | 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. Papers will be posted shortly. If you are interested in leading a particular week's discussion, please sign up below. |
| − | * can you ever say that a clade is basal?
| + | |
| − | * do non-uniform clade priors make sense?
| + | |
| − | * what can and can't fossils say about node age
| + | |
| − | * when gene trees and species trees are both right, but different
| + | |
| − | * the signature of an adaptive radiation
| + | |
| − | 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 == | + | == Schedule for Fall Semester 2008 == |
| | '''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. | | '''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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| − | === Tuesday, January 22, 2008: Basal clades === | + | === Tuesday, September 2nd, 2008: === |
| − | Discussion leader: Paul Lewis | + | Discussion leader: |
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| − | 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''.
| + | === Tuesday, September 9th, 2008 === |
| − | :{{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. | + | Discussion leader: |
| − | :{{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 === | + | === Tuesday, September 16th, 2008 === |
| − | Discussion leader: Frank Smith | + | Discussion leader: |
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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.
| + | === Tuesday, September 23rd, 2008 === |
| − | | + | Discussion leader: |
| − | In this paper, Kevin de Queiroz considers how to define names for clades, and discusses tree terms such as ''crown group'', ''stem lineage'', etc.
| + | |
| − | | + | |
| − | === Friday, February 8, 2008 === | + | |
| − | Discussion leader: Karolina Fucikova | + | |
| − | :{{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.
| + | |
| − | | + | |
| − | === Friday, February 15, 2008 ===
| + | |
| − | Discussion leader: Yu(Daniel) Fan
| + | |
| − | :{{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
| + | |
| − | | + | |
| − | :{{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.
| + | |
| − | | + | |
| − | === Friday, February 22, 2008 ===
| + | |
| − | ''Cancelled due to snow storm''
| + | |
| − | | + | |
| − | === Friday, February 26, 2008 ===
| + | |
| − | Discussion leader: Juan Carlos Villarreal Aguilar
| + | |
| − | | + | |
| − | :{{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.
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pagel-1.etal.20006.science.suppl.pdf}} '''Supporting online material'''
| + | |
| − | | + | |
| − | === Friday, February 29, 2008 ===
| + | |
| − | Discussion leader:
| + | |
| − | | + | |
| − | === Friday, March 7, 2008 ===
| + | |
| − | Discussion leader: [[Nic Tippery]]
| + | |
| − | | + | |
| − | :{{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 ===
| + | |
| − | No meeting (Spring Break)
| + | |
| − | | + | |
| − | === Friday, March 21, 2008 ===
| + | |
| − | Discussion leader: Roberta Engel
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Introduction.pdf}} Introduction of David Baum's book on Tree Thinking
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%201.pdf}} Chapter 1 of David Baum's book on Tree Thinking
| + | |
| − | | + | |
| − | === Friday, March 28, 2008 ===
| + | |
| − | Discussion leader: Thiago Rangel
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%202.pdf}} Chapter 2 of David Baum's book on Tree Thinking
| + | |
| − | | + | |
| − | === Friday, April 4, 2008 ===
| + | |
| − | Discussion leader: Geert Goemans
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter%203.pdf}} Chapter 3 of David Baum's book on Tree Thinking
| + | |
| − | | + | |
| − | === Friday, April 11, 2008 ===
| + | |
| − | Discussion leader: Carrie Fyler
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter4.pdf}} Chapter 4 of David Baum's book on Tree Thinking
| + | |
| − | | + | |
| − | === Friday, April 18, 2008 ===
| + | |
| − | Discussion leader: everyone and no one
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter5.pdf}} Chapter 5 of David Baum's book on Tree Thinking
| + | |
| − | | + | |
| − | === Friday, April 25, 2008 ===
| + | |
| − | Discussion leader: free for all
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chapter6.pdf}} Chapter 6 of David Baum's book on Tree Thinking
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| − | | + | |
| − | === Friday, May 2, 2008 (final meeting of Spring 2008) ===
| + | |
| − | Discussion leader: Dave Wagner
| + | |
| − | | + | |
| − | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Rabosky_Lovette_evo_6.pdf}} Rabosky, D. L., and I. J. Lovette. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Submitted manuscript.
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| | [[#top|Back to top]] | | [[#top|Back to top]] |
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.
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. Papers will be posted shortly. If you are interested in leading a particular week's discussion, please sign up below.
