Seminar in Comparative Biology

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This is the home page of the UConn EEB department's Seminar in Comparative Biology. This (Fall 2007) semester, we are meeting each '''Monday''' at '''11:30am''' in the [[Bamford Conference Room]] in the [[Torrey Life Science]] building.
 
This is the home page of the UConn EEB department's Seminar in Comparative Biology. This (Fall 2007) semester, we are meeting each '''Monday''' at '''11:30am''' in the [[Bamford Conference Room]] in the [[Torrey Life Science]] building.
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== Possible papers for discussion ==
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A separate EEBedia page, [[Comparative Biology Papers]], has been created for listing possible papers for discussion. Feel free to add to it!
  
 
== Schedule for Fall Semester 2007 ==
 
== Schedule for Fall Semester 2007 ==
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=== October 1, 2007 ===
 
=== October 1, 2007 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Caro_etal.pdf}}Caro, Graham, Stoner and Flores. 2003. Correlates of horn and antler shape in bovids and cervids. Behav. Ecol. Sociobiol. 55:32-41.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Caro_etal.pdf}}Caro, T. M., C. M. Graham, C. J. Stoner, and M. M. Flores. 2003. Correlates of horn and antler shape in bovids and cervids. Behav. Ecol. Sociobiol. 55:32-41.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PDTREE_Mesquite-1.pdf}} PDTREE_Mesquite-1.pdf
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=== October 8, 2007 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cavender-Bares%202004%20AmNat.pdf}} Cavender-Bares, J., D. D. Ackerly, D. A. Baum, and F. A. Bazzaz. 2004 American Naturalist 163(6): 823-843.
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=== October 15, 2007 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Phillimore%20et%20al%20Am%20Nat%2006.pdf}}  Phillimore, A. B., R. P. Freckleton, C. D. L. Orme and I. P. F. Owens. 2006. Ecology predicts large-scale patterns of phylogenetic diversification in birds. American Naturalist 168: 220-229.
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=== October 22, 2007 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hulsey%20et%20al%20PRSB%2007.pdf}}  Hulsey, C. D., M. C. Mims and J. T. Streelman. 2007. Do constructional constraints influence cichlid craniofacial diversification? Proceedings of the Royal Society London B 274: 1867-1875.
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=== November 5, 2007 ===
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Some more Mesquite workshopping, using a tree with equal branch lengths, and looking at ancestral character reconstruction.
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Here is a nexus file that can be opened in Mesquite containing the data matrix and tree:
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[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/carl3.nex carl3.nex]
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=== November 12, 2007 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/garlandetal1993.pdf}} Phylogenetic ANOVA/ANCOVA - Garland et al. 1993
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pcm_applications.pdf}} Phylogenetic comparative methods & applications   
 +
:Here is a table outlining some of the prevailing phylogeny-based analytical methods, in relation to their traditional statistical counterparts, for approaching various types of questions.  This is a work in progress, so please email any comments, suggestions, or complaints to: diego.sustaita@uconn.edu
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=== November 26, 2007 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ives_et_al_2007_syst_biol.pdf}}Ives, A.R., P.E. Midford, and T. Garland Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56(2):252–270
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=== December 3, 2007 ===
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ackerly_Ecology_sup_06.pdf}}Ackerly, D.D., D. W. Schwilk, C. O. Webb. 2006. Niche evolution and adaptive radiation: testing the order of trait divergence. Ecology 87(7): S50-S61.
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[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

Latest revision as of 19:01, 28 November 2007

ComparativeMethod.png
Fall 2007 Instructor of Record: Carl Schlichting

This is the home page of the UConn EEB department's Seminar in Comparative Biology. This (Fall 2007) semester, we are meeting each Monday at 11:30am in the Bamford Conference Room in the Torrey Life Science building.

Contents

Possible papers for discussion

A separate EEBedia page, Comparative Biology Papers, has been created for listing possible papers for discussion. Feel free to add to it!

Schedule for Fall Semester 2007

The papers for discussion are available as PDF files, but to keep us from getting into hot water with the journals involved, a username and password are required for access. If you have forgotten the username/password, please contact Paul Lewis.

Note: in addition to this web site, we will be using the Systematics Listserv for communication because this seminar is taking the place of the Systematics Seminar this semester.

Click here for information about joining and using the Systematics email list

To upload a pdf use this form (username/password required)

August 29, 2007

Organizational meeting, Bamford Conference Room, 4pm

September 10, 2007

Pdficon small.gif Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15.
Pdficon small.gif Paul's notes explaining Felsenstein's paper in greater detail for those interested. The original has been updated to reflect some suggestions made by Eric Schultz and an explanation of why branch lengths should be lengthened to accommodate uncertainty in character values at interior nodes of the tree.

September 17, 2007

Pdficon small.gif The following eight papers have been bundled into one PDF:
Westoby, M., M. R. Leishman and J. M. Lord. 1995. On misinterpreting the 'phylogenetic correction'. Journal of Ecology 83: 531-534.
Harvey, P.H., A. F. Read and S. Nee. 1995. Why ecologists need to be phylogenetically challenged. Journal of Ecology 83: 535-536.
Westoby, M., M. R. Leishman and J. M. Lord. 1995. Further remarks on phylogenetic correction. Journal of Ecology 83: 727-730.
Fitter, A. H. 1995. Interpreting quantitative and qualitative characteristics in comparative analyses. Journal of Ecology 83: 730.
Ackerly, D. D. and M. J. Donoghue. 1995. Phylogeny and ecology reconsidered. Journal of Ecology 83: 730-733.
Harvey, P.H., A. F. Read and S. Nee. 1995. Further remarks on the role of phylogeny in comparative ecology. Journal of Ecology 83: 733-734.
Rees, M. 1995. EC-PC comparative analyses? Journal of Ecology 83: 891-892.
Westoby, M., M. R. Leishman and J. M. Lord. 1995. Issues of interpretation after relating comparative datasets to phylogeny. Journal of Ecology 83: 892-893.

September 24, 2007

Pdficon small.gif Garland, T. Jr., P. H. Harvey, A. R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41: 18-32.
Pdficon small.gif Some additional references suggested by Jones, Schultz and Schlichting

October 1, 2007

Pdficon small.gifCaro, T. M., C. M. Graham, C. J. Stoner, and M. M. Flores. 2003. Correlates of horn and antler shape in bovids and cervids. Behav. Ecol. Sociobiol. 55:32-41.
Pdficon small.gif PDTREE_Mesquite-1.pdf

October 8, 2007

Pdficon small.gif Cavender-Bares, J., D. D. Ackerly, D. A. Baum, and F. A. Bazzaz. 2004 American Naturalist 163(6): 823-843.

October 15, 2007

Pdficon small.gif Phillimore, A. B., R. P. Freckleton, C. D. L. Orme and I. P. F. Owens. 2006. Ecology predicts large-scale patterns of phylogenetic diversification in birds. American Naturalist 168: 220-229.

October 22, 2007

Pdficon small.gif Hulsey, C. D., M. C. Mims and J. T. Streelman. 2007. Do constructional constraints influence cichlid craniofacial diversification? Proceedings of the Royal Society London B 274: 1867-1875.

November 5, 2007

Some more Mesquite workshopping, using a tree with equal branch lengths, and looking at ancestral character reconstruction. Here is a nexus file that can be opened in Mesquite containing the data matrix and tree: carl3.nex

November 12, 2007

Pdficon small.gif Phylogenetic ANOVA/ANCOVA - Garland et al. 1993
Pdficon small.gif Phylogenetic comparative methods & applications
Here is a table outlining some of the prevailing phylogeny-based analytical methods, in relation to their traditional statistical counterparts, for approaching various types of questions. This is a work in progress, so please email any comments, suggestions, or complaints to: diego.sustaita@uconn.edu

November 26, 2007

Pdficon small.gifIves, A.R., P.E. Midford, and T. Garland Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56(2):252–270

December 3, 2007

Pdficon small.gifAckerly, D.D., D. W. Schwilk, C. O. Webb. 2006. Niche evolution and adaptive radiation: testing the order of trait divergence. Ecology 87(7): S50-S61.
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