Phylogenetic Comparative Methods Seminar

Zoology 690B/696B: Fall, 2003

Instructor: Dr. Dean Adams
201 Science II

Office Hours: Anytime by appointment

Class Meetings
Lecture: Thursdays 11:00 – 12:30 (132 Science II)
Lab: meets occasionally in lieu of lecture (same time)

Recommended Readings
There is no formal text for this seminar course. In lieu of a textbook I will provide readings each week for the following week’s topic. One book that will be referred to repeatedly throughout the semester is Harvey and Pagel, 1991. This is a book that I keep on my shelf, and have found to be useful reference material (and is one that you may wish to purchase for your own reference following the seminar). The full reference is:

Harvey, P. H., and M. D. Pagel. 1991. The Comparative Method in Evolutionary Biology. Oxford Series in Ecology and Evolution. Oxford University Press, Oxford. 239 pp.

Course Description and Objectives
Comparative biology has long been the cornerstone of ecological and evolutionary research. This research program began with early 18th and 19th century naturalists, who observed large numbers of organisms from populations, geographic regions, and species, described the emergent patterns of various features, and posited ecological and evolutionary explanations for those patterns. Among modern evolutionary ecologists, a relatively standardized protocol has emerged: 1) generate ecological or evolutionary hypothesis, 2) quantify various traits (ecological, morphological, behavioral, etc.) for members of populations and species, and 3) statistically assess the patterns of covariation among these traits. However, in the past two decades the methods employed in such research have changed drastically; as it has become apparent that shared evolutionary history among taxa can significantly alter interpretations of patterns of covariation. Thus, to accurately assess whether or not two traits covary in an adaptive manner, the phylogenetic relatedness of the species must first be taken into account. If it is not, then assigning a causal mechanism to the observed correlation of traits may be difficult (e.g., is it due to selection, or evolutionary history?).
In this seminar, we will review the major advances in comparative methodology for both discrete and continuous data, and compare the different procedures that have been proposed for these tasks. We will meet once a week for 1 ½ hours. I tend to run seminars a bit differently than most, and this one is no exception. Each week, we will read one or more papers and discuss them. However, rather than discussing the biological theory and results of the papers, we will instead focus on the methodology that was used. I will provide additional mathematical details as needed. There will be several laboratory periods throughout the semester where you will have a chance to try out the methods we have discussed in previous class periods. It is hoped that the exercises in laboratory will reinforce the concepts discussed during class, so that you can apply these methods in your own research.

Schedule of Lectures and Laboratories
Below is a tentative schedule of topics to be discussed, and the papers we will read for each discussion. Papers can be found outside my office (201 Science II) the week prior to class.

(DM = discrete methods, CM = continutous methods)




Aug 28

Introduction & Basic Concepts


Sept 4

Why worry about phylogeny?

Harvey & Pagel, 1991 (CH 2); Westoby et al. 1995. J. Ecol. 83:531-534; Harvey eta al., 1995. J. Ecol. 83:535-536

Sept 11

DM: Chi-Squared Changes Method

Ridley, 1982 (parts); Harvey & Pagel, 1991 (CH 4 parts)

Sept 18

DM: Concentrated Changes

Harvey & Pagel, 1991 (CH 4 parts); Maddison, 1990. Evol. 44:539-557

Sept 25

DM: Maximum Likelihood

Harvey & Pagel, 1991 (CH 4 parts); Pagel, 1994. Proc. Roy. Soc. Lon. B. 255:37-45

Oct 2

LAB WORK: Discrete Methods

Maclade, Discrete

Oct 9

CM: Phylogenetic Autocorrelation

Cheverud and Dow, 1985. Am. J. Phys. Anthrop. 67:113-121

Oct 16

CM: Independent Contrasts

Felsenstein, 1985. Am. Net. 125:1-15

Oct 23

CM: Phylogenetic Regression

Grafen, 1989. Phil. Trans. Roy. Soc. LOnd. 326:119-156

Oct 30

CM: Phylogenetic Least Squares and Phylogenetic regression

Martins and Hansen, 1997. Am. Nat. 149:646-667 Grafen, 1989. Phil. Trans. Roy. Soc. Lond. 326:119-156.

Nov 6

Incomplete Phylogenies I: Branch Lengths

Branches=1, Grafen's (1989) method; Pagel's (1992) method

Nov 13

Incomplete Phylogenies II: Polytomies

Martins, 1996. Evol. 50:12-22; Abouheif, 1998. Evol. 52:1197-1204

Nov 20

CM: Synthesis

Rohlf, 2001. Evol. 55:2143-2160

Nov 27



Dec 4

LAB WORK: Continuous Methods

PDAP, Compare, NTSYS

Dec 11

Phylogenies and Community Ecology

Losos, 1992. Syst. Biol. 41:403-420; Webb et al., 2002. Ann. Rev. Ecol. Syst