Winter 2003 - Topic: Phylogenies and the Comparative Method

Instructor: Theodore Garland, Jr., Professor of Biology

Phone: 787-3524; Email: tgarland@citrus.ucr.edu; Office: 109 ULB

8 Jan. 2003 - Organize

15 Jan. 2003 - Lecture
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1-15.
    [Note typo in Table 1]
Garland, T., Jr., and S. C. Adolph. 1994. Why not to do two-species comparative studies:
    limitations on inferring adaptation. Physiological Zoology 67:797-828.
    [Note worked example of independent contrasts in Fig. 2]

22 Jan. 2003 - Lecture
Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of continuous characters.
    Systematic Biology 42:569-575.
Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of
    covariance by computer simulation. Systematic Biology 42:265-292.

29 Jan. 2003 - Lecture by Mark Springer
Reznick, D. N., M. Mateos, and M. S. Springer. 2002. Independent origins and rapid evolution
    of the placenta in the fish genus Poeciliopsis. Science 298:1018-1020.
Schluter, D., T. Price, A. O. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in
    adaptive radiation. Evolution 51:1699-1711.

5 Feb. 2003 - Lecture
Garland, T., Jr., and A. R. Ives. 2000. Using the past to predict the present: Confidence intervals
    for regression equations in phylogenetic comparative methods. American Naturalist 155:346-364.

12 Feb. 2003 - Discussion; Present outline of project idea

Student leaders:
Jessica Bunkers
Losos, J. B., and D. B. Miles. 2002. Testing the hypothesis that a clade has adaptively radiated:
    iguanid lizard clades as a case study. American Naturalist 160:147-157.
Enrico Rezende
Housworth, E. A., and E. P. Martins. 2001. Random sampling of constrained phylogenies:
    conducting phylogenetic analyses when the phylogeny is partially known. Syst. Biol. 50:628-639.

19 Feb. 2003 - Discussion; Pointers for your presentations
(e.g., font, fill frame, maximize ratio of data ink/non-data ink)

Student leaders:
Cathy Chmura
Crespi, B. J., and R. Teo. 2002. Comparative phylogenetic analysis of the evolution of semelparity
    and life history in salmonid fishes. Evolution 56:1008–1020.
Marcelo Pires
Reynolds, J. D., N. B. Goodwin, and R. P. Freckleton. 2002. Evolutionary transitions in parental
    care and live bearing in vertebrates. Phil. Trans. R. Soc. Lond. B 357:269–281.

26 Feb. 2003 - Discussion; Guidelines for paper format

Student leaders:
Veronique Campbell
Bininda-Emonds, O. R. P., and J. L. Gittleman. 2000. Are pinnipeds functionally different from
    fissiped carnivores? The importance of phylogenetic comparative analyses. Evolution 54:1011-1023.
Robert Meredith
Bininda-Emonds, O. R. P., J. L. Gittleman, and A. Purvis. 1999. Building large trees by combining
    phylogenetic information: a complete phylogeny of the extant Carnivora. Biological Reviews 74:143-175.

5 Mar. 2003 - PowerPoint presentations (half); Discussion

Student leader: James ("Chris") Sagebiel
Ferguson, S. H., and S. Lariviere. 2002. Can comparing life histories help conserve carnivores?
    Animal Conservation 5:1-12.

12 Mar. 2003 - PowerPoint presentations (half); Discussion

Student leader: Greg Russell
Hochachka, P. W. 2000. Pinniped diving response mechanism and evolution: a window on the paradigm
    of comparative biochemistry and physiology. Comparative Biochemistry and Physiology Part A 126:435–458.

Papers due duirng Final's Week

No Final Exam