Genetics 590

The Evolution and Population Genetics Seminar will cover the topic of "The Comparative Method" during Autumn Quarter of 1996. Here is a syllabus with references.

The weekly references will be available to be copied in the copy room of the Genetics Department, J205 Health Sciences Building. The four general references will be available at the Health Sciences Library Reserve.

I will be leading the seminar, which will involve readings and student presentations. The first session (on week 2 of the quarter) there will be no presentation but we will all read the readings and discuss them. The seminar meets on Tuesdays at 12:30pm (that's just after noon, not just after midnight). It is scheduled for room J280 Health Sciences Building, but will actually take place in J182 HSB, a much cozier room, unless too many people register.

This will be a working seminar, where we all read readings and 1 or 2 people give presentations on them each week. Students will be required to give a presentation to get credit.

The syllabus below is tentative. It will evolve rapidly, and I will post any changes in the papers or the names of presenters. Watch this space.

Joe Felsenstein (joe@genetics.washington.edu)

General References in the Area

• Harvey, P. H. and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford. (The only reasonably comprehensive text).
• Felsenstein, J. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19: 445-471. (Brief coverage of comparative methods, emphasizing the author's favorite approaches. Brilliant on evolutionary models).
• Miles, D. B. and A. E. Dunham. 1993. Historical perspectives in ecology and evolutionary biology: the use of phylogenetic comparative analyses. Annual Review of Ecology and Systematics 24: 587-619.
• E. P. Martins (ed.). 1996. Phylogenies and the Comparative Method in Animal Behavior. Oxford University Press, New York and Oxford. (A multi-author volume with some methdological papers and a lot of behavioral applications).
• Harvey, P. H. and A. Purvis. 1991. Comparative methods for explaining adaptations. Nature 351: 619-24.

Syllabus and reading list

Already done:

• October 1. (Joe is away so we start on week 2). Copy and start reading the papers for week 2.
• October 8: The problem. No presenter: we all read these and discuss them. These are fairly long but we're not really going through them in detail.
  • Clutton-Brock, T. H., and P. H. Harvey. 1984. Comparative approaches to investigating adaptation. Pages 7-29 in Behavioral ecology: An evolutionary approach, ed. J. R. Krebs and N. B. Davies. 2nd ed. Blackwell, Oxford.
  • Huey, R. B. 1987. Phylogeny, history, and the comparative method. pp. 76-101 in New Directions in Ecological Physiology, ed. M. Feder, A. F. Bennett, W. W. Burggren, and R. B. Huey. Cambridge University Press, Cambridge.
  • Garland, T., Jr. and S. C. Adolph. 1994. Why not to do two-species comparative studies: limitations in inferring adaptation. Physiological Zoology 67: 797-828. (especially pages 797-805 and 821-824)
• October 15: Contrasts methods. Presenter: Art Woods
  • Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 126: 1-25.
  • Harvey, P. H. and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford. (pages 115-170)
  • Bjorklund, M. 1994. The independent contrast method in comparative biology. Cladistics 10: 425-433.
• October 22: Unresolved phylogenies. Presenters: Do Peterson and Hopi Hoekstra
  • Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society of London, Biological Sciences 326: 119-157.
  • Gittleman, J. L. and M. Kot. 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Systematic Zoology 39: 227-241.
  • Pagel, M. D. and P. H. Harvey. 1989. Comparative methods for examining adaptation depend on evolutionary models. Folia Primatologica 53: 203-220. (the stuff on pages 214-215 is most relevant; the rest is a useful review).
  • Martins, E. P. 1996. Conducting phylogenetic comparative analyses when the phylogeny is not known. Evolution 50: 12-22. Note -- newly added at last minute.
• October 29: Discrete characters. Presenter: Peter Beerli
  • Maddison, W. P. 1990. A method for testing the correlated evolution of two binary characters: are gains and losses concentrated on certain branches of a phylogenetic tree Evolution 44: 539-557. (Can skim over the algorithmic stuff as long as you know what he is trying to compute).
  • Pagel, M. D. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London, series B 255: 37-45.
  • Ridley, M. and A. Grafen. 1996. How to study discrete comparative methods. pp. 76-103 in Phylogenies and the Comparative Method in Animal Behavior, ed. E. P. Martins. Oxford University Press, New York and Oxford.
  • A number of papers that attempt comparative method inferences on discrete characters, but not use statistical analysis, will be found in the most recent (September, 1996) issue of Systematic Biology -- the papers by Losos, McLennan, Emerson, Basolo, and Wray.
• November 5: Ancestral character states. Presenter: Wendy Schackwitz
  • Huey, R. B. and A. F. Bennett. 1987. Phylogenetic studies of co-adaptation: preferred temperatures versus optimal performance temperatures of lizards. Evolution 41: 1098-1115.
  • Maddison, W. P. 1991. Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Systematic Zoology 40: 304-314.
• November 12: Criticisms of statistical comparative methods. Presenter: Lindsey Dubb
  • Wenzel, J. W., and J. M. Carpenter. 1994. Comparing methods: adaptive traits and tests of adaptation. Pages 79-101 in Phylogenetics and ecology, ed. P. Eggleton and R. I. Vane-Wright. Linnean Society Symposium Series Number 17. Academic Press, London.
  • Bjorklund, M. 1994. The independent contrast method in comparative biology. Cladistics 10: 425-433. (This was used on Oct. 15 too).
  • If you want to see a number of papers that do not use statistical analysis, but deal with this sort of data, you might look at the most recent (September, 1996) issue of Systematic Biology, at the papers by Losos, McLennan, Emerson, Basolo, and Wray.
• November 19: (Class was cancelled because Joe was not able to get to it through the snow).
• November 26: Better models of evolution? Presenters: Anthu Hoang and Carol Lee.
  • Felsenstein, J. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19: 445-471. (especially pages 460 ff.)
  • Hansen, T. F. and E. P. Martins. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50: 1404-1417.
• December 3: Sampling variation within species. Presenter: Eric Anderson.
  • Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080.
• December 10: Geographic variation within species. Presenters: Stacey Coombes, Caity Conley.
  • Edwards, S. V. and M. Kot. 1995. Comparative methods at the species level: geographic variation in morphology and group size in Grey-Crowned Babblers (Pomatostomus temporalis). Evolution 49: 1134-1146.