Evolution and Population Genetics Seminar

Genetics 590

Autumn, 2000

The Evolution and Population Genetics seminar will meet on Tuesdays in Autumn quarter in J112 Health Sciences Building (note: this is a new location) from 12:30pm - 1:20pm. This quarter the topic will be morphometrics, quantitative characters, and phylogenies. Participants will read papers in this area and will be expected to lead discussion once during the quarter. Some of the material we hope to cover includes methods of morphometrics (landmark and outline methods) and use of quantitative characters for inferring phylogenies (whether to, how to). I will try to make a list of references available at the first meeting and on the course web page.

The weekly references will be available to be copied in the copy room of the Genetics Department, J205 Health Sciences Building, and they are to be listed below.

The course will presuppose knowledge of elementary statistics and genetics. It is a graduate course with prerequisite Genetics 562 or permission of the instructor.

Joe Felsenstein (joe@genetics.washington.edu)

Readings for the sessions (session leader given for each):

(The readings are available in the Xerox room of the Genetics Department office, J205 HSB. If you ask the secretary at the front desk she will permit you to copy for free the reading, from the originals in the course file folder in the copy room).

Rough topics are given -- readings will gradually follow)

September 26

This will be an organizational session.

October 3

Landmark methods -- Biorthogonal grids (Joe Felsenstein)

The reading for this session is pp. 127-142 of

Bookstein, F. L., B. Chernoff, R. Elder, J. Humphries, G. Smith, and R. Strauss. 1985. Morphometrics in Evolutionary Biology. Special Publication No. 15. Academy of Natural Sciences, Philadelphia.

Also relevant though not required:

Bookstein, F. L. 1978. The Measurement of Biological Shape and Shape Change. Lecture Notes in Biomathematics, vol. 24. Springer-Verlag, 191 pp.

October 10

Landmark methods -- Thin-plate splines (Joe Felsenstein)

(Either one of these will do:)

October 17

Outline methods -- Elliptical Fourier transform (Lindsey Dubb)

October 24

Combining outline and landmark data

One of these ...

October 31

(we need a scary topic for this one, so ...) Is there any hope of a developmental or phylogenetic morphometrics instead of a geometric morphometrics?

November 7

Character coding methods for quantitative characters

November 14

Brownian motion models of quantitative characters

November 21

(No seminar as Joe will be out of town)

November 28

How to correct for covariances (and which covariances, anyway?)

References

Here are some references which include some of the papers we will read (plus some we won't read):

Archie, J. W. 1985. Methods for coding variable morphological features for numerical taxonomic analysis. Systematic Zoology 34: 326-345.

Björklund, M. 1994. The independent contrast method in comparative biology. Cladistics 10: 425-433.

Bookstein, F. L. 1977. The study of shape transformation after D'Arcy Thompson. Mathematical Biosciences 34: 177-219.

Bookstein, F. L. 1978. The Measurement of Biological Shape and Shape Change. Lecture Notes in Biomathematics, vol. 24. Springer-Verlag, 191 pp.

Bookstein, F. L. 1982. Foundations of morphometrics. Annual Reviews of Ecology and Systematics 13: 451-470.

Bookstein, F. L. 1984. A statistical method for biological shape comparisons. Journal of Theoretical Biology 107: 475-520.

Bookstein, F. L., B. Chernoff, R. Elder, J. Humphries, G. Smith, and R. Strauss. 1985. Morphometrics in Evolutionary Biology. Special Publication No. 15. Academy of Natural Sciences, Philadelphia.

Bookstein, F. L. 1988. Random walk and the biometrics of morphological characters. Evolutionary Biology 23: 369-398.

Bookstein, F. L. 1989. Principal warps: Thin-plate splines and the decomposition of deformations. I.E.E.E. Transactions on Pattern Analysis and Machine Intelligence 11: 567-585.

Bookstein, F. L. 1991. Morphometric tools for landmark data: geometry and biology. Cambridge Univ. Press, New York. 435 pp.

Bookstein, F. L. 1995. The Morphometric Synthesis for landmarks and edge-elements in images. Terra Nova 7: 393-407.

Bookstein, F. L. 1996. The morphometric synthesis. Computing Science and Statistics 27: 240-249.

Bookstein, F. L. 1996. Combining the tools of geometric morphometrics. pp. 131--151 in L. F. Marcus, M. Corti, A. Loy, G. J. P. Naylor and D. E. Slice, eds., Advances in Morphometrics. NATO ASI Series A: Life Sciences, volume 284. Plenum, 1996.

Bookstein, F. L. 1996. Biometrics, biomathematics, and the morphometric synthesis. Bulletin of Mathematical Biology 58: 313--365, 1996.

Bookstein, F. L. 1996. Applying landmark methods to biological outline data. pp. 59--70 in K. V. Mardia, C. A. Gill, and I. L. Dryden, eds., Proceedings in Image Fusion and Shape Variability Techniques. Leeds University Press, 1996.

Bookstein, F. L. 1996. Landmark methods for forms without landmarks: Localizing group differences in outline shape. pp. 279--289 in A. Amini, F. L. Bookstein, and D. Wilson, eds., Proceedings of the Workshop on Mathematical Methods in Biomedical Image Analysis, San Francisco, June 1996. IEEE Computer Society Press.

Dryden, I. L. and K. V. Mardia. 1998. Statistical shape analysis. Wiley: New York. 347 pp. ISBN 0-471-95816-6.

Felsenstein, J. 1973. Maximum likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics 25: 471-492.

Felsenstein, J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35: 1229-1242.

Felsenstein, J. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19: 445-471.

Felsenstein, J. 2000?. Quantitative characters, phylogenies and morphometrics. To appear in a volume edited by N. MacLeod.

Kuhl, F. P. and C. R. Giardina. 1982. Elliptic Fourier features of a closed contour. Computer Graphics and Image Processing. 18: 236-258.

Rohlf, F. J. and J. Archie. 1984. A comparison of Fourier methods for the description of wing shapes in mosquitoes (Diptera:Culicidae). Systematic Zoology 33: 302-317.

Rohlf, F. J. and F. L. Bookstein. (eds.) 1990. Proceedings of the Michigan Morphometrics Workshop. Special Publ. No. 2, The University of Michigan Museum of Zoology. 380 pp.

Wiens, J. J. (ed.). 2000. Phylogenetic Analysis of Morphological Data Smithsonian Institution Press, Washington.

Zelditch, M. L., W. L. Fink, and D. L. Swiderski. 1995. Morphometrics, homology, and phylogenetics - quantified characters as synapomorphies. Systematic Biology 44: 179-189.

Web resources

An enormously useful set of web resources on morphometrics is:
The WWW Morphometrics pages

Futher morphometrics software is listed at the Digital Taxonomy pages Morphometric Software list.