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Integrative Biology 200B Spring 2007

"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"

Most important recommended readings are in bold face; required readings also have two asterisks

Jan. 16 - 25: GENERAL PHYLOGENETIC TREE-BUILDING

Albert, V. A., B. D. Mishler and M. W. Chase. 1992. Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. Pages 369-403 in Molecular Systematics of Plants (Soltis, P. S., D. E. Soltis and J. J. Doyle, ed.). Chapman & Hall, New York.

Bremer, K. 1994. Branch support and tree stability. Cladistics 10(3):295-304

Donoghue, M.J. and J.W. Kadereit. 1992. Walter Zimmermann and the growth of phylogenetic theory. Systematic Biology 41(1): 74-84.

de Queiroz, K. and J. Gauthier. 1992. Phylogenetic taxonomy. Ann. Rev. Ecol. Syst. 23: 449-480.

Farris J.S. 1983. The logical basis of phylogenetic analysis. In N Platnick and V Funk (eds.): Advances in Cladistics, Volume 2. NY.:Columbia Univ. Press, pp. 7-36.

Felsenstein, J. 1978. The number of evolutionary trees. Syst. Zool. 27:27-33.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17:368-376.

Felsenstein, J. 1981. A likelihood approach to character weighting and what it

tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16:183-196.

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the

bootstrap. Evolution 39:783-791.

Forey, P. L., C. J. Humphries, I. L. Kitching, R. W. Scotland, D. J. Siebert, and D. M. Williams. 1992. Cladistics. The Systematics Association Publication No.10. Oxford University Press, New York

Hennig, W. 1965. Phylogenetic systematics. Ann. Rev. of Entomology 10: 97-116.

Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana.

Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.

Hillis, D. M., and J. J. Bull. 1993. An empirical test of boot strapping as a method for assessing

confidence in phylogenetic analysis. Syst. Biol.

42:182-192.

Huelsenbeck, J. P. 1995. The performance of phylogenetic methods in simulation. Syst. Biol.

44:17-48.

Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny.

Bioinformatics 17:754-755.

Hull, D. L. 1988. Science as a process: an evolutionary account of the social and conceptual development of science. University of Chicago Press, Chicago. [an already classic work on the recent, violent history of systematics; used as data for Hull's general theories about scientific change].

Kluge, A.G. 1994. Moving targets and shell games. Cladistics 10(4): 403-413.

Larget, B., and D. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.

Lewis, P. O. 2001. Phylogenetic systematics turns over a new leaf. Trends Ecol.

Evol. 16:30-37.

Lundberg, J. G. and L. A. McDade. 1990. Systematics. Pages 65-108 in Methods for Fish Biology, American Fisheries Society.

Lindberg, D.R. Systematic paleontology, pp. 31-37.

Maddison, D. R. 1991. The discovery and importance of multiple islands of

most-parsimonious trees. Syst. Zool. 40:315-328.

Maddison, W. P., and D. R. Maddison. 1992. MacClade: Analysis of Phylogeny and Character Evolution (version 3). Sinauer Associates, Sunderland, MA.

Mau, B., M. Newton, and B. Larget. 1999. Bayesian phylogenetic inference

via Markov chain Monte Carlo methods. Biometrics 55:1-12.

Mishler, B. D. and E. De Luna. 1991. The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology 4:121-167. [especially pages 129-143]

Mishler, B. D. 1994. The cladistic analysis of molecular and morphological data. American Journal of Physical Anthropology 94: 143-156.

**Mishler, B. D.2005. The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, pp. 57-70. Oxford University Press.

Patterson, C. 1982. Morphological characters and homology. pp. 21-74 in Josey, K.A. and Friday, A.E. (eds.) Problems of Phylogenetic Reconstruction. Academic Press.

Posada, D. and K. A. Crandall. 1998. MODELTEST: testing the model of

DNA substitution. Bioinformatics 14:817-818.

Rannala, B., and Z. Yang. 1996. Probability distribution of molecular

evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol.

43:304-311.

Sanderson, M. J. and M. J. Donoghue. 1989. Patterns of variation in levels of homoplasy. Evol. 43:1781-1795.

Sober, E. 1988. Reconstructing the past. MIT Press.

Stevens, P. F. 1994. The development of biological systematics. Columbia University Press, New York.

Swofford, D. L. 2001. PAUP*. Phylogenetic analysis using parsimony (*and other methods).

Version 4. Sinauer Associates, Sunderland, Massachusetts.

Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inferencs.

Pages 407-514 in Molecular systematics second edition (D. M. Hillis, C. Moritz, and B.

K. Mable, eds.). Sinauer, Sunderland, MA.

Wiley, E. O. 1975. Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists. Syst. Zool. 24: 233-243.

Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte carlo method. Molecular Biology and Evolution. 14:717-724.