References about Phylogenetic Biology

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Eldredge, N. and J. Cracraft. 1980. Phylogenetic Patterns and the Evolutionary Process: Method and Theory in Comparative Biology. Columbia Univ. Press, N.Y.

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Farris, J. S. 1983. The logical basis of phylogenetic analysis. Pp. 7-36 in N. I. Platnick and V. A. Funk (eds.), Advances in Cladistics, Vol. 2. Proceedings of the Second Meeting of the Willi Hennig Society. Columbia Univ. Press, N.Y.

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1-15.

Felsenstein, J. 1979. Alternative methods of phylogenetic inference and their interrelationship. Systematic Zoology 28:49-62.

Felsenstein, J. 1988a. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22:521-565.

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

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Futuyma, D. J. and S. S. McCafferty. 1991. Phylogeny and the evolution of host plant associations in the leaf beetle genus Ophraella (Coleoptera, Chrysomelidae). Evolution 44:1885-1913.

Futuyma, D. J. 1988. Sturm und Drang and the evolutionary synthesis. Evolution 42:217-226.

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Huey, R. B. and A. F. Bennett. 1987. Phylogenetic studies of coadaptation: Preferred temperatures versus optimal performance temperatures of lizards. Evolution 41:1098-1115.

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Maddison, D. R., M. Ruvolo, and D. L. Swofford. 1992. Geographic origins of human mitochondrial DNA: Phylogenetic evidence from control region sequences. Systematic Biology 41:111-124.

Maddison, W. P. 1995. Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees. Systematic Biology 44:474-481.

Maddison, W. P. 1990. A method for testing the correlated evolution of two binary characters: Are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44:539-557.

Maddison, W. P. 1996. Molecular approaches and the growth of phylogenetic biology. Pages 47-63 in J.D. Ferraris and S.R. Palumbi (eds.). Molecular zoology: Advances, strategies, and protocols. Wiley-Liss, New York.

Maddison, W. P. 1997. Gene trees in species trees. Systematic Biology 46:523-536.

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

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Swofford, D. L., G.J. Olsen, P.J. Waddell, and D.M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B.K. Mable (eds.), Molecular Systematics, Second Edition. Sinauer Associates, Sunderland, Mass.

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Yang, Z. H. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 10:1396-1401.

Yang, Z. H. 1994a. Maximum-likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. Journal of Molecular Evolution 39:306-314.

Yang, Z. 1994b. Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution 39:105-111.

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