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References about Phylogenetic Biology

Baum, D. A. and A. Larson. 1991. Adaptation reviewed: A phylogenetic methodology for studying character macroevolution. Systematic Zoology 40:1-18.

Brooks, D. R. and D. A. McLennan. 1991. Phylogeny, Ecology and Behavior: A Research Program in Comparative Biology. Chicago: Univ. Chicago Press.

Carpenter, J. M. 1989. Testing scenarios: Wasp social behavior. Cladistics 5:131-144.

Chang, B. S. W. and M. J. Donoghue. 2000. Recreating ancestral proteins. Trends in Ecology and Evolution 15:109-114.

Coddington, J. A. 1988. Cladistic tests of adaptational hypotheses. Cladistics 4:3-22.

Cunningham, C. W., K. E. Omland, and T. H. Oakley. 1998. Reconstructing ancestral character states: A critical reappraisal. Trends in Ecology and Evolution 13:361-366.

Donoghue, M. J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43:1137-1156.

Donoghue, M. J., and M. J. Sanderson. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pp. 340-368 in P. S. Soltis, D. E. Soltis, and J. J. Doyle (eds.), Molecular Systematics of Plants. Chapman and Hall, N.Y.

Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.

Edwards, A. W. F., and L. L. Cavalli-Sforza. 1964. Reconstruction of evolutionary trees. Pp. 67-76 in V. H. Heywood and J. McNeill (eds.), Phenetic and Phylogenetic Classification. Systematics Assoc., Publ. No. 6, London.

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

Farrell, B. D., C. Mitter, and D. J. Futuyma. 1992. Diversification at the insect-plant interface: Insights from phylogenetics. Bioscience 42:34-42.

Farris, J. S. 1970. Methods for computing Wagner Trees. Systematic Zoology 19:83-92.

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.

Felsenstein, J. 2004. Inferring Phylogenies. Sinauer, Sunderland, MA.

Fink, W. L. 1982. The conceptual relationship between ontogeny and phylogeny. Paleobiology 8:254-264.

Fitch, W. M. 1971. Toward defining the course of evolution: Minimal change for a specific tree topology. Systematic Zoology 20:406-416.

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.

Gittleman, J. L. 1988. The comparative approach in ethology: Aims and limitations. Perspectives in Ethology 8:55-83.

Goodman, M., J. Czelusniak, G. W. , Moore, A. E. Romero-Herrera, and G. Matsuda. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28:132-163.

Graur, D. and W.-H. Li. 1999. Fundamentals of Molecular Evolution, Second Edition. Sinauer Associates, Sunderland, Massachusetts.

Harvey, P. H., and M. D. Pagel. 1991. The Comparative Method in Evolutionary Biology. Oxford Univ. Press, Oxford.

Harvey, P. H., A. J. Leigh Brown, and J. Maynard Smith. 1995. New uses for phylogenies: editor's introduction. Philosophical Transactions of the Royal Society London Series B 349:3-4.

Hennig, W. 1966. Phylogenetic Systematics. Univ. Illinois Press, Urbana.

Hillis, D. M. 1987. Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics 18:23-42.

Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1992. Experimental phylogenetics: Generation of a known phylogeny. Science 255:589-592.

Huelsenbeck, J.P. and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics 28:437-466

Huelsenbeck, J. P. and B. Rannala. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276:227-232.

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

Koshi, J. M. and R. A. Goldstein. 1996. Probabilistic reconstruction of ancestral protein sequences. Journal of Molecular Evolution 42:313-320.

Lauder, G. V. 1982. Historical biology and the problem of design. Journal of Theoretical Biology 97:57-67.

Maddison, D. R. 1994. Phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters. Annual Review of Entomology 39:267-292.

Maddison, D. R. and W.P. Maddison. 2000. MacClade 4: Analysis of phylogeny and character evolution. Sunderland, Massachusetts: Sinauer Associates.

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.

Mitter, C., B. Farrell, and B. Wiegmann. 1988. The phylogenetic study of adaptive zones: Has phytophagy promoted insect diversification? American Naturalist 132:107-128.

Morrison, D. A. 1996. Phylogenetic tree-building. International Journal for Parasitology 26:549-617.

Nelson, G. and N. I. Platnick. 1981. Systematics and Biogeography: Cladistics and Vicariance. New York: Columbia Univ. Press.

O'Hara, R. J. 1988. Homage to Clio, or, Toward an historical philosophy for evolutionary biology. Systematic Zoology 37:142-155.

Page, R. D. M. and E. C. Holmes. 1998. Molecular Evolution. A Phylogenetic Approach. Blackwell Science, Oxford.

Pagel, M. 1994. Detecting correlated evolution on phylogenies: A general-method for the comparative analysis of discrete characters. Proceedings of the Royal Society London Series B 255:37-45.

Pagel, M. 1997. Inferring evolutionary processes from phylogenies. Zoological Scripta 26:331-348.

Pagel, M. 1999a. Inferring the historical patterns of biological evolution. Nature 401:877-884.

Pagel, M. 1999b. The maximum likelihood approach to reconstructing ancestral states of discrete characters on phylogenies. Systematic Biology 48:612-622.

Penny, D., M.D. Hendy, and M.A. Steel. 1992. Progress with methods for constructing evolutionary trees. Trends in Ecology and Evolution 7:73-79.

Ridley, M. 1983. The Explanation of Organic Diversity. Oxford Univ. Press, Oxford.

Sessions, S. R. and A. Larson. 1987. Developmental correlates of genome size in plethodontid salamanders and their implications for genome evolution. Evolution 41:1239-1251.

Sillén-Tullberg, B. 1988. Evolution of gregariousness in aposematic butterfly larvae: A phylogenetic analysis. Evolution 42:293-305.

Steel, M. and D. Penny. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Molecular Biology and Evolution 17:839-850.

Swofford, D. L. and W. P. Maddison. 1992. Parsimony, character-state reconstructions, and evolutionary inferences. In Mayden, R. L. (ed.) Systematics, Historical Ecology, and North American Freshwater Fishes. Stanford: Stanford University Press, pp. 187-223.

Swofford, D. L., and G. J. Olsen. 1990. Phylogeny reconstruction. Pp. 411-501 in D. M. Hillis and G. Moritz (eds.), Molecular Systematics. Sinauer Associates, Sunderland, Mass.

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.

Tuffley, C. and M. Steel. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bulletin of Mathematical Biology 59:581-607.

Wanntorp, H.-E., D. R. Brooks, T. Nilsson, S. Nylin, F. Ronquist, S. C. Stearns, and N. Wedell. 1990. Phylogenetic approaches in ecology. Oikos 57:119-132.

Wiley, E. O. 1981. Phylogenetics. The Theory and Practice of Phylogenetic Systematics. Wiley, N.Y.

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.

Yang, Z., S. Kumar, and M. Nei. 1995. A new method of inference of ancestral nucleotide and amino-acid sequences. Genetics 141:1641-1650.

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