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Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis: modelsand estimation procedures. Evolution 32: 550-570.
Christoffersen, M. L. 1995. Cladistic taxonomy, phylogenetic systematics,and evolutionary ranking. Systematic Biology 44: 440-454.
Colless, D. H. 1982. Review of phylogenetics: the theory and practice ofphylogenetic systematics. Systematic Zoology 31: 100-104.
Crandall, K. and A. R. Templeton. 1993. Empirical tests of some predictionsfrom coalescent theory with applications to intraspecific phylogeny reconstruction.Genetics 134:989-99.
Day, W. H. E. and D. Sankoff. 1986. Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35: 224-229.
Duncan, T. and T. Steussey [eds.]. 1984. Cladistics: perspectives on the reconstruction of evolutionary history, 24-38. Columbia University Press, New York.
Estabrook, G. F. 1972. Cladistic methodology: a discussion ofthe theoretical basis for the induction of evolutionary history. Annual Review of Ecology and Systematics 3: 427-456.
Felsenstein, J. 1982. Numerical methods for inferring evolutionary trees. Quarterly Review of Biology 57: 379-404.
Felsenstein, J. 1983. Parsimony in systematics: biological and statistical issues. Annual Review of Ecology and Systematics 14: 313-333.
Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 2: 521-565.
Forey, P. L., C. J. Humphries, I. L. Kitching, R .W. Scotland, D. J. Siebert, and D. M. Williams. 1992. Cladistics: a practical course in systematics. The Systematics Association Publication No. 10, Oxford Science Publications, Clarendon Press,Oxford.
Garey, M. and D. S. Johnson. 1979. Computers and intractability: a guide to the theory of NP-Completeness. W. H. Freeman and Co., New York.
Harvey P. H. and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, New York.
Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana.
Hillis, D. M. 1995. Approaches for assessing phylogenetic accuracy. Systematic Biology 44: 3-16.
Noreen, E. W. 1989. Computer intensive methods for resting hypotheses: and introduction. John Wiley & Sons, NY.
Penny, D. L.R. Foulds, and M.D. Hendy. 1982. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297: 197-200.
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.
Patterson, C. [ed.]. 1987. Molecules and morphology in evolution: conflict or compromise. Cambridge University Press, Cambridge.
Ridley, M. 1986. Evolution and classification: the reformation of cladism. Longman Press, London.
Salthe, S. M. 1985. Evolving hierarchial systems: their structure and representation. Columbia University Press, NewYork.
Sneath, P. H. A. and R. R. Sokal. 1973. Numerical taxonomy. The principles and practice of numerical classification. W. H. Freeman, San Francisco.
Steel, M., P. J. Lockhart, and D. Penny. 1993. Confidence in evolutionarytrees from biological sequence data. Nature 364: 440-442.
Stevens, P. F. 1980. Evolutionary polarity of character states. Annual Review of Ecology and Systematics 11: 333-358.
Warnow, T. J. 1993. Constructing phylogenetic trees using compatibility criteria. New Zealand Journal of Botany 31: 239-248.
Wheeler, W. C. 1992. Extinction, sampling, and molecular phylogenetics. Columbia University Press, New York.
Wiley, E. O. 1981. Phylogenetic systematics: the theory and practice of phylogeneticsystematics. John WIley & Sons, NY.
Bottjer, P. D. 1980. Farris' "Information Content" and phylogenetic versus evolutionary classification: the philosophical differences remain. Systematic Zoology 29: 382-386.
Brooks, D. R., R. T. O'Grady, and E. O. Wiley. 1986. A measure of the information content of phylogenetic trees, and its use as an optimality criterion. Systematic Zoology 35: 571-581.
Farris, J. S. 1979. The information content of the phylogenetic system. Systematic Zoology 28: 483-519.
Mickevich, M. F. and N. I. Platnick. 1989. On the information content of classifications. Cladistics 5: 33-47.
Page, R. D. M. 1992. On the information content of classifications. Cladistics 8: 87-95.
Sanderson, M. J. and G. Bharathan. 1993. Does cladistic information affect inferences about branching rates? Systematic Biology 42: 1-17.
Wicken, J. S. 1983. Entropy, information, and nonequilibrium evolution. Systematic Zoology 32: 438-443.
Wicken, J. S. 1986. Entropy and evolution: Ground rules for discourse. Systematic Zoology 35: 22-36.
Barriel, V. and P. Tassy. 1993. Characters, observations and steps: comment on Lipscomb's "Parsimony, homology and the analysis of multistate characters." Cladistics 9: 223-232.
Hillis, D. M. 1993. Homology in molecular biology. In: B. Hall [ed.], Homology. Academic Press, San Diego.
Patterson, C. 1988. Homology in classical and molecular biology. Molecular Biology and Evolution 5: 603-625.
Roth, V. L.1984. On homology. Biological Journal of the Linnean Society 22: 13-29.
Roth, V. L. 1988. The biological basis of homology. In: C. J. Humpries [ed.], Ontogeny and Systematics. Columbia University Press, New York.
Roth, V. L. 1991. Homology and hierarchies: problems solved and unresolved. Journal of Evolution Biology 4: 167-194.
Valen, L. M. V. 1982. Homology and causes. Journal of Morphology 173: 305-312.
Wagner, G. P. 1989. The origin of morphological characters and the biological basis of homology. Evolution 43: 1157-1171.
Williams, D. M. 1993. A note of molecular homology: Multiple patterns from single data sets. Cladistics 9: 233-245.
Zelditch, M. L., W. L. Fink, and D. L. Swiderski. 1995. Morphometrics, homology, and phylogenetics: quantified characters as synapomorphies. Systematic Biology 44: 179-189.
Albrecht, G. H. 1978. Some comments on the use of ratios. Systematic Zoology 27: 67-71.
Archie, J. W. 1989. Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Systematic Zoology 38: 253-269.
Archie, J. W. 1990. Homoplasy excess statistics and retention indices: a reply to Farris. Systematic Zoology 39: 169-174.
Atchley W. R. 1978. Ratios, regression intercepts, and the scaling of data. Systematic Zoology 27: 78-83.
Atchley, W. R. and D. Anderson. 1978. Ratios and the statistical analysis of biological data. Systematic Zoology 27: 71-78.
Dodson, P. 1978. On the use of ratios in growth studies. Systematic Zoology 27: 62-67.
Donoghue M. J. and M. J. Sanderson. 1989. Patterns in variation in levels ofhomoplasy. Evolution 43: 1781-1795. Faith, D. P. 1989. Homoplasy as pattern: multivariate analysis of morphological convergence in Anseriformes. Cladistics 5: 235-258.
Farris, J. S. 1989. The retention index and homoplasy excess. Systematic Zoology 38: 406-407.
Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 47-419.
Farris, J. S. 1991. Excess homoplasy ratios. Cladistics 7: 81-91.
Goloboff, P. A. 1991. Homoplasy and the choice among cladograms. Cladistics 7: 215-232.
Hillis, D. M. 1978. On ratios- a response to Atchly, Gaskins, and Anderson. Systematic Zoology 27: 61-62.
Klassen, G. J., R. D. Mooi, and A. Locke. 1991. Consistency indices and random data. Systematic Zoology 40: 446-457.
Meier, R., P. Kores, and S. Darwin. 1991. Homoplasy slope ratio: a better measurement of observed homoplasy in cladistic analyses. Systematic Zoology 40: 74-88.
Sanderson, M. J. 1990. Estimating rates of speciation and evolution: a bias due to homoplasy. Cladistics 6: 387-391.
Sanderson, M. J. 1991. In search of homoplastic tendencies: statistical inference of typological patterns in homoplasy. Evolution 45: 351-358.
Sharkey M. J. 1993. Exact indices, criteria to select from minimum length trees. Cladistics 9: 211-222.
Wilkinson, M. 1991. Homoplasy and parsimony analysis. Systematic Zoology 40: 105-109.
Alroy, J. 1994. Four permutation tests for the presence of phylogenetic structure. Systematic Biology 43: 430-437.
Archie, J. W. 1989. A randomization test for phylogenetic information in systematic data. Systematic Zoology 38: 239-252.
Bryant, H. N. 1992. The role of permutation tail probability tests in phylogenetic systematics. Systematic Biology 41: 258-263.
Carpenter, J. M. 1992. Random cladistics. Cladistics 8: 147-153.
Faith, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40: 366-375.
Faith, D. P. 1992. On corroboration: a reply to Carpenter. Cladistics 8: 265-273.
Faith, D. P. and J. W. O. Ballard. 1994. Length differences and topology-dependent tests: a response to Källersjö: et al. Cladistics 10: 57-64.
Faith, D. P. and P. S. Cranston. 1991. Could a cladogram this short have arisen by chance alone?: on permutationtests for cladistic structure. Cladistics 7: 1-28.
Faith, D. P. and P. S. Cranston. 1992. Probability, parsimony, and Popper. Systematic Biology 41: 252-257.
Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1994. Permutations. Cladistics 10: 65-76.
Fishman, G. S. and L. R. Moore. 1982. A statistical evaluation of multiplicative congruential random number generators with modulus 231-1. Journal of American Statistical Association 77: 129-136.
Goloboff, P. A. 1991. Random data, homoplasy and infomation. Cladistics 7: 395-406.
Källersjö, M., J. S. Farris, A.G. Kluge, and C. Bult.1992. Skewness and permutation. Cladistics 8: 275-287. Page 1991. Random dendrograms and null hypotheses in cladistic biogeography. Systematic Zoology 40: 54-62.
Trueman, J. W. H. 1993. Randomization confounded: a response to Carpenter. Cladistics 9: 101-109.
Trueman, J. W. H. 1995. Sponges, plants and T-PTP. Systematic Biology 44: 429-434
Wilkinson, M. 1994. The permutation method and character compatibility. Systematic Biology 43: 274-277.
Hillis, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences. In: M. M. Miyamoto and J. Cracraft [eds.], Phylogenetic Analysis of DNA Sequences, 278-294. Oxford University Press, New York, N.Y.
Hillis, D. M., and J. P. Huelsenbeck. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. Journal of Heredity 83: 189-195.
Huelsenbeck, J. P. 1991. Tree-length distribution skewness: an indicator of phylogenetic information. Systematic Zoology 40: 257-270.
Källersjö, M., J. S. Farris, A.G. Kluge, and C. Bult.1992. Skewness and permutation. Cladistics 8: 275-287.
Le Quesne, W. J 1989. Frequency distributions of lengths of possible networks from a data matrix. Cladistics 5: 395-407.
Novacek, M. J. 1991. "All tree histograms" and the evaluation of cladistic evidence: some ambiguities. Cladistics 7: 345-349.
Forster, M. R. 1986. Statistic covariance as measure of phylogenetic relationship. Cladistics 2: 297-317.
Lyons-Weiler, J., G.A. Hoelzer, and R.J. Tausch. 1996. Relative apparent synapomorphy analysis (RASA) I: the statistical measurement of phylogenetic signal. Molecular Biology and Evolution (in press).
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Efron, B. 1982. The jacknife, the bootstrap, and other resampling plans. CBMS-NSF Regional Conference Series in Applied Mathematics, Philadelphia, PA.
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Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
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Felsenstein, J. 1978. The number of evolutionary trees. Systematic Zoology 27: 27-33.
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Penny, D. and M. D. Hendy. 1985. The use of tree comparison metrics. Systematic Zoology 34: 75-82.
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Felsenstein, J. 1983. Statistical inference of phylogenies. Journal of the Royal Statistical Society A146: 246-272.
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