REFERENCES FOR THE DOCUMENTATION FILES

In the documentation files that follow I frequently refer to papers in the literature. In order to centralize the references they are given in this section. If you want to find further papers beyond these, my Quarterly Review of Biology review of 1982 and my Annual Review of Genetics review of 1988 list many further references. The chapter by David Swofford and Gary Olsen (1990) is also an excellent review of the issues in phylogeny reconstruction.

• Adams, E. N. 1972. Consensus techniques and the comparison of taxonomic trees. Systematic Zoology 21: 390-397.
• Adams, E. N. 1986. N-trees as nestings: complexity, similarity, and consensus. Journal of Classification 3: 299-317.
• Archie, J. W. 1989. A randomization test for phylogenetic information in systematic data. Systematic Zoology 38: 219-252.
• Astolfi, P., K. K. Kidd, and L. L. Cavalli-Sforza. 1981. A comparison of methods of reconstructing evolutionary trees. Systematic Zoology 30: 156-169.
• Baum, B. R. 1989. PHYLIP: Phylogeny Inference Package. Version 3.2. (Software review). Quarterly Review of Biology 64: 539-541.
• Bron, C., and J. Kerbosch. 1973. Algorithm 457: Finding all cliques of an undirected graph. Communications of the Association for Computing Machinery 16: 575-577.
• Camin, J. H., and R. R. Sokal. 1965. A method for deducing branching sequences in phylogeny. Evolution 19: 311-326.
• Carpenter, J. 1987a. A report on the Society for the Study of Evolution workshop "Computer Programs for Inferring Phylogenies". Cladistics 3: 363-375.
• Carpenter, J. 1987b. Cladistics of cladists. Cladistics 3: 363-375.
• Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 32: 550-570 (also Amer. J. Human Genetics 19: 233-257).
• Cavender, J. A. and J. Felsenstein. 1987. Invariants of phylogenies in a simple case with discrete states. Journal of Classification 4: 57-71.
• Churchill, G.A. 1989. Stochastic models for heterogeneous DNA sequences. Bulletin of Mathematical Biology 51: 79-94.
• Conn, E. E. and P. K. Stumpf. 1963. Outlines of Biochemistry. John Wiley and Sons, New York.
• Day, W. H. E. 1983. Computationally difficult parsimony problems in phylogenetic systematics. Journal of Theoretical Biology 103: 429-438.
• Dayhoff, M. O. 1979. Atlas of Protein Sequence and Structure, Volume 5, Supplement 3, 1978. National Biomedical Research Foundation, Washington, D.C.
• DeBry, R. W. and N. A. Slade. 1985. Cladistic analysis of restriction endonuclease cleavage maps within a maximum-likelihood framework. Systematic Zoology 34: 21-34.
• Dempster, A. P., N. M. Laird, and D. B. Rubin. 1977. Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society B 39: 1-38.
• Eck, R. V., and M. O. Dayhoff. 1966. Atlas of Protein Sequence and Structure 1966. National Biomedical Research Foundation, Silver Spring, Maryland.
• Edwards, A. W. F., and L. L. Cavalli-Sforza. 1964. Reconstruction of evolutionary trees. pp. 67-76 in Phenetic and Phylogenetic Classification, ed. V. H. Heywood and J. McNeill. Systematics Association Volume No. 6. Systematics Association, London.
• Estabrook, G. F., C. S. Johnson, Jr., and F. R. McMorris. 1976a. A mathematical foundation for the analysis of character compatibility. Mathematical Biosciences 23: 181-187.
• Estabrook, G. F., C. S. Johnson, Jr., and F. R. McMorris. 1976b. An algebraic analysis of cladistic characters. Discrete Mathematics16: 141-147.
• Estabrook, G. F., F. R. McMorris, and C. A. Meacham. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Systematic Zoology 34: 193-200.
• Faith, D. P. 1990. Chance marsupial relationships. Nature 345: 393-394.
• Faith, D. P. and P. S. Cranston. 1991. Could a cladogram this short have arisen by chance alone?: On permutation tests for cladistic structure. Cladistics 7: 1-28.
• Farris, J. S. 1977. Phylogenetic analysis under Dollo's Law. Systematic Zoology 26: 77-88.
• Farris, J. S. 1978a. Inferring phylogenetic trees from chromosome inversion data. Systematic Zoology 27: 275-284.
• Farris, J. S. 1981. Distance data in phylogenetic analysis. pp. 3-23 in Advances in Cladistics: Proceedings of the first meeting of the Willi Hennig Society, ed. V. A. Funk and D. R. Brooks. New York Botanical Garden, Bronx, New York.
• Farris, J. S. 1983. The logical basis of phylogenetic analysis. pp. 1-47 in Advances in Cladistics, Volume 2, Proceedings of the Second Meeting of the Willi Hennig Society. ed. Norman I. Platnick and V. A. Funk. Columbia University Press, New York.
• Farris, J. S. 1985. Distance data revisited. Cladistics 1: 67-85.
• Farris, J. S. 1986. Distances and statistics. Cladistics 2: 144-157.
• Farris, J. S. ["T. N. Nayenizgani"]. 1990. The systematics association enters its golden years (review of "Prospects in Systematics", ed. D. Hawksworth). Cladistics 6: 307-314.
• Felsenstein, J. 1973a. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22: 240-249.
• Felsenstein, J. 1973b. Maximum-likelihood estimation of evolutionary trees from continuous characters. Amer. J. Human Genetics 25: 471-492.
• Felsenstein, J. 1978a. The number of evolutionary trees. Systematic Zoology 27: 27-33.
• Felsenstein, J. 1978b. Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.
• Felsenstein, J. 1979. Alternative methods of phylogenetic inference and their interrelationship. Systematic Zoology 28: 49-62.
• Felsenstein, J. 1981a. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Molecular Evolution 17: 368-376.
• Felsenstein, J. 1981b. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnean Society 16: 183-196.
• Felsenstein, J. 1981c. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35: 1229-1242.
• Felsenstein, J. 1982. Numerical methods for inferring evolutionary trees. Quarterly Review of Biology 57: 379-404.
• Felsenstein, J. 1983b. Parsimony in systematics: biological and statistical issues. Annual Review of Ecology and Systematics 14:313-333.
• Felsenstein, J. 1984a. Distance methods for inferring phylogenies: a justification. Evolution 38: 16-24.
• Felsenstein, J. 1984b. The statistical approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. pp. 169-191 in: Cladistics: Perspectives in the Reconstruction of Evolutionary History, edited by T. Duncan and T. F. Stuessy. Columbia University Press, New York.
• Felsenstein, J. 1985a. Confidence limits on phylogenies with a molecular clock. Systematic Zoology 34: 152-161.
• Felsenstein, J. 1985b. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
• Felsenstein, J. 1985c. Phylogenies from gene frequencies: a statistical problem. Systematic Zoology 34: 300-311.
• Felsenstein, J. 1985d. Phylogenies and the comparative method. American Naturalist 125: 1-12.
• Felsenstein, J. 1986. Distance methods: a reply to Farris. Cladistics 2: 130-144.
• Felsenstein, J. and E. Sober. 1986. Parsimony and likelihood: an exchange. Systematic Zoology 35: 617-626.
• Felsenstein, J. 1988a. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19: 445-471.
• Felsenstein, J. 1988b. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 22: 521-565.
• Felsenstein, J. 1992a. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research 59: 139-147.
• Felsenstein, J. 1992b. Phylogenies from restriction sites, a maximum likelihood approach. Evolution 46: 159-173.
• Felsenstein, J. 1992c. Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration approach. Genetical Research, (December issue), in press.
• Fink, W. L. 1986. Microcomputers and phylogenetic analysis. Science 234: 1135-1139.
• Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155: 279-284.
• Fitch, W. M. 1971. Toward defining the course of evolution: minimum change for a specified tree topology. Systematic Zoology 20: 406-416.
• Fitch, W. M. 1975. Toward finding the tree of maximum parsimony. pp. 189-230 in Proceedings of the Eighth International Conference on Numerical Taxonomy, ed. G. F. Estabrook. W. H. Freeman, San Francisco.
• Fitch, W. M. and E. Markowitz. 1970. An improved method for determining codon variability and its application to the rate of fixation of mutations in evolution. Biochemical Genetics 4: 579-593.
• George, D. G., L. T. Hunt, and W. C. Barker. 1988. Current methods in sequence comparison and analysis. pp. 127-149 in Macromolecular Sequencing and Synthesis, ed. D. H. Schlesinger. Alan R. Liss, New York.
• Gomberg, D. 1966. "Bayesian" post-diction in an evolution process. unpublished manuscript: University of Pavia, Italy.
• Graham, R. L., and L. R. Foulds. 1982. Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time. Mathematical Biosciences 60: 133-142.
• Hasegawa, M. and T. Yano. 1984a. Maximum likelihood method of phylogenetic inference from DNA sequence data. Bulletin of the Biometric Society of Japan No. 5: 1-7.
• Hasegawa, M. and T. Yano. 1984b. Phylogeny and classification of Hominoidea as inferred from DNA sequence data. Proceedings of the Japan Academy 60 B: 389-392.
• Hasegawa, M., Y. Iida, T. Yano, F. Takaiwa, and M. Iwabuchi. 1985a. Phylogenetic relationships among eukaryotic kingdoms as inferred from ribosomal RNA sequences. Journal of Molecular Evolution 22: 32-38.
• Hasegawa, M., H. Kishino, and T. Yano. 1985b. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
• Hendy, M. D., and D. Penny. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59: 277-290.
• Higgins, D. G. and P. M. Sharp. 1989. Fast and sensitive multiple sequence alignments on a microcomputer. Computer Applications in the Biological Sciences (CABIOS) 5: 151-153.
• Holmquist, R., M. M. Miyamoto, and M. Goodman. 1988. Higher-primate phylogeny -- why can't we decide? Molecular Biology and Evolution 5: 201-216.
• Inger, R. F. 1967. The development of a phylogeny of frogs. Evolution 21: 369-384.
• Jin, L. and M. Nei. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Molecular Biology and Evolution 7: 82-102.
• Jukes, T. H. and C. R. Cantor. 1969. Evolution of protein molecules. pp. 21-132 in Mammalian Protein Metabolism, ed. H. N. Munro. Academic Press, New York.
• Kim, J. and M. A. Burgman. 1988. Accuracy of phylogenetic-estimation methods using simulated allele-frequency data. Evolution 42: 596-602.
• Kimura, M. 1980. A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
• Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
• Kingman, J. F. C. 1982a. The coalescent. Stochastic Processes and Their Applications 13: 235-248.
• Kingman, J. F. C. 1982b. On the genealogy of large populations. Journal of Applied Probability 19A: 27-43.
• Kishino, H. and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution 29: 170-179.
• Kluge, A. G., and J. S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Systematic Zoology 18: 1-32.
• Kuensch, H. R. 1989. The jackknife and the bootstrap for general stationary observations. Annals of Statistics 17: 1217-1241.
• Lake, J. A. 1987. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Molecular Biology and Evolution 4: 167-191.
• Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205.
• Le Quesne, W. J. 1974. The uniquely evolved character concept and its cladistic application. Systematic Zoology 23: 513-517.
• Lewis, H. R., and C. H. Papadimitriou. 1978. The efficiency of algorithms. Scientific American 238: 96-109 (January issue)
• Luckow, M. and D. Pimentel. 1985. An empirical comparison of numerical Wagner computer programs. Cladistics 1: 47-66.
• Lynch, M. 1990. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080.
• Maddison, D. R. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Systematic Zoology 40: 315-328.
• Margush, T. and F. R. McMorris. 1981. Consensus n-trees. Bulletin of Mathematical Biology 43: 239-244.
• Nelson, G. 1979. Cladistic analysis and synthesis: principles and definitions, with a historical not on Adanson's Familles des Plantes (1763-1764). Systematic Zoology 28: 1-21.
• Nei, M. 1972. Genetic distance between populations. American Naturalist 106: 283-292.
• Nei, M. and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA 76: 5269-5273.
• Page, R. D. M. 1989. Comments on component-compatibility in historical biogeography. Cladistics 5: 167-182.
• Platnick, N. 1987. An empirical comparison of microcomputer parsimony programs. Cladistics 3: 121-144.
• Platnick, N. 1989. An empirical comparison of microcomputer parsimony programs. II. Cladistics 5: 145-161.
• Reynolds, J. B., B. S. Weir, and C. C. Cockerham. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767-779.
• Rohlf, F. J. and M. C. Wooten. 1988. Evaluation of the restricted maximum likelihood method for estimating phylogenetic trees using simulated allele- frequency data. Evolution 42: 581-595.
• Sanderson, M. J. 1990. Flexible phylogeny reconstruction: a review of phylogenetic inference packages using parsimony. Systematic Zoology 39: 414-420.
• Sankoff, D. D., C. Morel, R. J. Cedergren. 1973. Evolution of 5S RNA and the nonrandomness of base replacement. Nature New Biology 245: 232-234.
• Sokal, R. R. and P. H. A. Sneath. 1963. Principles of Numerical Taxonomy. W. H. Freeman, San Francisco.
• Smouse, P. E. and W.-H. Li. 1987. Likelihood analysis of mitochondrial restriction-cleavage patterns for the human-chimpanzee-gorilla trichotomy. Evolution 41: 1162-1176.
• Sober, E. 1983a. Parsimony in systematics: philosophical issues. Annual Review of Ecology and Systematics 14: 335-357.
• Sober, E. 1983b. A likelihood justification of parsimony. Cladistics 1: 209-233.
• Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press, Cambridge, Massachusetts.
• Sokal, R. R., and P. H. A. Sneath. 1963. Principles of Numerical Taxonomy. W. H. Freeman, San Francisco.
• Studier, J. A. and K. J. Keppler. 1988. A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution 5: 729-731.
• Swofford, D. L. and G. J. Olsen. 1990. Phylogeny reconstruction. Chapter 11, pages 411-501 in Molecular Systematics, ed. D. M. Hillis and C. Moritz. Sinauer Associates, Sunderland, Massachusetts.
• Templeton, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37: 221-244.
• Thompson, E. A. 1975. Human Evolutionary Trees. Cambridge University Press, Cambridge.
• Wu, C. F. J. 1986. Jackknife, bootstrap and other resampling plans in regression analysis. Annals of Statistics 14: 1261-1295.
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Please note this was copied from the Stanford Bioinformatics group at Stanford It has been adapted (and will be further adapted) by Rob Edwards