Britten, R. J. 1993. Forbidden synonymous substitutions in coding regions. Molecular Biology and Evolution 10:205-220.
Brown, W. M., E. M. Prager, A. Wang, and A. C. Wilson. 1982. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. Journal of Molecular Evolution 18:225-239.
Bulmer, M. 1991. Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Molecular Biology and Evolution 8:868-883.
Burke, W. D., D. G. Eickbush, Y. Xiong, J. Jacubczak, and T. H. Eickbush. 1993. Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species . Molecular Biology and Evolution 10:163-1 85.
Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis: Models and estimation procedures. American Journal of Human Genetics 19:233-257.
Chakraborty, R. 1977. Estimation of time of divergence from phylogenetic studies. Canadian Journal of Genetics and Cytology 19:217-223.
Cooper, A., C. Maourer-Chauviré, G. K. Chambers, A. von Haeseler, A. C. Wilson, and S. pääbo. 1992. Independent origins of New Zealand moas and kiwis. Proceedings of the National Academy of Sciences, USA 89:8741-8744.
Cunningham, C. W., N. W. Blackstone, and L. W. Buss. 1992. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.
Dayhoff, M. O. 1978. Survey of new data and computer methods of analysis. In M. O. Dayhoff, ed., Atlas of Protein Sequence and Structure, vol. 5, supp. 3, pp. 29, National Biomedical Research Foundation, Silver Springs, Maryland.
DeBry, R. W. 1992. The consistency of several phylogeny-inference methods under varying evolutionary rates. Molecular Biology and Evolution 9:537-551.
Eck, R. V. and M. O. Dayhoff. 1966. Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Springs, Maryland.
Efron, B. 1982. The Jackknife, the Bootstrap and Other Resampling Plans. CBMS-NSF Regional Conference Series in Applied Mathematics, Monograph 38, SIAM, Philadelphia.
Estabrook, G. F., C. S. Johnson, and F. R. McMorris. 1975. An idealized concept of the true cladistic character. Mathematical Biosciences 23:263-272.
Farris, J. S. 1981. Distance data in phylogenetic analysis. In V. A. Funk and D. R. Brooks, eds., Advances in Cladistics. Proceedings of the First Meeting of the Willi Hennig Society, pp. 3-23. New York Botanical Garden, Bronx.
Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27:401-410.
Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
Felsenstein, J. 1986. Distance Methods: Reply to Farris. Cladistics 2:130-143.
Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22:521-565.
Felsenstein, J. 1993. Phylogeny Inference Package (PHYLIP). Version 3.5. University of Washington, Seattle.
Felsenstein, J. and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42:193-200.
Fitch, W. M. 1971. Towards defining the course of evolution: Minimum change for a specific tree topology. Systematic Zoology 20:406-416.
Fitch, W. M. and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
Gojobori, T., E. N. Moriyama, and M. Kimura. 1990. Statistical methods for estimating sequence divergence. In R. F. Doolittle, ed., Methods in Enzymology, Vol. 183, Molecular Evolution.' Computer Analysis of Protein and Nucleic Acid Sequences, pp. 531-550. Academic Press, New York.
Goldman, N. 1993. Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36:182-198.
Goodman, M., A. E. Romero-Herrera, H. Dene, J. Czelusniak, and R. E. Tashian. 1982. Amino acid sequence evidence on the phylogeny of primates and other eutherians. In M. Goodman, ed., Macromolecular sequences in systematic and evolutionary biology, pp. 115-191. Plenum Press, New York and London.
Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
Hedges, S. B., S. Kumar, K. Tamura, and M. Stoneking. 1992. Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739.
Hendy, M. D. and D. Penny. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59:277-290.
Hendy, M. D. and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Systematic Zoology 38:297-309.
Hillis, D. M. and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42:182-192.
Hughes, A. L. and M. Nei. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
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. In H. N. Munro, ed., Mammalian Protein Metabolism, pp. 21-132, Academic Press, New York.
Kimura, M. 1980. A simple method for estimating evolutionary rate 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, Massachusetts.
Kimura, M. and T. Ohta. 1972. On the stochastic model for estimation of mutational distance between homologous proteins. Journal of Molecular Evolution 2:87-90.
Kishino, H. and M. Hasegawa. 1989. Evaiuation 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.
Kocher, T. D. and A. C. Wilson. 1991. Sequence evolution of mitochondrial DNA in humans and chimpanzees: Control region and a protein-coding region. In S. Osawa and T. Honjo, eds., Evolution of Life, pp. 391-413. Spring-Verlag, New York.
Kondo, R., S. Horai, Y. Satta, and N. Takahata. 1993. Evolution of hominoid mitochondrial DNA with special reference to the silent substitution rate over the genome. Journal of Molecular Evolution 36:517-531.
Lake, J. A. 1987. A rate-independent technique for analysis of nucleic acid sequences: Evolutionary parsimony. Molecular Biology and Evolution 4:167-191.
Lee, Y. H. and V. D. Vacquier. 1992. The divergence of species-specific abalone sperm lysins is promoted by positive Darwinian selection. Biological Bulletin 182:97-104.
Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18:201-205.
Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution 36:96-99.
Li, W.-H., C.-1. Wu, and C.-C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 2:150-174.Maddison, W. P. and D. R. Maddison. 1992. MacClade: Analysis of phylogeny and character evolution. Version 3. Sinauer Associates, Sunderland, Massachusetts.
Miyamoto, M. M. and J. Cracraft. 1991. Phylogenetic Analysis of DNA Sequences. Oxford University Press, New York.
Miyata, T. and T. Yasunaga. 1980. Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. Journal of Molecular Evolution 16:23-36.
Miyata, T., T. Yasunaga, and T. Nishida. 1980. Nucleotide sequence divergence and functional constraint in mRNA evolution. Proceedings of National Academy of Sciences, USA 77:7328-7332.
Nei, M. 1986. Stochastic errors in DNA evolution and molecular phylogeny. In H. Gershowitz, D. L. Rucknagel, and R. E. Tashian, eds., Evolutionary Perspectives and the New Genetics. pp. 133-147. Alan R. Liss, New York.
Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
Nei, M. 1991. Relative efficiencies of different tree making methods for molecular data. In M. M . Miyamoto and J . L. Cracraft, eds., Recent Advances in Phylogenetic Studies of DNA Sequences, pp. 90-128. Oxford University Press, Oxford.
Nei, M. and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3:418-426.
Nei, M. and A. L. Hughes. 1991. Polymorphism and evolution of the major histocompatibility complex loci in mammals. In R. K. Selander, A. G. Clark, and T. S. Whittam, eds., Evolution at the Molecular Level, pp. 222-247. Sinauer Associates, Sunderland, Massachusetts.
Nei, M. and L. Jin. 1989. Variances of the average numbers of nucleotide substitutions within and between populations . Molecular Biology and Evolution 6:290-300.
Nei, M. and A. Y. Rzhetsky. 1991 . Reconstruction of phylogenetic trees and evolution of major histocompatibility complex genes. In J. Klein and D. Klein, eds., Evolution of MHC Genes, pp. 13-27. Springer-Verlang, Heidelberg.
Nei, M. and F. Tajima. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97:145-163.
Nei, M., R. Chakraborty, and P. A. Fuerst. 1976. Infinite allele model with varying mutation rate. Proceedings of National Academy of Sciences, USA 73:4164-4168.
Nei, M., J. C. Stephens, and N. Saitou. 1985. Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. Molecular Biology and Evolution 2:66-85.
Neigel, J. E. and A. C. Avise. 1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In S. Karlin and E. Nevo, eds., Evolutionary Processes and Theory, pp. 515-534. Academic Press, New York.
Pamilo, P. and N. O. Bianchi. 1993. Evolution of the Zfx and Zfy, genes: Rates and interdependence between the genes. Molecular Biology and Evolution 10:271-281.
Pamilo, P. and M. Nei. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5:568-583.
Penny, D. 1982. Towards a basis for classification: Incompleteness of distance measures, incompatibility analysis, and phenetic classification. Journal of Theoretical Biology 96: 129- 142.
Penny, D. and M. D. Hendy. 1985. The use of tree comparison metrics. Systematic Zoology 34:75-82.
Rzhetsky, A. and M. Nei. 1992. A simple method for estimating and testing minimum-evolution trees . Molecular Biology and Evolution 9:945-967.
Rzhetsky, A. and M. Nei. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Molecular Biology and Evolution 10:1073-1095.
Rzhetsky, A. and M. Nei. 1994. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. Journal of Molecular Evolution 38:295-299.
Robinson, D. F. and L. R. Foulds. 1981. Comparison of phylogenetic trees. Mathematical Biosciences 53:131-147.
Saccone, C., C. Lanave, G. Pesole, and G. Preparata. 1990. Influence of base composition on quantitative estimates of gene evolution. In R. F. Doolittle, ed. , Methods in Enzymology, Vol. 183, Molecular Evolution.' Computer Analysis of Protein and Nucleic Acid Sequences, pp. 570-598. Academic Press, New York.
Saitou, N. and M. Imanishi. 1989. Relative efficiencies of the Fitch-Margolish, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree reconstruction in obtaining the correct tree. Molecular Biology and Evolution 6:514-525.
Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
Sankoff, D. and R. J. Cedergren. 1983. Simultaneous comparison of three or more sequences related by a tree. In D. Sankoff and J. B. Kruskal, eds., Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, pp. 253-263. Addison-Wesley, Reading, Massachusetts.
Schöniger, M. and A. von Haeseler. 1993. A simple method to improve the reliability of tree reconstructions . Molecular Biology and Evolution 10:471-483.
Sharp, P. M., T. M. F. Tuohy, and K. R. Mosurski. 1986. Codon usage in yeast: Cluster anaiysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Research 14:5125-5143.
Sneath, P. H. A. and R. R. Sokal. 1973. Numerical Taxonomy. Freeman, San Francisco.
Sober, E. 1988. Reconstructing the Past. MIT Press, Cambridge, Massachusetts.
Sourdis, J . and C. Krimbas. 1987. Accuracy of phylogenetic trees estimated from DNA sequence data. Molecular Biology and Evolution 4:159-166.
Sourdis, J. and M. Nei. 1988. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Molecular Biology and Evolution 5:298-311.
Studier, J. A. and K. L. Keppler. 1988. A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution 5:729-731.
Swofford, D. L. 1993. Phylogenetic Analysis Using Parsimony (PAUP), Version 3.1.1. University of Illinois, Champaign.
Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437460.
Tajima, F. 1993. Unbiased estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 10:677-688.
Tajima, F. and M. Nei. 1984. Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 1:269-285.
Tajima, F. and N. Takezaki. 1994. Estimation of evolutionary distance for reconstructing molecular phylogenetic trees. Molecular Biology and Evolution 11:278-286.
Tamura, K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution 9:678-687.
Tamura, K. 1994. Model selection in the estimation of the number of nucleotide substitutions. Molecular Biology and Evolution 11:154-157.
Tamura, K. and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10:512-526.
Tanaka, T. and M. Nei. 1989. Positive Darwinian selection observed at the variable-region genes of immnoglobulins. Molecular Biology and Evolution 6:447-459.
Tateno, Y., M. Nei, and F. Tajima. 1982. Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. Journal of Molecular Evolution 18:387-404.
Tateno, Y., N. Takezaki, and M. Nei. 1994. Relative efficiencies of the maximum likelihood, neighbor-joining, and maximum parsimony methods when substitution rate varies with site. Molecular Biology and Evolution 11:261-277.
Thomas, R. H. and J. A. Hunt. 1993. Phylogenetic relationships in Drosophila: A conflict between molecular and morphological data. Molecular Biology and Evolution 10:362-374.
Uzzell, T. and K. W. Corbin. 1971. Fitting discrete probability distribution to evolutionary events. Science 172:1089-1096.
Vigilant, L., M. Stoneking, H. Harpending, K. Hawkes, and A. C. Wilson. 1991. African populations and the evolution of human mitochondrial DNA. Science 253:1503-1507.
Wakeley, J. 1993. Substitution rate variation among sites in hypervariable region I of human mitochondrial DNA. Journal of Molecular Evolution 37:613-623.
Williams, P. L. and W. M. Fitch. 1990. Phylogeny determination using dynamically weighted parsimony method. In R. F. Doolittle, ed., Methods in Enzymology, Vol. 183, Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, pp. 615-626. Academic Press, New York.
Zharkikh, A. and W.-H. Li 1992a. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Molecular Biology and Evolution 9:1119-1147.
Zharkikh, A. and W.-H. Li. 1992b. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. II. Four taxa without a molecular clock. Journal of Molecular Evolution 35:356-366.