Jump to ContentJump to Main Navigation
Computational Molecular Evolution$

Ziheng Yang

Print publication date: 2006

Print ISBN-13: 9780198567028

Published to Oxford Scholarship Online: April 2010

DOI: 10.1093/acprof:oso/9780198567028.001.0001

Show Summary Details
Page of

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2018. All Rights Reserved. Under the terms of the licence agreement, an individual user may print out a PDF of a single chapter of a monograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: null; date: 17 August 2018

(p.319) References

(p.319) References

Source:
Computational Molecular Evolution
Publisher:
Oxford University Press

Bibliography references:

Adachi, J. and Hasegawa, M. 1996a. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459–468.

Adachi, J. and Hasegawa, M. 1996b. MOLPHY Version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs, 28:1–150. Institute of Statistical Mathematics, Tokyo.

Adachi, J., Waddell, P. J., Martin, W. and Hasegawa, M. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50:348–358.

Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Autom. Contr. ACM 19: 716–723.

Akam, M. 1995. Hox genes and the evolution of diverse body plans. Philos. Trans. R Soc. Lond. B Biol. Sci. 349: 313–319.

Akashi, H. 1995. Inferring weak selection from patterns of polymorphism and divergence at “silent” sites in Drosophila DNA. Genetics 139: 1067–1076.

Akashi, H. 1999a. Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics 151: 221–238.

Akashi, H. 1999b. Within- and between-species DNA sequence variation and the ‘footprint’ of natural selection. Gene 238: 39–51.

Akashi, H., Goel, P. and John, A. 2006. Ancestral state inference and the study of codon bias evolution: implications for molecular evolutionary analysis of the Drosophila melanogaster species subgroup. Genetics.

Alba, R., Kelmenson, P. M., Cordonnier-Pratt, M. -M. and Pratt, L. H. 2000. The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms. Mol. Biol. Evol. 17: 362–373.

Albert, V. A. 2005. Parsimony, Phylogeny, and Genomics. Oxford University Press, Oxford.

Alfaro, M. E., Zoller, S. and Lutzoni, F. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20: 255–266.

Altekar, G., Dwarkadas, S., Huelsenbeck, J. P. and Ronquist, F. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407–415.

Altschul, S. F., Gish, W., Miller, W. et al. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.

Anisimova, A. and Yang, Z. 2004. Molecular evolution of hepatitis delta virus antigen gene: recombination or positive selection? J. Mol. Evol. 59: 815–826.

(p.320) Anisimova, A. and Yang, Z. 2006. Searching for positive selection affecting a few sites and lineages. Submitted.

Anisimova, M., Bielawski, J. P. and Yang, Z. 2001. The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Mol. Biol. Evol. 18: 1585–1592.

Anisimova, M., Bielawski, J. P. and Yang, Z. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19: 950–958.

Anisimova, M., Nielsen, R. and Yang, Z. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229–1236.

Aris-Brosou, S. and Yang, Z. 2002. The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny. Syst. Biol. 51: 703–714.

Atkinson, A. C. 1970. A method of discriminating between models. J. R. Statist. Soc. B 32: 323–353.

Bailly, X., Leroy, R., Carney, S. et al. 2003. The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection. Proc. Natl. Acad. Sci. U.S.A. 100: 5885–5890.

Bargelloni, L., Marcato, S. and Patarnello, T. 1998. Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperatures. Proc. Natl. Acad. Sci. U.S.A 95: 8670–8675.

Barker, D. 2004. LVB: parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics 20: 274–275.

Barkman, T. J. 2003. Evidence for positive selection on the floral scent gene isoeugenol-O-methyltransferase. Mol. Biol. Evol. 20: 168–172.

Barrier, M., Robichaux, R. H. and Purugganan, M. D. 2001. Accelerated regulatory gene evolution in an adaptive radiation. Proc. Natl. Acad. Sci. U.S.A. 98:10208–10213.

Barry, D. and Hartigan, J. A. 1987a. Asynchronous distance between homologous DNA sequences. Biometrics 43: 261–276.

Barry, D. and Hartigan, J. A. 1987b. Statistical analysis of hominoid molecular evolution. Statist. Sci. 2: 191–210.

Baudry, E. and Depaulis, F. 2003. Effect of misoriented sites on neutrality tests with outgroup. Genetics 165: 1619–1622.

Baum, J., Ward, R. and Conway, D. 2002. Natural selection on the erythrocyte surface. Mol. Biol. Evol. 19: 223–229.

Beerli, P. and Felsenstein, J. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. U.S.A. 98: 4563–4568.

Belda, E., Moya, A. and Silva, F. J. 2005. Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Mol. Biol. Evol. 22: 1456–1467.

Benner, S. A. 2001. Natural progression. Nature 409: 459.

Benner, S. A. 2002. The past as the key to the present: resurrection of ancient proteins from eosinophils. Proc. Natl. Acad. Sci. U.S.A. 99: 4760–4761.

Benton, M. J., Wills, M. and Hitchin, R. 2000. Quality of the fossil record through time. Nature 403: 534–538.

Berry, V. and Gascuel, O. 1996. On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain. Mol. Biol. Evol. 13: 999–1011.

Betran, E. and Long, M. 2003. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164: 977–988.

(p.321) Bielawski, J. P. and Yang, Z. 2001. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18:523–529.

Bielawski, J. P. and Yang, Z. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J. Mol. Evol. 59:121–132.

Bielawski, J. P., Dunn, K. and Yang, Z. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156:1299–1308.

Bielawski, J. P., Dunn, K. A., Sabehi, G. and Beja, O. 2004. Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc. Natl. Acad. Sci. U.S.A. 101:14824–14829.

Bierne, N. and Eyre-Walker, A. 2003. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics 165:1587–1597.

Bininda-Emonds, O. R. P. 2004. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic, Dordrecht.

Birdsey, G. M., Lewin, J., Cunningham, A. A. et al. 2004. Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora. Mol. Biol. Evol. 21:632–646.

Bishop, J. G. 2005. Directed mutagenesis confirms the functional importance of positively selected sites in polygalacturonase inhibitor protein (PGIP). Mol. Biol. Evol. 22: 1531–1534.

Bishop, J. G., Dean, A. M. and Mitchell-Olds, T. 2000. Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc. Natl. Acad. Sci. U.S.A. 97:5322–5327.

Bishop, J. G., Ripoll, D. R., Bashir, S. et al. 2005. Selection on glycine β-1, 3-endoglucanase genes differentially inhibited by a phytophthora glucanase inhibitor protein. Genetics 169:1009–1019.

Bishop, M. J. and Friday, A. E. 1985. Evolutionary trees from nucleic acid and protein sequences. Proc. R. Soc. Lond. B Biol. Sci. 226:271–302.

Bishop, M. J. and Friday, A. E. 1987. Tetropad relationships: the molecular evidence. Molecules and Morphology in Evolution: Conflict or Compromise? in (ed. C. Patterson) Cambridge University Press, Cambridge, pp. 123–139.

Bishop, M. J. and Thompson, E. A. 1986. Maximum likelihood alignment of DNA sequences. J. Mol. Biol. 190:159–165.

Bjorklund, M. 1999. Are third positions really that bad? A test using vertebrate cytochrome b. Cladistics 15:191–197.

Bjorkman, P. J., Saper, S. A., Samraoui, B. et al. 1987a. Structure of the class I histocompatibility antigen, HLA-A2. Nature 329:506–512.

Bjorkman, P. J., Saper, S. A., Samraoui, B. et al. 1987b. The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329:512–518.

Bonhoeffer, S., Holmes, E. C. and Nowak, M. A. 1995. Causes of HIV diversity. Nature 376:125.

Box, G. E. P. 1979. Robustness in the strategy of scientific model building. In Robustness in Statistics (ed. R. L. Launer, and G. N. Wilkinson), p. 202. Academic Press, New York.

Box, G. E. P. and Muller, M. E. 1958. A note on the generation of random normal deviates. Ann. Math. Statist. 29:610–611.

Braverman, J. M., Hudson, R. R., Kaplan, N. L. et al. 1995. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140:783–796.

(p.322) Bremer, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795–803.

Brent, R. P. 1973. Algorithms for Minimization Without Derivatives. Prentice-Hall Inc., Englewood Cliffs, NJ.

Brinkmann, H., van der Giezen, M., Zhou, Y. et al. 2005. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst. Biol. 54:743–757.

Britten, R. J. 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science 231:1393–1398.

Bromham, L. 2002. Molecular clocks in reptiles: life history influences rate of molecular evolution. Mol. Biol. Evol. 19:302–309.

Bromham, L. and Penny, D. 2003. The modern molecular clock. Nat. Rev. Genet. 4:216–224.

Bromham, L., Rambaut, A. and Harvey, P. H. 1996. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43:610–621.

Bromham, L., Penny, D., Rambaut, A. and Hendy, M. D. 2000. The power of relative rates tests depends on the data. J. Mol. Evol. 50:296–301.

Brown, W. M., Prager, E. M., Wang, A. and Wilson, A. C. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18:225–239.

Brunet, M., Guy, F., Pilbeam, D. et al. 2002. A new hominid from the upper Miocene of Chad, central Africa. Nature 418:145–151.

Bruno, W. J. 1996. Modeling residue usage in aligned protein sequences via maximum likelihood. Mol. Biol. Evol. 13:1368–1374.

Bruno, W. J. and Halpern, A. L. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564–566.

Bruno, W. J., Socci, N. D. and Halpern, A. L. 2000. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17:189–197.

Bryant, D. 2003. A classication of consensus methods for phylogenetics. In BioConsensus, DIMACS Series in Discrete Mathematics and Theoretical Computer Science. (ed. M. Janowitz, F. -J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts), pp. 163–184. American Mathematical Society, Providence, RI.

Bryant, D. and Waddell, P. J. 1998. Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Mol. Biol. Evol. 15:1346–1359.

Buckley, T. R. 2002. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51:509–523.

Bulmer, M. G. 1990. Estimating the variability of substitution rates. Genetics 123:615–619.

Bulmer, M. S. and Crozier, R. H. 2004. Duplication and diversifying selection among termite antifungal peptides. Mol. Biol. Evol. 21:2256–2264.

Bush, R. M., Fitch, W. M., Bender, C. A. and Cox, N. J. 1999. Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol. Biol. Evol. 16:1457–1465.

Bustamante, C. D., Wakeley, J., Sawyer, S. and Hartl, D. L. 2001. Directional selection and the site-frequency spectrum. Genetics 159:1779–1788.

Bustamante, C. D., Nielsen, R., Sawyer, S. A. et al. 2002. The cost of inbreeding in Arabidopsis. Nature 416:531–534.

Bustamante, C. D., Nielsen, R. and Hartl, D. L. 2003. Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor. Popul. Biol. 63:91–103.

Camin, J. H. and Sokal, R. R. 1965. A method for deducing branching sequences in phylogeny. Evolution 19:311–326.

(p.323) Cao, Y., Adachi, J., Janke, A. et al. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 39:519–527.

Cao, Y., Janke, A., Waddell, P. J. et al. 1998. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47:307–322.

Cao, Y., Kim, K. S., Ha, J. H. and Hasegawa, M. 1999. Model dependence of the phylogenetic inference: relationship among Carnivores, Perissodactyls and Cetartiodactyls as inferred from mitochondrial genome sequences. Genes Genet. Syst. 74:211–217.

Carlin, B. P. and Louis, T. A. 2000. Bayes and Empirical Bayes Methods for Data Analysis. Chapman and Hall, London.

Carroll, S. B. 1995. Homeotic genes and the evolution of the arthropods and chordates. Nature 376:479–485.

Cavalli-Sforza, L. L. and Edwards, A. W. F. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570.

Cavender, J. A. 1978. Taxonomy with confidence. Math. Biosci. 40:271–280.

Chang, B. S. and Donoghue, M. J. 2000. Recreating ancestral proteins. Trends Ecol. Evol. 15:109–114.

Chang, J. T. 1996a. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math. Biosci. 137:51–73.

Chang, J. T. 1996b. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Math. Biosci. 134:189–215.

Charleston, M. A. 1995. Toward a characterization of landscapes of combinatorial optimization problems, with special attention to the phylogeny problem. J. Comput. Biol. 2:439–450.

Chenna, R., Sugawara, H., Koike, T. et al. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497–3500.

Chernoff, H. 1954. On the distribution of the likelihood ratio. Ann. Math. Stat. 25:573–578.

Choisy, M., Woelk, C. H., Guegan, J. F. and Robertson, D. L. 2004. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J. Virol. 78:1962–1970. [Erratum in J. Virol. 2004 78:4381–2].

Chor, B. and Snir, S. 2004. Molecular clock fork phylogenies: closed form analytic maximum likelihood solutions. Syst. Biol. 53:963–967.

Chor, B., Holland, B. R., Penny, D. and Hendy, M. D. 2000. Multiple maxima of likelihood in phylogenetic trees: an analytic approach. Mol. Biol. Evol. 17:1529–1541.

Clark, A. G., Glanowski, S., Nielsen, R. et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960–1963.

Clark, B. 1970. Selective constraints on amino-acid substitutions during the evolution of proteins. Nature 228:159–160.

Clark, N. L., Aagaard, J. E. and Swanson, W. J. 2006. Evolution of reproductive proteins from animals and plants. Reproduction 131:11–22.

Collins, T. M., Wimberger, P. H. and Naylor, G. J. P. 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43:482–496.

Comeron, J. M. 1995. A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J. Mol. Evol. 41:1152–1159.

Consuegra, S., Megens, H.-J., Schaschl, H. et al. 2005. Rapid evolution of the MHC Class I locus results in different allelic compositions in recently diverged populations of Atlantic salmon. Mol. Biol. Evol. 22:1095–1106.

Cooper, A. and Fortey, R. 1998. Evolutionary explosions and the phylogenetic fuse. Trends Ecol. Evol. 13:151–156.

(p.324) Cooper, A. and Penny, D. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275:1109–1113.

Cox, D. R. 1961. Tests of separate families of hypotheses. Proc. 4th Berkeley Symp. Math. Stat. Prob. 1:105–123.

Cox, D. R. 1962. Further results on tests of separate families of hypotheses. J. R. Statist. Soc B 24:406–424.

Cox, D. R. and Hinkley, D. V. 1974. Theoretical Statistics. Chapman and Hall, London.

Cummings, M. P., Otto, S. P. and Wakeley, J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814–822.

Cutler, D.J. 2000. Understanding the overdispersed molecular clock. Genetics 154:1403–1417.

Dagan, T., Talmor, Y. and Graur, D. 2002. Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol. Biol. Evol. 19:1022–1025.

Davison, A. C. 2003. Statistical Models. Cambridge University Press, Cambridge.

Dawkins, R. and Krebs, J. R. 1979. Arms races between and within species. Proc. R. Soc. Lond. B. Biol. Sci. 205:489–511.

Dayhoff, M. O., Eck, R. V. and Park, C. M. 1972. Evolution of a complex system: the immunoglobulins. Pp. 31–40. Atlas of protein sequence and structure, pp. 31–40. National Biomedical Research Foundation, Silver Spring, MD.

Dayhoff, M. O., Schwartz, R. M. and Orcutt, B. C. 1978. A model of evolutionary change in proteins. Atlas of protein sequence and structure, Vol 5, Suppl. 3, pp. 345–352. National Biomedical Research Foundation, Washington DC.

DeBry, R. W. 1992. The consistency of several phylogeny-inference methods under varying evolutionary rates. Mol. Biol. Evol. 9:537–551.

DeBry, R. 2001. Improving interpretation of the decay index for DNA sequences. Syst. Biol. 50:742–752.

Deely, J. J. and Lindley, D. V. 1981. Bayes empirical Bayes. J. Amer. Statist. Assoc. 76:833–841.

DeGroot, M. H. and Schervish, M. J. 2002. Probability and Statistics. Addison-Wesley, Boston, MA.

Delson, E., Tattersall, I., Van Couvering, J. A. and Brooks, A. S. 2000. In Encyclopedia of Human Evolution and Prehistory (ed. E. Delson, I. Tattersall, J. A. Van Couvering, and A. S. Brooks), pp. 166–171. Garland, New York.

Desper, R. and Gascuel, O. 2005. The minimum-evolution distance-based approach to phylogenetic inference. In Mathematics of Evolution and Phylogeny (ed. O. Gascuel), pp. 1–32. Oxford University Press, Oxford.

Diggle, P. J. 1990. Time Series: a Biostatistical Introduction. Oxford University Press, Oxford.

Doolittle, F. W. 1998. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14:307–311.

Doolittle, R. F. and Blomback, B. 1964. Amino-acid sequence investigations of fibrinopeptides from various mammals: evolutionary implications. Nature 202:147–152.

Douzery, E. J., Delsuc, F., Stanhope, M. J. and Huchon, D. 2003. Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J. Mol. Evol. 57:S201–S213.

Drummond, A. J., Nicholls, G. K., Rodrigo, A. G. and Solomon, W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307–1320.

Duda, T. F. and Palumbi, S. R. 2000. Evolutionary diversification of multigene families: allelic selection of toxins in predatory cone snails. Mol. Biol. Evol. 17:1286–1293.

(p.325) Duda, T. F., Jr and Palumbi, S. R. 1999. Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc. Natl. Acad. Sci. U.S.A. 96:6820–6823.

Duret, L. 2002. Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12:640–649.

Duret, L., Semon, M., Piganeau, G. et al. 2002. Vanishing GC-rich isochores in mammalian genomes. Genetics 162:1837–1847.

Dutheil, J., Pupko, T., Jean-Marie, A. and Galtier, N. 2005. A model-based approach for detecting coevolving positions in a molecule. Mol. Biol. Evol. 22:1919–1928.

Eck, R. V. and Dayhoff, M. O. 1966. Inference from protein sequence comparisons. In Atlas of protein sequence and structure (ed. M. O. Dayhoff). National Biomedical Research Foundation, Silver Spring, MD.

Edwards, A. W. F. 1970. Estimation of the branch points of a branching diffusion process (with discussion). J. R. Statist. Soc. B. 32:155–174.

Edwards, A. W. F. 1992. Likelihood, expanded edition. Johns Hopkins University Press, London.

Edwards, A. W. F. and Cavalli-Sforza, L. L. 1963. The reconstruction of evolution (abstract). Ann. Hum. Genet. 27:105.

Efron, B. 1979. Bootstrap methods: another look at the jackknife. Ann. Stat. 7:1–26.

Efron, B. 1986. Why isn’t everyone a Bayesian? (with discussion). Am. J. Statist. Assoc. 40:1–11.

Efron, B. and Hinkley, D. V. 1978. Assessing the accuracy of the maximum likelihood estimator: observed and expected information. Biometrika 65:457–487.

Efron, B. and Tibshirani, R. J. 1993. An Introduction to the Bootstrap. Chapman and Hall, London.

Efron, B., Halloran, E. and Holmes, S. 1996. Bootstrap confidence levels for phylogenetic trees [corrected and republished article originally printed in Proc. Natl. Acad. Sci. U.S.A. 1996 93:7085–7090]. Proc. Natl. Acad. Sci. U.S.A. 93:13429–13434.

Emes, R. D., Riley, M. C., Laukaitis, C. M. et al. 2004. Comparative evolutionary genomics of androgen-binding protein genes. Genome Res. 14:1516–1529.

Enard, W., Przeworski, M., Fisher, S. E. et al. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869–872.

Erixon, P., Svennblad, B., Britton, T. and Oxelman, B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52:665–673.

Evans, P. D., Anderson, J. R., Vallender, E. J. et al. 2004. Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Hum. Mol. Genet. 13:1139–1145.

Everitt, B. S., Landau, S. and Leese, M. 2001. Cluster Analysis. Arnold, London.

Excoffier, L. and Yang, Z. 1999. Substitution rate variation among sites in the mitochondrial hypervariable region I of humans and chimpanzees. Mol. Biol. Evol. 16: 1357–1368.

Eyre-Walker, A. 1998. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47:686–690.

Fan, C., Purugganan, M. D., Thomas, D. T. et al. 2004. Heterogeneous evolution of the Myc-like anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae). Mol. Phylogenet. Evol. 33:580–594.

Fares, M. A. and Wolfe, K. H. 2003. Positive selection and subfunctionalization of duplicated CCT chaperonin subunits. Mol. Biol. Evol. 20:1588–1597.

(p.326) Fares, M.A., Barrio, E., Sabater-Munoz, B. and Moya, A. 2002. The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Mol. Biol. Evol. 19:1162–1170.

Farris, J. S. 1969. A successive approximation approach to character weighting. Syst. Zool. 18:374–385.

Farris, J. S. 1973. A probability model for inferring evolutionary trees. Syst. Zool. 22:250–256.

Farris, J. S. 1977. Phylogenetic analysis under Dollo’s law. Syst. Zool. 26:77–88.

Farris, J. S. 1983. The logical basis of phylogenetic analysis. Advances in Cladistics. (ed. N. Platnick, and V. Funk), pp. 7–26. Columbia University Press, New York.

Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 417–419.

Fay, J. C. and Wu, C. I. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405–1413.

Fay, J. C. and Wu, C. -I. 2001. The neutral theory in the genomic era. Curr. Opinion Genet. Dev. 11:642–646.

Fay, J. C. and Wu, C. I. 2003. Sequence divergence, functional constraint, and selection in protein evolution. Annu. Rev. Genomics Hum. Genet. 4:213–235.

Fay, J. C., Wyckoff, G. J. and Wu, C. -I. 2001. Positive and negative selection on the human genome. Genetics 158:1227–1234.

Felsenstein, J. 1973a. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471–492.

Felsenstein, J. 1973b. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22:240–249.

Felsenstein, J. 1978a. The number of evolutionary trees. Syst. Zool. 27:27–33.

Felsenstein, J. 1978b. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401–410.

Felsenstein, J. 1981. Evolutionary trees from DNAsequences: a maximum likelihood approach. J. Mol. Evol. 17:368–376.

Felsenstein, J. 1983. Statistical inference of phylogenies. J. R. Statist. Soc. A 146:246–272.

Felsenstein, J. 1985a. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.

Felsenstein, J. 1985b. Phylogenies and the comparative method. Amer. Nat. 125:1–15.

Felsenstein, J. 1985c. Confidence limits on phylogenies with a molecular clock. Evolution 34:152–161.

Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521–565.

Felsenstein, J. 2001a. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J. Mol. Evol. 53:447–455.

Felsenstein, J. 2001b. The troubled growth of statistical phylogenetics. Syst. Biol. 50: 465–467.

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

Felsenstein, J. and Churchill, G.A. 1996. Ahidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93–104.

Felsenstein, J. and Kishino, H. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42:193–200.

Felsenstein, J. and Sober, E. 1986. Parsimony and likelihood: an exchange. Syst. Zool. 35: 617–626.

(p.327) Filip, L. C. and Mundy, N. I. 2004. Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates. Mol. Biol. Evol. 21:1504–1511.

Fisher, R. 1930a. The Genetic Theory of Natural Selection. Clarendon Press, Oxford.

Fisher, R. 1930b. Inverse probability. Proc. Camb. Phil. Soc. 26:528–535.

Fisher, R. 1970. Statistical Methods for Research Workers. Oliver and Boyd, Edinburgh.

Fitch, W. M. 1971a. Rate of change of concomitantly variable codons. J. Mol. Evol. 1:84–96.

Fitch, W. M. 1971b. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406–416.

Fitch, W. M. 1976. Molecular evolutionary clocks. In Molecular Evolution. (ed. F. J. Ayala), pp. 160–178. Sinauer Associates, Sunderland, MA.

Fitch, W. M. and Margoliash, E. 1967. Construction of phylogenetic trees. Science 155: 279–284.

Fitch, W. M., Bush, R. M., Bender, C.A. and N.J. 1997. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl. Acad. Sci. U.S.A. 94:7712–7718.

Fleissner, R., Metzler, D. and von Haeseler, A. 2005. Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst. Biol. 54:548–561.

Fletcher, R. 1987. Practical Methods of Optimization. Wiley, New York.

Foote, M., Hunter, J. P., Janis, C. M. and Sepkoski, J. J. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283:1310–1314.

Ford, M. J. 2001. Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 18:639–647.

Ford, M. J., Thornton, P. J. and Park, L. K. 1999. Natural selection promotes divergence of transferrin among salmonid species. Mol. Ecol. 8:1055–1061.

Forsberg, R. and Christiansen, F. B. 2003. A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol. Biol. Evol. 20:1252–1259.

Freeland, S. J. and Hurst, L. D. 1998. The genetic code is one in a million. J. Mol. Evol. 47:238–248.

Fu, Y. 1994. Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics 138:1375–1386.

Fu, Y. X. and Li, W. H. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693–709.

Fu, Y. -X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and backgroud selection. Genetics 147:915–925.

Fukami, K. and Tateno, Y. 1989. On the maximum likelihood method for estimating molecular trees: uniqueness of the likelihood point. J. Mol. Evol. 28:460–464.

Fukami-Kobayashi K. and Tateno, Y.1991. Robustness of maximum likelihood tree estimation against different patterns of base substitutions. J. Mol. Evol. 32:79–91.

Gadagkar, S. R. and Kumar, S. 2005. Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol. Biol. Evol. 22:2139–2141.

Galtier, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:866–873.

Galtier, N. and Gouy, M. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871–879.

Galtier, N., Tourasse, N. and Gouy, M. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283:220–221.

(p.328) Gascuel, O.1994. A note on Sattath and Tversky’s, Saitou and Nei’s, and Studier and Keppler’s algorithms for inferring phylogenies from evolutionary distances. Mol. Biol. Evol. 11: 961–963.

Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685–695.

Gascuel, O. 2000. On the optimization principle in phylogenetic analysis and the minimum-evolution criterion. Mol. Biol. Evol. 17:401–405.

Gaucher, E. A. and Miyamoto, M. M. 2005. A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol. Phylogenet. Evol. 37:928–931.

Gaut, B. S. and Lewis, P. O. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12:152–162.

Gelfand, A. E. and Smith, A. F. M. 1990. Sampling-based approaches to calculating marginal densities. J. Amer. Stat. Assoc. 85:398–409.

Gelman, A. and Rubin, D. B. 1992. Inference from iterative simulation using multiple sequences (with discussion). Statist. Sci. 7:457–511.

Gelman, A., Roberts, G. O. and Gilks, W. R. 1996. Efficient Metropolis jumping rules. In Bayesian Statistics 5 (ed. J. M. Bernardo, J. O. Berger, A. P. Dawid, and A. F. M. Smith), pp. 599–607. Oxford University Press, Oxford.

Gelman, S. and Gelman, G. D. 1984. Stochastic relaxation, Gibbs distributions and the Bayes restoration of images. IEEE Trans. Pattern Anal. Mach. Intel. 6:721–741.

Gerrard, D. T. and Filatov, D. A. 2005. Positive and negative selection on mammalian Y chromosomes. Mol. Biol. Evol. 22:1423–1432.

Geyer, C. J. 1991. Markov chain Monte Carlo maximum likelihood. In Computing Science and Statistics: Proc. 23rd Symp. Interface (ed. E. M. Keramidas), pp. 156–163. Interface Foundation, Fairfax Station, VA.

Gilks, W. R., Richardson, S. and Spielgelhalter, D. J. 1996. Markov Chain Monte Carlo in Practice. Chapman and Hall, London.

Gill, P. E., Murray, W. and Wright, M. H. 1981. Practical Optimization. Academic Press, London.

Gillespie, J. H. 1984. The molecular clock may be an episodic clock. Proc. Natl. Acad. Sci. U.S.A. 81:8009–8013.

Gillespie, J. H. 1986a. Rates of molecular evolution. Ann. Rev. Ecol. Systemat. 17:637–665.

Gillespie, J. H. 1986b. Natural selection and the molecular clock. Mol. Biol. Evol. 3:138–155.

Gillespie, J. H. 1991. The Causes of Molecular Evolution. Oxford University Press, Oxford.

Gillespie, J. H. 1998. Population Genetics: a Concise Guide. Johns Hopkins University Press, Baltimore, MD.

Gogarten, J. P., Kibak, H., Dittrich, P. et al. 1989. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 86:6661–6665.

Gojobori, T. 1983. Codon substitution in evolution and the “saturation” of synonymous changes. Genetics 105:1011–1027.

Gojobori, T., Li, W. H. and Graur, D. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18:360–369.

Golding, G. B. 1983. Estimates of DNA and protein sequence divergence: an examination of some assumptions. Mol. Biol. Evol. 1:125–142.

Golding, G. B. and Dean, A. M. 1998. The structural basis of molecular adaptation. Mol. Biol. Evol. 15:355–369.

(p.329) Goldman, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis. Syst. Zool. 39:345–361.

Goldman, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36: 182–198.

Goldman, N. 1994. Variance to mean ratio, R(t), for Poisson processes on phylogenetic trees. Mol. Phylogenet. Evol. 3:230–239.

Goldman, N. 1998. Phylogenetic information and experimental design in molecular systematics. Proc. R. Soc. Lond. B Biol. Sci. 265:1779–1786.

Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725–736.

Goldman, N., Thorne, J. L. and Jones, D. T. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445–458.

Goldman, N., Anderson, J. P. and Rodrigo, A. G. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652–670.

Goldstein, D. B. and Pollock, D. D. 1994. Least squares estimation of molecular distance—noise abatement in phylogenetic reconstruction. Theor. Popul. Biol. 45:219–226.

Goloboff, P. A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15:415–428.

Goloboff, P. A. and Pol, D. 2005. Parsimony and Bayesian phylogenetics. In Parsimony, Phylogeny, and Genomics (ed. V. A. Albert), pp. 148–159. Oxford University Press, Oxford.

Golub, G. H. and Van Loan, C. F. 1996. Matrix Computations. Johns Hopkins University Press, Baltimore, MD.

Gonnet, G. H., Cohen, M. A. and Benner, S. A. 1992. Exhaustive matching of the entire protein sequence database. Science 256:1443–1445.

Goodwin, R. L., Baumann, H. and Berger, F. G. 1996. Patterns of divergence during evolution of α 1-Proteinase inhibitors in mammals. Mol. Biol. Evol. 13:346–358.

Götesson, A., Marshall, J. S., Jones, D. A. and Hardham, A. R. 2002. Characterization and evolutionary analysis of a large polygalacturonase gene family in the oomycete pathogen Phytophthora cinnamomi. Mol. Plant Microbe Interact. 15:907–921.

Grantham, R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862–864.

Graur, D. and Li, W. -H. 2000. Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, MA.

Graur, D. and Martin, W. 2004. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20:80–86.

Griffiths, R. C. and Tavaré, S. 1997. Computational methods for the coalescent. In Progress in Population Genetics and Human Evolution: IMA Volumes in Mathematics and its Applications (ed. P. Donnelly and S. Tavaré), pp. 165–182. Springer-Verlag, Berlin.

Grimmett, G. R. and Stirzaker, D. R. 1992. Probability and Random Processes. Clarendon Press, Oxford.

Gu, X. 2001. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18:453–464.

Gu, X. and Li, W. -H. 1996. A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc. Natl. Acad. Sci. U.S.A. 93:4671–4676.

Gu, X., Fu, Y. X. and Li, W. H. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546–557.

(p.330) Guindon, S. and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696–704.

Guindon, S., Rodrigo, A. G., Dyer, K. A. and Huelsenbeck, J. P. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc. Natl. Acad. Sci. U.S.A. 101:12957–12962.

Haldane, J. B. S. 1932. The Causes of Evolution. Longmans Green & Co., London.

Harris, H. 1966. Enzyme polymorphism in man. Proc. R. Soc. Lond. B Biol. Sci. 164:298–310.

Hartigan, J. A. 1973. Minimum evolution fits to a given tree. Biometrics 29:53–65.

Hartl, D. L. and Clark, A. G. 1997. Principles of Population Genetics. Sinauer Associates, Sunderland, MA.

Hartl, D. L., Moriyama, E. N. and Sawyer, S. A. 1994. Selection intensity for codon bias. Genetics 138:227–234.

Harvey, P. H. and Pagel, M. 1991. The Comparative Method in Evlutionary Biology. Oxford University Press, Oxford.

Harvey, P. H. and Purvis, A. 1991. Comparative methods for explaining adaptations. Nature 351:619–624.

Hasegawa, M. and Fujiwara, M. 1993. Relative efficiencies of the maximum likelihood, maximum parsimony, and neihbor joining methods for estimating protein phylogeny. Mol. Phyl. Evol. 2:1–5.

Hasegawa, M. and Kishino, H. 1989. Confidence limits on the maximum-likelihood estimate of the Hominoid tree from mitochondrial DNA sequences. Evolution 43:672–677.

Hasegawa, M. and Kishino, H. 1994. Accuracies of the simple methods for estimating the bootstrap probability of a maximum likelihood tree. Mol. Biol. Evol. 11:142–145.

Hasegawa, M., Yano, T. and Kishino, H. 1984. A new molecular clock of mitochondrial DNA and the evolution of Hominoids. Proc. Japan Acad. B. 60:95–98.

Hasegawa, M., Kishino, H. and Yano, T. 1985. Dating the human–ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160–174.

Hasegawa, M., Kishino, H. and Saitou, N. 1991. On the maximum likelihood method in molecular phylogenetics. J. Mol. Evol. 32:443–445.

Hasegawa, M., Cao, Y. and Yang, Z. 1998. Preponderance of slightly deleterious polymorphism in mitochondrial DNA: replacement/synonymous rate ratio is much higher within species than between species. Mol. Biol. Evol. 15:1499–1505.

Hasegawa, M., Thorne, J. L. and Kishino, H. 2003. Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes Genet. Syst. 78:267–283.

Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their application. Biometrika 57:97–109.

Haydon, D. T., Bastos, A. D., Knowles, N. J. and Samuel, A. R. 2001. Evidence for positive selection in foot-and-mouth-disease virus capsid genes from field isolates. Genetics 157: 7–15.

Hedges, S. B. and Kumar, S. 2004. Precision of molecular time estimates. Trends Genet. 20:242–247.

Hedges, S. B., Parker, P. H., Sibley, C. G. and Kumar, S. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226–229.

Hein, J., Wiuf, C., Knudsen, B. et al. 2000. Statistical alignment: computational properties, homology testing and goodness-of-fit. J. Mol. Biol. 302:265–279.

Hein, J., Jensen, J. L. and Pedersen, C. N. 2003. Recursions for statistical multiple alignment. Proc. Natl. Acad. Sci. U.S.A. 100:14960–14965.

(p.331) Hein, J., Schieriup, M. H. and Wiuf, C. 2005. Gene Genealogies, Variation and Evolution: a Primer in Coalescent Theory. Oxford University Press, Oxford.

Hellberg, M. E. and Vacquier, V. D. 2000. Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein. Mol. Biol. Evol. 17: 458–466.

Hendy, M. D. 2005. Hadamard conjugation: an analytical tool for phylogenetics. In Mathematics of Evolution and Phylogeny (ed. O. Gascuel), pp. 143–177. Oxford University Press, Oxford.

Hendy, M. D. and Penny, D. 1982. Branch and bound algorithms ro determine minimum-evolution trees. Math. Biosci. 60:133–142.

Hendy, M. D. and Penny, D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297–309.

Henikoff, S. and Henikoff, J. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89:10915–10919.

Hey, J. and Nielsen, R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747–760.

Higgins, D. G. and Sharp, P. M. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237–244.

Hillis, D. M. and Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182–192.

Hillis, D. M., Bull, J. J., White, M. E. et al. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255:589–592.

Holbrook, J. D., Birdsey, G. M., Yang, Z. et al. 2000. Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates. Mol. Biol. Evol. 17:387–400.

Holder, M. and Lewis, P. O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4:275–284.

Holmes, I. 2005. Using evolutionary expectation maximization to estimate indel rates. Bioinformatics 21:2294–2300.

Holmes, S. 2003. Bootstrapping phylogenetic trees: theory and methods. Stat. Sci. 18:241–255.

Horai, S., Hayasaka, K., Kondo, R. et al. 1995. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. U.S.A. 92:532–536.

Hudson, R. R. 1990. Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology (ed. D. J. Futuyma, and J. D. Antonovics), pp. 1–44. Oxford University Press, New York.

Hudson, R. R. 2001. Two-locus sampling distributions and their application. Genetics 159:1805–1817.

Hudson, R. R., Kreitman, M. and Aguade, M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153–159.

Huelsenbeck, J. P. 1995a. The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12:843–849.

Huelsenbeck, J. P. 1995b. The performance of phylogenetic methods in simulation. Syst. Biol. 44:17–48.

Huelsenbeck, J. P. 1998. Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved? Syst. Biol. 47:519–537.

(p.332) Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698–707.

Huelsenbeck, J. P. and Bollback, J. P. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50:351–366.

Huelsenbeck, J. P. and Dyer, K. A. 2004. Bayesian estimation of positively selected sites. J. Mol. Evol. 58:661–672.

Huelsenbeck, J.P. and Lander, K. M. 2003. Frequent inconsistency of parsimony under a simple model of cladogenesis. Syst Biol 52:641–648.

Huelsenbeck, J.P. and Rannala, B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904–913.

Huelsenbeck, J. P. and Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755.

Huelsenbeck, J. P., Larget, B. and Swofford, D. 2000a. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879–1892.

Huelsenbeck, J. P., Rannala, B. and Larget, B. 2000b. A Bayesian framework for the analysis of cospeciation. Evolution 54:352–364.

Huelsenbeck, J. P., Rannala, B. and Masly, J. P. 2000c. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349–2350.

Huelsenbeck, J. P., Ronquist, F., Nielsen, R. and Bollback, J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314.

Huelsenbeck, J. P., Larget, B. and Alfaro, M. E. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123–1133.

Hughes, A. L. 1999. Adaptive Evolution of Genes and Genomes. Oxford University Press, Oxford.

Hughes, A. L. and Nei, M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167–170.

Hughes, A. L., Ota, T. and Nei, M. 1990. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol. Biol. Evol. 7:515–524.

Huttley, G. A., Easteal, S., Southey, M. C. et al. 2000. Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Nature Genet. 25:410–413.

Ina, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40:190–226.

Ivarsson, Y., Mackey, A. J., Edalat, M. et al. 2002. Identification of residues in glutathione transferase capable of driving functional diversification in evolution: a novel approach to protein design. J. Biol. Chem. 278:8733–8738.

Iwabe, N., Kuma, K., Hasegawa, M. et al. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. U.S.A. 86:9355–9359.

Jeffreys, H. 1939. Theory of Probability. Clarendon Press, Oxford.

Jeffreys, H. 1961. Theory of Probability. Oxford University Press, Oxford.

Jermann, T. M., Opitz, J. G., Stackhouse, J. and Benner, S. A. 1995. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374: 57–59.

(p.333) Jiggins, F. M., Hurst, G. D. D. and Yang, Z. 2002. Host–symbiont conflicts: positive selection on the outer membrane protein of parasite but not mutualistic Rickettsiaceae. Mol. Biol. Evol. 19:1341–1349.

Jin, L. and Nei, M. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis [erratum in Mol. Biol. Evol. 1990 7:201]. Mol. Biol. Evol. 7:82–102.

Johannesson, H., Vidal, P., Guarro, J. et al. 2004. Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives. Mol. Biol. Evol. 21:1134–1145.

Johnson, M. E., Viggiano, L., Bailey, J. A. et al. 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature 413:514–519.

Jones, D. T., Taylor, W. R. and Thornton, J. M. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275–282.

Jordan, I. K., Kondrashov, F. A., Adzhubei, I. A. et al. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature 433:633–638.

Jukes, T. H. 1987. Transitions, transversions, and the molecular evolutionary clock. J. Mol. Evol. 26:87–98.

Jukes, T. H. and Cantor, C. R. 1969. Evolution of protein molecules. In Mammalian protein metabolism (ed. H. N. Munro), pp. 21–123. Academic Press, New York.

Jukes, T. H. and King, J. L. 1979. Evolutionary nucleotide replacements in DNA. Nature 281:605–606.

Kafatos, F. C., Efstratiadis, A., Forget, B. G. and Weissman, S. M. 1977. Molecular evolution of human and rabbit ß-globin mRNAs. Proc. Natl. Acad. Sci. U.S.A. 74:5618–5622.

Kalbfleisch, J. G. 1985. Probability and Statistical Inference, Vol. 2: Statistical Inference. Springer-Verlag, New York.

Kalbfleisch, J. G. and Sprott, D. A. 1970. Application of likelihood methods to models involving large numbers of parameters (with discussions). J. R. Statist. Soc. B 32:175–208.

Kao, E. P. C. 1997. An Introduction to Stochastic Processes. ITP, Belmont, CA.

Karlin, S. and Taylor, H. M. 1975. A First Course in Stochastic Processes. Academic Press, San Diego, CA.

Karn, R. C. and Nachman, M. W. 1999. Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection. Mol. Biol. Evol. 16:1192–1197.

Katoh, K., Kuma, K. and Miyata, T. 2001. Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J. Mol. Evol. 53:477–484.

Keilson, J. 1979. Markov Chain Models: Rarity and Exponentiality. Springer-Verlag, New York.

Kelly, C. and Rice, J. 1996. Modeling nucleotide evolution: a heterogeneous rate analysis. Math. Biosci. 133:85–109.

Kelly, F. 1979. Reversibility and Stochastic Networks. Springer-Verlag, Berlin.

Kendall, D. G. 1948. On the generalized birth-and-death process. Ann. Math. Stat. 19:1–15.

Kidd, K. K. and Sgaramella-Zonta, L. A. 1971. Phylogenetic analysis: concepts and methods. Am. J. Hum. Genet. 23:235–252.

Kim, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363–374.

Kimura, M. 1968. Evolutionary rate at the molecular level. Nature 217:624–626.

Kimura, M. 1977. Prepondence of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275–276.

(p.334) Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111–120.

Kimura, M. 1981. Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. USA 78:454–458.

Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Kimura, M. 1987. Molecular evolutionary clock and the neutral theory. J. Mol. Evol. 26:24–33.

Kimura, M. and Ohta, T. 1971. Protein polymorphism as a phase of molecular evolution. Nature 229:467–469.

Kimura, M. and Ohta, T. 1972. On the stochastic model for estimation of mutational distance between homologous proteins. J. Mol. Evol. 2:87–90.

King, C. E. and Jukes, T. H. 1969. Non-Darwinian evolution. Science 164:788–798.

Kirkpatrick, S., Gelatt, C. D. and Vecchi, M. P. 1983. Optimization by simulated annealing. Science 220:671–680.

Kishino, H. and Hasegawa, M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:170–179.

Kishino, H. and Hasegawa, M. 1990. Converting distance to time: application to human evolution. Methods Enzymol. 183:550–570.

Kishino, H., Miyata, T. and Hasegawa, M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:151–160.

Kishino, H., Thorne, J. L. and Bruno, W. J. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352–361.

Kitano, T., Sumiyama, K., Shiroishi, T. and Saitou, N. 1998. Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene. Biochem. Biophys. Res. Commun. 249:78–85.

Kluge, A. G. and Farris, J. S. 1969. Quantitateive phyletics and the evolution of anurans. Syst. Zool. 18:1–32.

Knoll, A. H. and Carroll, S. B. 1999. Early animal evolution: emerging views from comparative biology and geology. Science 284:2129–2137.

Knudsen, B. and Miyamoto, M. M. 2001. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc. Natl. Acad. Sci. U.S.A. 98:14512–14517.

Knuth, D. E. 1997. The Art of Computer Programming: Fundamental Algorithms. Addison-Wesley, Reading, MA.

Kocher, T. D. 2004. Adaptive evolution and explosive speciation: the cichlid fish model. Nature Rev. Genet. 5:288–298.

Kolaczkowski, B. and Thornton, J. W. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980–984.

Kosakovsky Pond, S. L. and Frost, S. D. W. 2005a. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 22:478–485.

Kosakovsky Pond, S. L. and Frost, S. D. W. 2005b. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22:1208–1222.

Kosakovsky Pond, S. L. and Muse, S. V. 2004. Column sorting: rapid calculation of the phylogenetic likelihood function. Syst. Biol. 53:685–692.

Kosakovsky Pond, S. L. and Muse, S. V. 2005. Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. 22:2375–2385.

Koshi, J. M. and Goldstein, R. A. 1996a. Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol. 42:313–320.

(p.335) Koshi, J. M. and Goldstein, R. A. 1996b. Correlating structure-dependent mutation matrices with physical-chemical properties. In Pacific Symposium on Biocomputing ’96 (ed. L. Hunter and J. E. Klein), pp. 488–499. World Scientific, Singapore.

Koshi, J. M. Mindell, D. P. and Goldstein, R. A. 1999. Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes. Mol. Biol. Evol. 16:173–179.

Kosiol, C. and Goldman, N. 2005. Different versions of the Dayhoff rate matrix. Mol. Biol. Evol. 22:193–199.

Kreitman, M. 2000. Methods to detect selection in populations with applications to the human. Annu. Rev. Genomics Hum. Genet. 1:539–559.

Kreitman, M. and Akashi, H. 1995. Molecular evidence for natural selection. Annu. Rev. Ecol. Syst. 26:403–422.

Kronmal, R. A. and Peterson, A. V. 1979. On the alias method for generating random variables from a discrete distribution. Amer. Statist. 33:214–218.

Kuhner, M. K. and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates [erratum in Mol. Biol. Evol. 1995 12:525]. Mol. Biol. Evol. 11:459–468.

Kuhner, M. K., Yamato, J. and Felsenstein, J. 1995. Estimating effective population size and mutation rate from sequence data using Metropolis–Hastings sampling. Genetics 140: 1421–1430.

Kumar, S. 2005. Molecular clocks: four decades of evolution. Nat. Rev. Genet. 6:654–662.

Kumar, S. and Hedges, S. B. 1998. A molecular timescale for vertebrate evolution. Naturet 392:917–920.

Kumar, S. and Subramanian, S. 2002. Mutation rate in mammalian genomes. Proc. Natl. Acad. Sci. U.S.A. 99:803–808.

Kumar, S., Tamura, K. and Nei, M. 2005a. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150–163.

Kumar, S., Filipski, A., Swarna, V. et al. 2005b. Placing confidence limits on the molecular age of the human–chimpanzee divergence. Proc. Natl. Acad. Sci. U.S.A. 102:18842–18847.

Laird, C. D., McConaughy, B. L. and McCarthy, B. J. 1969. Rate of fixation of nucleotide substitutions in evolution. Nature 224:149–154.

Lake, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. U.S.A. 91:1455–1459.

Lang, S. 1987. Linear Algebra. Springer-Verlag, New York.

Langley, C. H. and Fitch, W. M. 1974. An examination of the constancy of the rate of molecular evolution. J. Mol. Evol. 3:161–177.

Larget, B. and Simon, D. L. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750–759.

Larget, B., Simon, D. L., Kadane, J. B. and Sweet, D. 2005. A Bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol. Evol. 22:486–495.

Lee, M. S. Y. 2000. Tree robustness and clade significance. Syst. Biol. 49:829–836.

Lee, Y. and Nelder, J. A. 1996. Hierarchical generalized linear models. J. R. Statist. Soc. B. 58:619–678.

Lee, Y. -H., Ota, T. and Vacquier, V. D. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12:231–238.

Lehmann, P. 2002. Structure and evolution of plant disease resistance genes. J. Appl. Genet. 43:403–414.

(p.336) Lemmon, A. R. and Milinkovitch, M. C. 2002. The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation. Proc. Natl. Acad. Sci. U.S.A. 99:10516–10521.

Lemmon, A. R. and Moriarty, E. C. 2004. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 53:265–277.

Leonard, T. and Hsu, J. S. J. 1999. Bayesian Methods. Cambridge University Press, Cambridge.

Lewis, P. O. 1998. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol. 15:277–283.

Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913–925.

Lewis, P. O., Holder, M. T. and Holsinger, K. E. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241–253.

Lewontin, R. 1989. Inferring the number of evolutionary events from DNA coding sequence differences. Mol. Biol. Evol. 6:15–32.

Lewontin, R. C. and Hubby, J. L. 1966. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54:595–609.

Li, S., Pearl, D. and Doss, H. 2000. Phylogenetic tree reconstruction using Markov chain Monte Carlo. J. Amer. Statist. Assoc. 95:493–508.

Li, W. H. and Tanimura, M. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 326:93–96.

Li, W. -H. 1986. Evolutionary change of restriction cleavage sites and phylogenetic inference. Genetics 113:187–213.

Li, W. H. 1989. A statistical test of phylogenies estimated from sequence data. Mol. Biol. Evol. 6:424–435.

Li, W. -H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96–99.

Li, W. -H. 1997. Molecular Evolution. Sinauer Associates, Sunderland, MA.

Li, W. -H. and Gouy, M. 1991. Statistical methods for testing molecular phylogenies. In Phylogenetic Analysis of DNA Sequences (ed. M. Miyamoto, and J. Cracraft), pp. 249–277. Oxford University Press, Oxford.

Li, W. H., Tanimura, M. and Sharp, P. M. 1987. An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J. Mol. Evol. 25:330–342.

Li, W. -H., Wu, C. -I. and Luo, C. -C. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150–174.

Libertini, G. and Di Donato, A. 1994. Reconstruction of ancestral sequences by the inferential method, a tool for protein engineering studies. J. Mol. Evol. 39:219–229.

Lindley, D. V. 1957. A statistical paradox. Biometrika 44:187–192.

Lindley, D. V. 1962. Discussion on “Confidence sets for the mean of a multivariate normal distribution” by C. Stein. J. R. Statist. Soc. B 24:265–296.

Lindley, D. V. and Phillips, L. D. 1976. Inference for a Bernoulli process (a Bayesian view). Amer. Statist. 30:112–119.

Lindsey, J. K. 1974a. Comparison of probability distributions. J. R. Statist. Soc. B 36:38–47.

Lindsey, J. K. 1974b. Construction and comparison of statistical models. J. R. Statist. Soc. B. 36:418–425.

(p.337) Linhart, H. 1988. A test whether two AIC’s differ significantly. S. Afr. Stat. J. 22: 153–161.

Lockhart, P., Novis, P., Milligan, B. G. et al. 2006. Heterotachy and tree building: a case study with plastids and Eubacteria. Mol. Biol. Evol. 23:40–45.

Lockhart, P. J., Steel, M. A., Hendy, M. D. and Penny, D. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605–612.

Lunter, G. A., Miklos, I., Song, Y. S. and Hein, J. 2003. An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. J Comput Biol 10:869–889.

Lunter, G., Miklos, I., Drummond, A. et al. 2005. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 6:83.

Lynch, M. and Conery, J. S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155.

Maddison, D. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 33:83–103.

Maddison, D. R. and Maddison, W. P. 2000. MacClade 4: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA.

Maddison, W. P. and Maddison, D. R. 1982. MacClade: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA.

Makova, K. D., Ramsay, M., Jenkins, T. and Li, W. H. 2001. Human DNA sequence variation in a 6.6-kb region containing the melanocortin 1 receptor promoter. Genetics 158: 1253–1268.

Malcolm, B. A., Wilson, K. P., Matthews, B. W. et al. 1990. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345:86–89.

Margoliash, E. 1963. Primary structure and evolution of cytochrome c. Proc. Natl. Acad. Sci. U.S.A. 50:672–679.

Maritz, J. S. and Lwin, T. 1989. Empirical Bayes Methods. Chapman and Hall, London.

Martin, A. P. and Palumbi, S. R. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci U.S.A. 90:4087–4091.

Massingham, T. and Goldman, N. 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753–1762.

Maston, G. A. and Ruvolo, M. 2002. Chorionic gonadotropin has a recent origin within primates and an evolutionary history of selection. Mol. Biol. Evol. 19:320–335.

Mateiu, L. M. and Rannala, B. 2006. Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation. Syst. Biol. 55: 259–269.

Mau, B. and Newton, M. A. 1997. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J. Computat. Graph. Stat. 6:122–131.

Mau, B., Newton, M. A. and Larget, B. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Biometrics 55:1–12.

Maynard Smith, J. and Haigh, J. 1974. The hitch-hiking effect of a favorable gene. Genet. Res. 23:23–35.

Mayrose, I., Friedman, N. and Pupko, T. 2005. A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics 21:151–158.

McDonald, J. H. and Kreitman, M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652–654.

McGuire, G., Denham, M. C. and Balding, D. J. 2001. Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol. 18:481–490.

(p.338) McVean, G. A. and Charlesworth, D. J. 2000. The effects of Hill–Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155:929–944.

McVean, M., Awadalla, P. and Fearnhead, P. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231–1241.

Messier, W. and Stewart, C. -B. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151–154.

Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N. et al. 1953. Equations of state calculations by fast computing machines. J. Chem. Physi. 21:1087–1092.

Metz, E. C. and Palumbi, S. R. 1996. Positive selection and sequence arrangements generate extensive polymorphism in the gamete recognition protein bindin. Mol. Biol. Evol. 13: 397–406.

Metzler, D. 2003. Statistical alignment based on fragment insertion and deletion models. Bioinformatics 19:490–499.

Meyer, A., Kocher, T. D., Basasibwaki, P. and Wilson, A. C. 1990. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347: 550–553.

Mindell, D. P. 1996. Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees. Proc. Natl. Acad. Sci. U.S.A. 93:3284–3288.

Miyata, T. and Yasunaga, T. 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applications. J. Mol. Evol. 16:23–36.

Miyata, T., Miyazawa, S. and Yasunaga, T. 1979. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:219–236.

Moler, C. and Van Loan, C. F. 1978. Nineteen dubious ways to compute the exponential of a matrix. SIAM Review 20:801–836.

Mondragon-Palomino, M., Meyers, B. C., Michelmore, R. W. and Gaut, B. S. 2002. Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 12:1305–1315.

Mooers, A. Ø. and Schluter, D. 1999. Reconstructing ancestor states with maximum likelihood: support for one- and two-rate models. Syst. Biol. 48:623–633.

Moore, R. C. and Purugganan, M. D. 2003. The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. U.S.A. 100:15682–15687.

Moore, R. C. and Purugganan, M. D. 2005. The evolutionary dynamics of plant duplicate genes. Curr. Opin. Plant Biol. 8:122–128.

Morgan, G. J. 1998. Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock. J. Hist. Biol. 31:155–178.

Moriyama, E. N. and Powell, J. R. 1997. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45:378–391.

Mossel, E. and Vigoda, E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207–2209.

Mundy, N. I. and Cook, S. 2003. Positive selection during the diversification of class I vomeronasal receptor-like (V1RL) genes, putative pheromone receptor genes, in human and primate evolution. Mol. Biol. Evol. 20:1805–1810.

Murphy, W. J., Larkin, D. M., der Wind, A. E. -v. et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613–617.

(p.339) Muse, S. V. 1996. Estimating synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 13:105–114.

Muse, S. V. and Gaut, B. S. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715–724.

Muse, S. V. and Gaut, B. S. 1997. Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. Genetics 146:393–399.

Muse, S. V. and Weir, B. S. 1992. Testing for equality of evolutionary rates. Genetics 132: 269–276.

Nachman, M. W., Boyer, S. and Aquadro, C. F. 1996. Non-neutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice. Proc. Natl. Acad. Sci. U.S.A. 91:6364–6368.

Needleman, S. G. and Wunsch, C. D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443–453.

Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.

Nei, M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30:371–403.

Nei, M. and Gojobori, T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418–426.

Nei, M., Stephens, J. C. and Saitou, N. 1985. Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. Mol. Biol. Evol. 2:66–85.

Nielsen, R. 1997. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst. Biol. 46:346–353.

Nielsen, R. 2001a. Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations. Genetics 159:401–411.

Nielsen, R. 2001b. Statistical tests of selective neutrality in the age of genomics. Heredity 86:641–647.

Nielsen, R. and Wakeley, J. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885–896.

Nielsen, R. and Yang, Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936.

Nielsen, R., Bustamante, C., Clark, A. G. et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3:e170.

Nixon, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407–414.

Norris, J. R. 1997. Markov Chains. Cambridge University Press, Cambridge.

Nylander, J. A. A., Ronquist, F., Huelsenbeck, J. P. and Nieves-Aldrey, J. L. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53:47–67.

O’Hagan, A. and Forster, J. 2004. Kendall’s Advanced Theory of Statistics: Bayesian Inference. Arnold, London.

Ohno, S. 1970. Evolution by Gene Duplication. Springer-Verlag, New York.

Ohta, T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96–98.

Ohta, T. 1992. Theoretical study of near neutrality. II. Effect of subdivided population structure with local extinction and recolonization. Genetics 130:917–923.

Ohta, T. 1995. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 40:56–63.

(p.340) Ohta, T. 2002. Near-neutrality in evolution of genes and gene regulation. Proc. Natl. Acad. Sci. U.S.A. 99:16134–16137.

Ohta, T. and Gillespie, J. H. 1996. Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49:128–142.

Ohta, T. and Kimura, M. 1971. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1:18–25.

Ohta, T. and Tachida, H. 1990. Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. Genetics 126:219–229.

Olsen, G. J., Matsuda, H., Hagstrom, R. and Overbeek, R. 1994. fastDNAML: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood4. Comput. Appl. Biosci. 10:41–48.

Opazo, J. C., Palma, R. E., Melo, F. and Lessa, E. P. 2005. Adaptive evolution of the insulin gene in caviomorph rodents. Mol. Biol. Evol. 22:1290–1298.

Osawa, S. and Jukes, T. H. 1989. Codon reassignment (codon capture) in evolution. J. Mol. Evol. 28:271–278.

Ota, S. and Li, W. H. 2000. NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. Mol. Biol. Evol. 17:1401–1409.

Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B Biol. Sci. 255:37–45.

Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48:612–622.

Pagel, M. and Meade, A. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst. Biol. 53:571–581.

Pagel, M., Meade, A. and Barker, D. 2004. Bayesian estimation of ancestral character states on phylogenies. Syst. Biol. 53:673–684.

Palmer, C. A., Watts, R. A., Gregg, R. G. et al. 2005. Lineage-specific differences in evolutionary mode in a salamander courtship pheromone. Mol. Biol. Evol. 22:2243–2256.

Palumbi, S. R. 1994. Genetic divergence, reproductive isolation and marine speciation. Annu. Rev. Ecol. Syst. 25:547–572.

Pamilo, P. and Bianchi, N. O. 1993. Evolution of the Zfx and Zfy genes—rates and interdependence between the genes. Mol. Biol. Evol. 10:271–281.

Pamilo, P. and O’Neill, R. W. 1997. Evolution of Sry genes. Mol. Biol. Evol. 14:49–55.

Pauling, L. and Zuckerkandl, E. 1963. Chemical paleogenetics: molecular “restoration studies” of extinct forms of life. Acta Chem. Scand. 17:S9–S16.

Pechirra, P., Nunes, B., Coelho, A. et al. 2005. Molecular characterization of the HA gene of influenza type B viruses. J. Med. Virol. 77:541–549.

Penny, D. and Hendy, M. D. 1985. The use of tree comparison metrics. Syst. Zool. 34:75–82.

Perler, F., Efstratiadis, A., Lomedica, P. et al. 1980. The evolution of genes: the chicken preproinsulin gene. Cell 20:555–566.

Perna, N. T. and Kocher, T. D. 1995. Unequal base frequencies and the estimation of substitution rates. Mol. Biol. Evol. 12:359–361.

Pfister, P. and Rodriguez, I. 2005. Olfactory expression of a single and highly variable V1r pheromone receptor-like gene in fish species. Proc. Natl. Acad. Sci. U.S.A. 102:5489–5494.

Philippe, H., Zhou, Y., Brinkmann, H. et al. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 5:50.

Pickett, K. M. and Randle, C. P. 2005. Strange Bayes indeed: uniform topological priors imply non-uniform clade priors. Mol. Phylogenet. Evol. 34:203–211.

(p.341) Polley, S. D. and Conway, D. J. 2001. Strong diversifying selection on domains of the Plasmodium falciparum apical membrane antigen 1 gene. Genetics 158:1505–1512.

Posada, D. and Buckley, T. R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Informtaion Criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793–808.

Posada, D. and Crandall, K. A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818.

Posada, D. and Crandall, K. 2001. Simple (wrong) models for complex trees: a case from retroviridae. Mol. Biol. Evol. 18:271–275.

Prince, V. E. and Pickett, F. B. 2002. Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3:827–837.

Pupko, T., Pe’er, I., Shamir, R. and Graur, D. 2000. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol. 17:890–896.

Pupko, T., Pe’er, I., Hasegawa, M. et al. 2002a. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: application to the evolution of five gene families. Bioinformatics 18:1116–1123.

Pupko, T., Huchon, D., Cao, Y. et al. 2002b. Combining multiple data sets in a likelihood analysis: which models are the best? Mol. Biol. Evol. 19:2294–2307.

Raaum, R. L., Sterner, K. N., Noviello, C. M. et al. 2005. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J. Human Evol. 48:237–257.

Rambaut, A. 2000. Estimating the rate of molecular evolution: incorporating non-comptemporaneous sequences into maximum likelihood phylogenetics. Bioinformatics 16:395–399.

Rambaut, A. and Bromham, L. 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:442–448.

Rambaut, A. and Grassly, N. C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235–238.

Rand, D., Dorfsman, M. and Kann, L. 1994. Neutral and nonneutral evolution of Drosophila mitochondrial DNA. Genetics 138:741–756.

Rand, D. M., Weinreich, D. M. and Cezairliyan, B. O. 2000. Neutrality tests of conservative-radical amino acid changes in nuclear- and mitochondrially-encoded proteins. Gene 261:115–125.

Rannala, B. 2002. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Syst. Biol. 51:754–760.

Rannala, B. and Yang, Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304–311.

Rannala, B. and Yang, Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645–1656.

Rannala, B. and Yang, Z. 2006. Inferring speciation times under an episodic molecular clock in preparation.

Ranwez, V. and Gascuel, O. 2002. Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets. Mol. Biol. Evol. 19:1952–1963.

Redelings, B. D. and Suchard, M. A. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54:401–418.

Ren, F., Tanaka, T. and Yang, Z. 2005. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst. Biol. 54:808–818.

(p.342) Ripley, B. 1987. Stochastic Simulation. Wiley, New York.

Robbins, H. 1955. An empirical Bayes approach to statistics. Proc. 3rd Berkeley Symp. Math. Stat. Prob. 1:157–164.

Robbins, H. 1983. Some thoughts on empirical Bayes estimation. Ann. Statist. 1:713–723.

Robert, C. P. and Casella, G. 2004. Monte Carlo Statistical Methods. Springer-Verlag, New York.

Robinson, D. F. and Foulds, L. R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131–147.

Rodriguez, F., Oliver, J. F., Marin, A. and Medina, J. R. 1990. The general stochastic model of nucleotide substitutions. J. Theor. Biol. 142:485–501.

Rodriguez-Trelles, F., Tarrio, R. and Ayala, F. J. 2003. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc. Natl. Acad. Sci. U.S.A. 100:13413–13417.

Rogers, J. S. 1997. On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences. Syst. Biol. 46:354–357.

Rogers, J. S. and Swofford, D. L. 1998. A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst. Biol. 47:77–89.

Rogers, J. S. and Swofford, D. L. 1999. Multiple local maxima for likelihoods of phylogenetic trees: a simulation study. Mol. Biol. Evol. 16:1079–1085.

Rokas, A., Kruger, D. and Carroll, S. B. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933–1938.

Ronquist, F. 1998. Fast Fitch-parsimony algorithms for large data sets. Cladistics 14:387–400.

Ronquist, F. and Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574.

Rooney, A. P. and Zhang, J. 1999. Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Mol. Biol. Evol. 16:706–710.

Ross, R. 1997. Simulation. Academic Press, London.

Ross, S. 1996. Stochastic Processes. Springer-Verlag, New York.

Roth, C., Betts, M. J., Steffansson, P. et al. 2005. The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. Nucl. Acids Res. 33:D495–D497.

Rubin, D. B. and Schenker, N. 1986. Efficiently simulating the coverage properties of interval estimates. Appl. Statist. 35:159–167.

Russo, C. A., Takezaki, N. and Nei, M. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525–536.

Rzhetsky, A. and Nei, M. 1992. Asimple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945–967.

Rzhetsky, A. and Nei, M. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10:1073–1095.

Rzhetsky, A. and Nei, M. 1994. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J. Mol. Evol. 38:295–299.

Rzhetsky, A. and Sitnikova, T. 1996. When is it safe to use an oversimplified substitution model in tree-making? Mol. Biol. Evol. 13:1255–1265.

Saitou, N. 1988. Property and efficiency of the maximum likelihood method for molecular phylogeny. J. Mol. Evol. 27:261–273.

Saitou, N. and Imanishi, T. 1989. Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum likelihood, minimum evolution, and neighbor joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6:514–525.

(p.343) Saitou, N. and Nei, M. 1986. The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence. J. Mol. Evol. 24: 189–204.

Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.

Salter, L. A. 2001. Complexity of the likelihood surface for a large DNA dataset. Syst. Biol. 50: 970–978.

Salter, L. A. and Pearl, D. K. 2001. Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Syst. Biol. 50: 7–17.

Sanderson, M. J. 1997.Anonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14: 1218–1232.

Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19: 101–109.

Sanderson, M. J. and Kim, J. 2000. Parametric phylogenetics? Syst. Biol. 49: 817–829.

Sankoff, D. 1975. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28: 35–42.

Sarich, V. M. and Wilson, A. C. 1967. Rates of albumin evolution in primates. Proc. Natl. Acad. Sci. U.S.A. 58: 142–148.

Sarich, V. M. and Wilson, A. C. 1973. Generation time and genomic evolution in primates. Science 179: 1144–1147.

Savage, L. J. 1962. The Foundations of Statistical Inference. Metheun & Co., London.

Sawyer, K. R. 1984. Multiple hypothesis testing. J. R. Statist. Soc. B 46: 419–424.

Sawyer, S. A. and Hartl, D. L. 1992. Population genetics of polymorphism and divergence. Genetics 132: 1161–1176.

Sawyer, S. L.,Emerman M. and Malik, H. S. 2004. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2:E275.

Sawyer, S. L., Wu, L. I., Emerman, M. and Malik, H. S. 2005. Positive selection of primate TRIM5α identifies a critical species-specific retroviral restriction domain. Proc. Natl. Acad. Sci. U.S.A. 102: 2832–2837.

Scheffler, K.,Seoighe C. 2005.A Bayesian model comparison approach to inferring positive selection. Mol. Biol. Evol. 22:2531–2540.

Schluter, D. 1995. Uncertainty in ancient phylogenies. Nature 377: 108–110.

Schluter, D. 2000. The Ecology of Adaptive Radiation. Oxford University Press, Oxford.

Schmidt, H. A., Strimmer, K., Vingron, M. and von Haeseler, A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502–504.

Schoeniger, M. and von Haeseler, A. 1993. A simple method to improve the reliability of tree reconstructions. Mol. Biol. Evol. 10: 471–483.

Schott, J. R. 1997. Matrix Analysis for Statistics. Wiley, New York.

Schultz, T. R. and Churchill, G.A. 1999. The role of subjectivity in reconstructing ancestral character states: a Bayesian approach to unknown rates, states, and transformation asymmetries. Syst. Biol. 48: 651–664.

Schwarz, G. 1978. Estimating the dimension of a model. Ann. Statist. 6: 461–464.

Self, S. G. and Liang, K. -Y. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82: 605–610.

Shackelton, L. A., Parrish, C. R., Truyen, U. and Holmes, E. C. 2005. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc. Natl. Acad. Sci. U.S.A. 102: 379–384.

(p.344) Shapiro, B., Rambaut, A. and Drummond, A. J. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 23: 7–9.

Sharp, P. M. 1997. In search of molecular Darwinism. Nature 385: 111–112.

Shields, D. C., Harmon, D. L. and Whitehead, A. S. 1996. Evolution of hemopoietic ligands and their receptors: influence of positive selection on correlated replacements throughout ligand and receptor proteins. J. Immunol. 156: 1062–1070.

Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51: 492–508.

Shimodaira, H. and Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16: 1114–1116.

Shimodaira, H. and Hasegawa, M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246–1247.

Shindyalov, I. N., Kolchanov, N. A. and Sander, C. 1994. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7: 349–358.

Shriner, D., Nickle, D. C., Jensen, M. A. and Mullins, J. I. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81: 115–121.

Siddall, M. E. 1998. Success of parsimony in the four-taxon case: long branch repulsion by likelihood in the Farris zone. Cladistics 14: 209–220.

Silverman, B. W. 1986. Density Estimation for Statistics and Data Analysis. Chapman and Hall, London.

Simes, R. J. 1986. An improved Bonferroni procedure for multiple tests of significance. Biometrika 73: 751–754.

Simonsen, K. L., Churchill, G. A. and Aquadro, C. F. 1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141: 413–429.

Sitnikova, T., Rzhetsky, A. and Nei, M. 1995. Interior-branch and bootstrap tests of phylogenetic trees. Mol. Biol. Evol. 12: 319–333.

Slowinski, J. B. and Arbogast, B. S. 1999. Is the rate of molecular evolution inversely related to body size? Syst. Biol. 48: 396–399.

Smith, A. B. and Peterson, K. J. 2002. Dating the time of origin of major clades: molecular clocks and the fossil record. Ann. Rev. Earth Planet. Sci. 30: 65–88.

Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press, Cambridge, MA.

Sober, E. 2004. The contest between parsimony and likelihood. Syst. Biol. 53: 644–653.

Sokal, R. R. and Sneath, P. H. A. 1963. Numerical Taxonomy. W.H. Freeman and Co., San Francisco, CA.

Sourdis, J. and Nei, M. 1988. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol. Biol. Evol. 5: 298–311.

Spady, T. C., Seehausen, O., Loew, E. R. et al. 2005. Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Mol. Biol. Evol. 22: 1412–1422.

Spencer, M., Susko, E. and Roger, A. J. 2005. Likelihood, parsimony, and heterogeneous evolution. Mol. Biol. Evol. 22: 1161–1164.

Springer, M. S., Murphy, W. J., Eizirik, E. and O’Brien, S. J. 2003. Placental mammal diversification and the Cretaceous–Tertiary boundary. Proc. Natl. Acad. Sci. U.S.A. 100: 1056–1061.

Stackhouse, J., Presnell, S. R., McGeehan, G. M. et al. 1990. The ribonuclease from an ancient bovid ruminant. FEBS Lett. 262: 104–106.

(p.345) Steel, M. A. 1994a. The maximum likelihood point for a phylogenetic tree is not unique. Syst. Biol. 43:560–564.

Steel, M. A. 1994b. Recovering a tree from the leaf colourations it generates under a Markov model. Appl. Math. Lett. 7:19–24.

Steel, M. A. and Penny, D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839–850.

Stein, C. 1956. Inadmissibility of the usual estimator for the mean of a multivariate normal distribution. Proc. Third Berkeley Symp. Math. Stat. Prob. 1:197–206.

Stein, C. 1962. Confidence sets for the mean of a multivariate normal distribution. J. R. Statist. Soc. B. 24:265–296.

Steiper, M. E., Young, N. M. and Sukarna, T. Y. 2004. Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence. Proc. Natl. Acad. Sci. U.S.A. 101:17021–17026.

Stephens, M. and Donnelly, P. 2000. Inference in molecular population genetics (with discussions). J. R. Statist. Soc. B 62:605–655.

Stewart, C. -B., Schilling, J. W. and Wilson, A. C. 1987. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330:401–404.

Stotz, H. U., Bishop, J. G., Bergmann, C. W. et al. 2000. Identification of target amino acids that affect interactions of fungal polygalacturonases and their plant inhibitors. Mol. Physiol. Plant Pathol. 56:117–130.

Strimmer, K. and von Haeseler, A. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964–969.

Stuart, A., Ord, K. and Arnold, S. 1999. Kendall’s Advanced Theory of Statistics. Arnold, London.

Studier, J. A. and Keppler, K. J. 1988. A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol. 5:729–731.

Su, C., Nguyen, V. K. and Nei, M. 2002. Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in Camelids. Mol. Biol. Evol. 19:205–215.

Suchard, M. A., Weiss, R. E. and Sinsheimer, J. S. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001–1013.

Suchard, M. A., Kitchen, C. M., Sinsheimer, J. S. and Weiss, R. E. 2003. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol. 52:649–664.

Sullivan, J. and Swofford, D. L. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723–729.

Sullivan, J., Holsinger, K. E. and Simon, C. 1995. Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents. Mol. Biol. Evol. 12:988–1001.

Sullivan, J., Swofford, D. L. and Naylor, G. J. P. 1999. The effect of taxon-sampling on estimating rate heterogeneity parameters on maximum-likelihood models. Mol. Biol. Evol. 16:1347–1356.

Sutton, K. A. and Wilkinson, M. F. 1997. Rapid evolution of a homeodomain: evidence for positive selection. J. Mol. Evol.s 45:579–588.

Suzuki, Y. 2004. New methods for detecting positive selection at single amino acid sites. J. Mol. Evol. 59:11–19.

Suzuki, Y. and Gojobori, T. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315–1328.

Suzuki, Y., Glazko, G. V. and Nei, M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. U.S.A. 99:16138–16143.

(p.346) Swanson, W. J. and Vacquier, V. D. 2002a. The rapid evolution of reproductive proteins. Nature Rev. Genet. 3:137–144.

Swanson, W. J. and Vacquier, V. D. 2002b. Reproductive protein evolution. Ann. Rev. Ecol. Systemat. 33:161–179.

Swanson, W. J., Yang, Z., Wolfner, M. F. and Aquadro, C. F. 2001a. Positive Darwinian selection in the evolution of mammalian female reproductive proteins. Proc. Natl. Acad. Sci. U.S.A. 98:2509–2514.

Swanson, W. J., Clark, A. G., Waldrip-Dail, H. M. et al. 2001b. Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 98:7375–7379.

Swofford, D. L. 2000. PAUP*: Phylogenetic Analysis by Parsimony, Version 4. Sinauer Associates, Sunderland, MA.

Swofford, D. L., Waddell, P. J., Huelsenbeck, J. P. et al. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50: 525–539.

Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437–460.

Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595.

Tajima, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599–607.

Tajima, F. and Takezaki N. 1994. Estimation of evolutionary distance for reconstructing molecular phylogenetic trees. Mol. Biol. Evol. 11:278–286.

Tajima, F. and Nei, M. 1982. Biases of the estimates of DNA divergence obtained by the restriction enzyme technique. J. Mol. Evol. 18:115–120.

Takahata, N. 1986. An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced. Genet. Res. 48: 187–190.

Takahata, N., Satta, Y. and Klein, J. 1995. Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48:198–221.

Takezaki, N. and Gojobori, T. 1999. Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol. Biol. Evol. 16:590–601.

Takezaki, N. and Nei, M. 1994. Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant. J. Mol. Evol. 39:210–218.

Takezaki, N., Rzhetsky, A. and Nei, M. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823–833.

Tamura, K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition/transversion and G+C content biases. Mol. Biol. Evol. 9:678–687.

Tamura, K. and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512–526.

Tanaka, T. and Nei, M. 1989. Positive darwinian selection observed at the variable-region genes of immunoglobulins. Mol. Biol. Evol. 6:447–459.

Tateno, Y., Takezaki, N. and Nei, M. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261–277.

Tavaré, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17:57–86.

(p.347) Tavaré, S., Marshall, C. R., Will, O. et al. 2002. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416:726–729.

Templeton, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of man and the apes. Evolution 37:221–224.

Terai, Y., Mayer, W. E., Klein, J. et al. 2002. The effect of selection on a long wavelength-sensitive (LWS) opsin gene of Lake Victoria cichlid fishes. Proc. Natl. Acad. Sci. U.S.A. 99:15501–15506.

Thomas, J. H., Kelley, J. L., Robertson, H. M. et al. 2005. Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proc. Natl. Acad. Sci. U.S.A. 102:4476–4481.

Thomas, J. W., Touchman, J. W., Blakesley, R. W. et al. 2003. Comparative analyses of multispecies sequences from targeted genomic regions. Nature 424:788–793.

Thompson, E. A. 1975. Human Evolutionary Trees. Cambridge University Press, Cambridge.

Thompson, J. D., Higgins, D. G. and Gibson, T. J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673–4680.

Thorne, J. L. and Kishino, H. 1992. Freeing phylogenies from artifacts of alignment. Mol. Biol. Evol. 9:1148–1162.

Thorne, J. L. and Kishino, H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689–702.

Thorne, J. L. and Kishino, H. 2005. Estimation of divergence times from molecular sequence data. In Statistical Methods in Molecular Evolution. (ed. R. Nielsen), pp. 233–256. Springer-Verlag, New York.

Thorne, J. L., Kishino, H. and Felsenstein, J. 1991. An evolutionary model for maximum likelihood alignment of DNA sequences [erratum in J. Mol. Evol. 1992 34:91]. J. Mol. Evol. 33:114–124.

Thorne, J. L., Kishino, H. and Felsenstein, J. 1992. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34:3–16.

Thorne, J. L., Goldman, N. and Jones, D. T. 1996. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:666–673.

Thorne, J. L., Kishino, H. and Painter, I. S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647–1657.

Thornton, J. 2004. Resurrecting ancient genes: experimental analysis of extinct molecules. Nat. Rev. Genet. 5:366–375.

Thornton, J. W., Need, E. and Crews, D. 2003. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301:1714–1717.

Tillier, E. R. M. 1994. Maximum likelihood with multiparameter models of substitution. J. Mol. Evol. 39:409–417.

Ting, C. T., Tsaur, S. C., Wu, M. L. and Wu, C. I. 1998. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282:1501–1504.

Torgerson, D. G. and Singh, R. S. 2004. Rapid evolution through gene duplication and sub-functionalization of the testes-specific a4 proteasome subunits in Drosophila. Genetics 168:1421–1432.

Tsaur, S. C. and Wu, C. -I. 1997. Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aα of Drosophila. Mol. Biol. Evol. 14:544–549.

Tucker, A. 1995. Applied Combinatorics. Wiley, New York.

Tuff, P. and Darlu, P. 2000. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol. Biol. Evol. 17:1753–1759.

(p.348) Tuffley, C. and Steel, M. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59:581–607.

Tuffley, C. and Steel, M. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:63–91.

Twiddy, S. S., Woelk, C. H. and Holmes, E. C. 2002. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J. Gen. Virol. 83:1679–1689.

Tzeng, Y. H., Pan, R. and Li, W. H. 2004. Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 21: 2290–2298.

Ugalde, J. A., Chang, B. S. W. and Matz, M. V. 2004. Evolution of coral pigments recreated. Science 305:1433.

Vacquier, V. D., Swanson, W. J. and Lee, Y. -H. 1997. Positive Darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence? J. Mol. Evol. 44:S15–S22.

Vallender, E. J. and Lahn, B. T. 2004. Positive selection on the human genome. Hum. Mol. Genet. 13:R245–R254.

Vinh, Y. and von Haeseler, A. 2004. IQPNNI: Moving fast through tree space and stopping in time. Mol. Biol. Evol. 21:1565–1571.

Vuong, Q. H. 1989. Likelihood ratio tests for model selection and non-nested hypotheses. Econometrica 57:307–333.

Waddell, P. J. and Steel, M. A. 1997. General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. Mol. Phylogenet. Evol. 8:398–414.

Waddell, P. J., Penny, D. and Moore, T. 1997. Hadamard conjugations and modeling sequence evolution with unequal rates across sites [erratum in Mol. Phylogenet. Evol. 1997 8:446]. Mol. Phylogenet. Evol. 8:33–50.

Wakeley, J. 1994. Substitution-rate variation among sites and the estimation of transition bias. Mol. Biol. Evol 11:436–442.

Wald, A. 1949. Note on the consistency of the maximum likelihood estimate. Ann. Math. Statist. 20:595–601.

Walker, A. J. 1974. New fast method for generating discrete random numbers with arbitrary frequency distributions. Electron. Lett. 10:127–128.

Wallace, D. L. 1980. The Behrens-Fisher and Fieller-Creasy problems. In R.A. Fisher: An Appreciation (ed. S. Fienberg, J. Gani, J. Kiefer, and K. Krickeberg) pp. 119–147. Springer-Verlag, New York.

Walsh, J. B. 1995. How often do duplicated genes evolve new functions? Genetics 139: 421–428.

Wang, X. and Zhang, J. 2004. Rapid evolution of mammalian X-linked testis-expressed homeobox genes. Genetics 167:879–888.

Wang, Y. -Q. and Su, B. 2004. Molecular evolution of microcephalin, a gene determining human brain size. Hum. Mol. Genet. 13:1131–1137.

Ward, T. J., Honeycutt, R. L. and Derr, J. N. 1997. Nucleotide sequence evolution at the k-casein locus: evidence for positive selection within the family Bovidae. Genetics 147: 1863–1872.

Ward, T. J., Bielawski, J. P., Kistler, H. C. et al. 2002. Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium. Proc. Natl. Acad. Sci. U.S.A. 99:9278–9283.

(p.349) Waterston, R. H., Lindblad-Toh, K., Birney, E. et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562.

Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7:256–276.

Weerahandi, S. 1993. Generalized confidence intervals. J. Amer. Statist. Assoc. 88: 899–905.

Weerahandi, S. 2004. Generalized Inference in Repeated Measures: Exact Methods in MANOVA and Mixed Models. Wiley, New York.

Whelan, S. and Goldman, N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Mol. Biol. Evol. 18:691–699.

Whelan, S., Liò, P. and Goldman, N. 2001. Molecular phylogenetics: state of the art methods for looking into the past. Trends Genet. 17:262–272.

White, H. 1982. Maximum likelihood estimation of misspecified models. Econometrica 50: 1–25.

Wiley, E. O. 1981. Phylogenetics. The Theory and Practice of Phylogenetic Systematics. John Wiley & Sons, New York.

Wilkinson, M., Lapointe, F. -J. and Gower, D. J. 2003. Branch lengths and support. Syst. Biol. 52:127–130.

Willett, C. S. 2000. Evidence for directional selection acting on pheromone-binding proteins in the genus Choristoneura. Mol. Biol. Evol. 17:553–562.

Williamson, S. and Orive, M. E. 2002. The genealogy of a sequence subject to purifying selection at multiple sites. Mol. Biol. Evol. 19:1376–1384.

Wilson, A. C., Carlson, S. S. and White, T. J. 1977. Biochemical evolution. Ann. Rev. Biochem. 46:573–639.

Wilson, D. J. and McVean, G. 2006. Estimating diversifying selection and functional constraint in the presence of recombination. Genetics 172:1411–1425.

Wilson, I. J., Weal, M. E. and Balding, D. J. 2003. Inference from DNA data: population histories, evolutionary processes and forensic match probabilities. J. R. Statist. Soc. A 166:155–201.

Wong, W. S. W., Yang, Z., Goldman, N. and Nielsen, R. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041–1051.

Wray, G. A., Levinton, J. S. and Shapiro, L. H. 1996. Molecular evidence for deep Precambrian divergences. Science 274:568–573.

Wright, F. 1990. The ‘effective number of codons’ used in a gene. Gene 87:23–29.

Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97–159.

Wu, C. -I. and Li, W. -H. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. U.S.A. 82:1741–1745.

Wu, Q. 2005. Comparative genomics and diversifying selection of the clustered vertebrate protocadherin genes. Genetics 169:2179–2188.

Wyckoff, G. J., Wang, W. and Wu, C. -I. 2000. Rapid evolution of male reproductive genes in the descent of man. Nature 403:304–309.

Xia, X. and Xie, Z. 2001. DAMBE: Data analysis in molecular biology and evolution. J. Hered. 92:371–373.

Yamaguchi-Kabata, Y. and Gojobori, T. 2000. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J. Virol. 74:4335–4350.

(p.350) Yang, W., Bielawski, J. P. and Yang, Z. 2003. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57:57:212–221.

Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396–1401.

Yang, Z. 1994a. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306–314.

Yang, Z. 1994b. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39: 105–111.

Yang, Z. 1994c. Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst. Biol. 43:329–342.

Yang, Z. 1995a. A space-time process model for the evolution of DNA sequences. Genetics 139:993–1005.

Yang, Z. 1995b. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. J. Mol. Evol. 40:689–697.

Yang, Z. 1996a. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294–307.

Yang, Z. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587–596.

Yang, Z. 1996c. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367–372.

Yang, Z. 1997a. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555–556(http://abacus.gene.ucl.ac.uk/software/paml.html://abacus.gene.ucl.ac.uk/software/paml.html).

Yang, Z. 1997b. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14:105–108.

Yang, Z. 1998a. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568–573.

Yang, Z. 1998b. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47: 125–133.

Yang, Z. 2000a. Complexity of the simplest phylogenetic estimation problem. Proc. R. Soc. B Biol. Sci. 267:109–116.

Yang, Z. 2000b. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51:423–432.

Yang, Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics 162:1811–1823.

Yang, Z. 2004. A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zoologica Sinica 50:645–656.

Yang, Z. and Kumar, S. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13:650–659.

Yang, Z. and Nielsen, R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46:409–418.

Yang, Z. and Nielsen, R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32–43.

Yang, Z. and Nielsen, R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908–917.

Yang, Z. and Rannala, B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo Method. Mol. Biol. Evol. 14:717–724.

Yang, Z. and Rannala, B. 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54:455–470.

(p.351) Yang, Z. and Rannala, B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23: 212–226.

Yang, Z. and Roberts, D. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12: 451–458.

Yang, Z. and Swanson, W. J. 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19: 49–57.

Yang, Z. and Wang, T. 1995. Mixed model analysis of DNA sequence evolution. Biometrics 51: 552–561.

Yang, Z. and Yoder, A. D. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52: 705–716.

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

Yang, Z., Lauder, I. J. and Lin, H. J. 1995b. Molecular evolution of the hepatitis B virus genome. J. Mol. Evol. 41: 587–596.

Yang, Z., Goldman, N. and Friday, A. E. 1995c. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44: 384–399.

Yang, Z., Nielsen, R. and Hasegawa, M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15: 1600–1611.

Yang, Z., Nielsen, R., Goldman, N. and Pedersen, A. -M. K. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431–449.

Yang, Z., Wong, W. S. W. and Nielsen, R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22: 1107–1118.

Yoder, A. D. and Yang, Z. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17: 1081–1090.

Yokoyama, S. 2002. Molecular evolution of color vision in vertebrates. Gene 300: 69–78.

York, T. L., Durrett, R. and Nielsen, R. 2002. Bayesian estimation of the number of inversions in the history of two chromosomes. J. Comp. Biol. 9: 805–818.

Yu, N., Zhao, Z., Fu, Y. X. et al. 2001. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol. Biol. Evol. 18: 214–222.

Zakon, H. H., Lu, Y., Zwickl, D. J. and Hillis, D. M. 2006. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution. Proc. Natl. Acad. Sci. U.S.A. 103: 3675–3680.

Zanotto, P. M., Kallas, E. G., Souza, R. F. and Holmes, E. C. 1999. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153: 1077–1089.

Zardoya, R. and Meyer, A. 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13: 933–942.

Zhang, J. 2000. Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 50: 56–68.

Zhang, J. 2003. Evolution of the human ASPM gene, amajor determinant of brain size. Genetics 165: 2063–2070.

Zhang, J. 2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21: 1332–1339.

Zhang, J. and Nei, M. 1997. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J. Mol. Evol. 44: S139–146.

Zhang, J. and Nei, M. 2000. Positive selection in the evolution of mammalian interleukin-2 genes. Mol. Biol. Evol. 17:1413–1416.

(p.352) Zhang, J. and Webb, D. M. 2004. Rapid evolution of primate antiviral enzyme APOBEC3G. Hum. Mol. Genet. 13: 1785–1791.

Zhang, J., Kumar, S. and Nei, M. 1997. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol. Biol. Evol. 14: 1335–1338.

Zhang, J., Nielsen, R. and Yang, Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22: 2472–2479.

Zhang, J., Rosenberg, H. F. and Nei, M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. U.S.A. 95: 3708–3713.

Zhang, J., Zhang, Y. P. and Rosenberg, H. F. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30: 411–415.

Zhang, L., Gaut, B. S. and Vision, T. J. 2001. Gene duplication and evolution. Science 293: 1551.

Zhao, Z., Jin, L., Fu, Y. X. et al. 2000. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. U.S.A. 97: 11354–11358.

Zharkikh, A. 1994. Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol. 39: 315–329.

Zharkikh, A. and Li, W. -H. 1993. Inconsistency of the maximum parsimony method: the case of five taxa with a molecular clock. Syst. Biol. 42: 113–125.

Zharkikh, A. and Li, W. -H. 1995. Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4: 44–63.

Zhu, L. and Bustamante, C. D. 2005. A composite likelihood approach for detecting directional selection from DNA sequence data. Genetics 170: 1411–1421.

Zhu, S., Bosmans, F. and Tytgat, J. 2004. Adaptive evolution of scorpion sodium channel toxins. J. Mol. Evol. 58: 145–153.

Zuckerkandl, E. 1964. Further principles of chemical paleogenetics as applied to the evolution of hemoglobin. In Protides of the Biological Fluids(ed. H. Peeters). pp. 102–109. Elsevier, Amsterdam.

Zuckerkandl, E. and Pauling, L. 1962. Molecular disease, evolution, and genetic heterogeneity. In Horizons in Biochemistry (ed. M. Kasha, and B. Pullman), pp. 189–225. Academic Press, New York.

Zuckerkandl, E. and Pauling, L. 1965. Evolutionary divergence and convergence in proteins. In Evolving Genes and Proteins (ed. V. Bryson, and H. J. Vogel), pp. 97–166. Academic Press, New York.