Y

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

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

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

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

Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 15:555-556.

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

Yang, Z. 2001. Adaptive molecular evolution, Chapter 12 (pp. 327-350) in Handbook of Statistical Genetics, eds. D. Balding, M. Bishop, and C. Cannings. Wiley, New York.

Yang, Z. 2002a. Inference of selection from multiple species alignments. Curr. Opinion Genet. Devel. 12:688-694.

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

Yang, Z. and J. P. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15:496-503.

Yang, Z. and S. Kumar. 1996. New parsimony-based methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites and comparison with likelihood methods. Mol. Biol. Evol. 13:650-659. PAML

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

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

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

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

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

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

Yang, Z. and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.

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

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Yang, Z., Swanson, W. J., and Vacquier, V. D. 2000. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Mol. Biol. Evol. 17: 1446-1455.

Yang, Z. and A. D. Yoder. 1999. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 48:274-283.

Yang Z, Ro S, Rannala B. 2003. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics. 165(2):695-705

Yang, Z. and A. D. Yoder. 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. Bio. 52(5):705-716.

Yang Z, Wong WS, Nielsen R. 2005. Bayes Empirical Bayes Inference of Amino Acid Sites under Positive Selection. Mol Biol Evol.

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Yoder, A. D., J. A.Irwin and B. A. Payseur. 2001. Failure of ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50:408-424.

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Yoder, J. A. Irwin, S. M. Goodman and S. V. Rakotoarisoa. 2000. Genetic tests of the taxonomic status of the ring-tailed lemur (Lemur catta) from the high mountain zone of the Andringitra Massif, Madagascar. J. of Zoology, London. 252:1-9.

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Yoder, A. D., Burns M. M., Zehr, S., Delefosse, T., Veron, G., Goodman, S. M., Flynn, J. J. 2003. Single origin of Malagasy Carnivora from an African ancestor. Nature. 421:734-737.

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Yokoyama, S. 2000. Molecular evolution of vertebrates visual pigments. Progress in Retinal and Eye Res. 19:385-419.

Yokoyama, S. (2002) Evaluating adaptive evolution (News & Views). Nature Genetics 30: 350-351.

Yokoyama, S., and F. B. Radlwimmer. 1999. The molecular genetics of red and green color vision in mammals. Genetics 153:919-932.

Yokoyama, S., F. B. Radlwimmer and N. S. Blow. 2000. Ultraviolet pigments in birds evolved from violet pigments by a single amino acid change. Proc. Natl. Acad. Sci. USA 97:7366-7371.

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Yokoyama, S. and Y. Shi. 2000. Genetics and evolution of ultraviolet vision in vertebrates. FEBS Lett. 486:167-172.

Yokoyama, S. and Takenaka, N. 2004. The molecular basis of rhodopsin evolution of squirrelfish and soldierfish (Holocentridae). Mol. Biol. Evol. 21: 2071-2078.

Yokoyama, S. and Takenaka, N. 2005. Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates. Mol. Biol. Evol. 22: 968-975.

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