Ziheng Yang's CV

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Academic degrees

Professional experience

Memberships

Service for Journals and Funding Agencies

Publications

Note 1 (Disclaimer): The listing of papers on this webpage is for my own use. Some of these files may be covered by publisher copyrights. Please ensure that your institution has the appropriate subscription before downloading.)

Note 2: Some typos are corrected in the pdf files.

Note 3: Total citations = 33k. H = 72 (1 September 2013, Google Scholar). My profile at Google Scholar

Note 4: Commonly used phrases in my papers.

2014

Yang, Z. 2014. Molecular Evolution: A Statistical Approach. Oxford University Press, Oxford, England. Book web site

Wang Y, Yang Z. 2014. Priors in Bayesian Phylogenetics, pp. in M-H C, L K, and P. L, eds. Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chapman & Hall/CRC, London.

Yang, Z., and B. Rannala. 2014. Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, in press. pdf

Zhang C, Rannala B, Yang Z. 2014. Bayesian species delimitation can be robust to guide tree inference errors. Systematic Biology in press. pdf

Angelis K, dos Reis M, Yang Z. 2014. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons. Molecular Biology and Evolution 31 (7): 1902-1913. pdf

dos Reis, M., T. Zhu, and Z. Yang. 2014. The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Systematic Biology 63(4): 555-565. pdf

dos Reis, M., M. J. Donoghue, and Z. Yang. 2014. Neither phylogenomic nor palaeontological data support a Paleogene origin of placental mammals. Biology Letters, 10: 20131003. pdf

Yoder, A. D., L. M. Chan, M. dos Reis, P. A. Larsen, C. R. Campbell, R. Rasolarison, M. Barrett, C. Roos, P. Kappeler, J. P. Bielawski, and Z. Yang. 2014. Molecular evolutionary characterization of a V1R subfamily unique to Strepsirrhine primates. Genome Biology and Evolution, 6: 213-227. pdf

Leaché AD, Harris RB, Rannala B, Yang Z. 2014. The influence of gene flow on species tree estimation: a simulation study. Systematic Biology 63:17-30. pdf

2013

Yang Z., and C.E. Rodríguez. 2013. Searching for efficient Markov chain Monte Carlo proposal kernels. Proceedings of the National Academy of Sciences of U.S.A. 110: 19307-19312. pdf and an extended version of the proof of equation (11)

Xu B, Yang Z. 2013. PamlX: A graphical user interface for PAML. Mol Biol Evol 30:2723-2724. pdf

Rannala B, Yang Z. 2013. Molecular clock dating. Pp. 68-74 in Losos JB, Baum DB, Futuyma DJ, Hoekstra HE, Lenski RE, Moore AJ, Peichel CL, Schluter D, and Whitlock MC, eds. The Princeton Guide to Evolution. Princeton University Press, New York.

dos Reis, M., and Z. Yang. 2013. Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics 195:195-204. pdf

Stadler T, Yang Z 2013. Dating phylogenies with sequentially sampled tips. Systematic Biology 62: 674-688. pdf

Zou X-H, Yang Z, Doyle JJ & Ge S. 2013. Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. New Phytologist 198: 1155-1164. pdf

Rannala, B, and Yang, Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics 194: 245-253. pdf

dos Reis, M., and Z. Yang. 2013. The unbearable uncertainty of Bayesian divergence time estimation. Journal of Systematics and Evolution 51:30-43. pdf

2012

Schabauer H, Valle M, Pacherz C, Stockingerx H, Stamatakis A, Robinson-Rechavi M, Yang Z, Salamin N. 2012. SlimCodeML: An optimized version of CodeML for the branch-site model. Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 2012 IEEE 26th International. IEEE. Pp. 700-708.

dos Reis M., Inoue J., Hasegawa M., Asher R., Donoghue P.C., Yang Z. 2012. Phylogenomic data sets provide both precision and accuracy in estimating the timescale of placental mammal evolution. Proc. R. Soc. Lond. B. Biol. Sci. 279: 3491-3500. pdf and Online Suppl. Mat.

Zhai W, Nielsen R, Goldman N, Yang Z. 2012. Looking for Darwin in genomic sequences - validity and success of statistical methods. Molecular Biology and Evolution 29: 2889-2893 pdf

Zhu T, Yang Z. 2012. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Molecular Biology and Evolution 29: 3131-3142 pdf

Zhang C, Rannala B, Yang Z. 2012. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Systematic Biology 61:779-784 pdf

Yang Z., Rannala B. 2012. Molecular phylogenetics: principles and practice. Nature Review Genetics 13: 303-314. pdf

Parham, J, Donoghue, P, Bell, C, Calway, T, Head, J, Holroyd, P, Inoue, J, Irmis, R, Joyce, W, Ksepka, D, Patane, J, Smith, N, Tarver, J, van Tuinen, M, Yang, Z, Angielczyk, K, Greenwood, J, Hipsley, C, Louis, J, Makovicky, P, Mueller, J, Smith, K, Theodor, J, Warnock, R and Benton, M, 2012. Systematic Biology 61: 346-359. pdf

Warnock, R.C.M., Z. Yang, and P.C.J. Donoghue. 2012. Exploring uncertainty in the calibration of the molecular clock. 8: 156-159. pdf

Rannala B., Zhu T., Yang Z. 2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Molecular Biology and Evolution 29: 325-335 pdf

2011

Zhang C., Zhang D.-X., Yang Z. 2011. Evaluation of a Bayesian coalescent method of species delimitation. Systematic Biology 60, 747-761 pdf

Brown RP, Yang Z. 2011. Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evolutionary Biology 11:271 pdf

Zang, L.-L., X.-H. Zou, F.-M. Zhang, Z. Yang, S. Ge, 2011 Phylogeny and species delimitation of the C-genome diploid species in Oryza. Journal of Systematics and Evolution 49: 386-395. pdf

Groussin M., Pawlowski J., Yang Z. 2011. Bayesian relaxed clock estimation of divergence times in Foraminifera. Molecular Phylogenetics and Evolution, 61: 157-166. pdf

Yoshida I, Sugiura W, Shibata J, Ren F, Yang Z, Tanaka H. 2011. Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLOS One 6:e18630. pdf

dos Reis M, Yang Z. 2011. Approximate likelihood calculation for Bayesian estimation of divergence times. Molecular Biology and Evolution 28:2161-2172. pdf

Zhu, T., Y. Hu, Z. Ma, D.-X. Zhang, T. Li, and Z. Yang. 2011. Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics 27:837-843. pdf

Yang Z., dos Reis M. 2011. Statistical properties of the branch-site test of positive selection. Molecular Biology and Evolution, 28: 1217-1228. pdf

Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang Z, Tavare S. 2011. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Systematic Biology 60:16-31. pdf

2010

Yang Z. 2010. Review of The Timetree of Life (Edited by S. Blair Hedges & Sudhir Kumar). Quart. Rev. Biol. 85:360-361. pdf

Chen M.-S., X. Liu, Z. Yang, H. Zhao, R. Shukle, J. Stuart, S. Hulbert. 2010. Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC Evolutionary Biology 10:296. abstract pdf

Fletcher W. and Z. Yang. 2010. The effect of insertions, deletions and alignment errors on the branch-site test of positive selection. Molecular Biology and Evolution 27: 2257-2267. abstract pdf

Yang Z. and B. Rannala. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of U.S.A. 107:9264-9269 abstract pdf

Yang Z. 2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biology and Evolution 2: 200-211. abstract pdf

Beaumont, M., R. Nielsen, C. Robert, J. Hey, O. Gaggiotti, L. Knowles, A. Estoup, M. Panchal, J. Corander, M. Hickerson, S. Sisson, N. Fagundes, L. Chikhi, P. Beerli, R. Vitalis, J.-M. Cornuet, J. Huelsenbeck, J. Novembre, M. Foll, Z. Yang, F. Rousset, D. Balding And L. Excoffier. 2010. In defence of model-based inference in phylogeography. Molecular Ecology 19: 436-446. abstract pdf

Brown R.P. and Z. Yang. 2010. Bayesian dating of shallow phylogenies with a relaxed clock. Systematic Biology 59:119-131. abstract pdf

Inoue, J., P. C. H. Donoghue, and Z. Yang. 2010. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology 59: 74-89. abstract pdf

2009

Yang Z, Nielsen R, Goldman N. 2009. In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA 106:E95-E95. pdf

Fletcher W. and Z. Yang. 2009. INDELible: A flexible simulator of biological sequence evolution. Molecular Biology and Evolution 26: 1879-1888. abstract pdf

Ren F, Tanaka H, Yang Z. 2009. A likelihood look at the supermatrix-supertree controversy. Gene 441:119-125. pdf

Rota-Stabelli, O., Z. Yang, and M. Telford. 2009. MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol. Phyl. Evol. 52:268-272. pdf

2008

Schmid, K.J. and Z. Yang. 2008. The trouble with sliding windows. PLoS One, 3: e3746. pdf

Goldman, N. and Z. Yang. 2008. Statistical and computational challenges in molecular phylogenetics and evolution, Introduction. Philosophical Transations of the Royal Society of London B: Biological Sciences 363: 3889-3892. pdf

Yang, Z. 2008 Empirical evaluation of a prior for Bayesian phylogenetic inference. Philosophical Transaction of the Royal Society of London B: Biological Sciences 363: 4031-4039. pdf

Vamathevan, J, S. Hasan, R. Emes, H. Amrine-Madsen, D. Rajagopalan, S. Topp, V. Kumar, M. Word, M. Simmons, S. Foord, P. Sanseau, Z. Yang, and J. Holbrook. 2008. The role of positive selection in determining the molecular cause of species differences in disease. BMC Evolutionary Biology 8: 273. pdf

Burgess, R. and Z. Yang. 2008 Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution 25: 1979-1994. abstract pdf

Rannala B, and Z. Yang. 2008. Phylogenetic inference using whole genomes. Annual Review of Genomics and Human Genetics 9: 217-231 pdf

Emes, R. D. and Z. Yang. 2008 Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS One 3: e2295. pdf

Furlong, R. F., and Z. Yang. 2008. Diversifying and purifying selection in the peptide binding region of DRB in mammals. Journal of Molecular Evolution 66: 384-394. pdf

Yang Z, and R. Nielsen. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular Biology and Evolution 25: 568-579. abstract pdf

2007

Zhou R., K. Zeng, W. Wu, X. Chen, Z. Yang, S. Shi, C.-I. Wu. 2007. Population genetics of speciation in nonmodel organisms: I. ancestral polymorphism in mangroves. Molecular Biology and Evolution 24:2746-2754. abstract pdf

Anisimova, M., J.P. Bielawski, K. Dunn, and Z. Yang. 2007. Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evolutionary Biology 7:154. pdf

Yang, Z. 2007. Fair-balance paradox, star-tree paradox and Bayesian phylogenetics. Molecular Biology and Evolution 24: 1639-1655. abstract pdf

Yang, Z. 2007. PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution 24: 1586-1591. abstract pdf

Rannala B, Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Systematic Biology, 56: 453-466 abstract pdf

Anisimova, M., and Z. Yang. 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Molecular Biology and Evolution 24: 1219-1228. abstract pdf

Hurley, I.A., R.L. Mueller, K.A. Dunn, E.J. Schmidt, M. Friedman, R.K. Ho, V.E. Prince, Z. Yang, M.G. Thomas, M.I. Coates, 2007. A new time-scale for ray-finned fish evolution. Proc. R. Soc. Lond. B. Biol. Sci. 274: 489-498. pdf and Online Suppl. Mat.

Yang, Z. 2007. Adaptive molecular evolution, Chapter 12 in Handbook of statistical genetics, 2nd Edition, eds. by D. Balding, M. Bishop, and C. Cannings. Wiley, New York.

2006

Yang, Z. 2006. Computational Molecular Evolution. Oxford University Press, Oxford, England. Book web site

Yang Z. 2006. On the varied pattern of evolution of two fungal genomes: a critique of Hughes and Friedman. Molecular Biology and Evolution 23:2279-2282. abstract pdf

Ren, F., A. Tsubota, T. Hirokawa, H. Kumada, Z. Yang, H. Tanaka. 2006. A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. Gene 383: 43-51. pdf

Aguileta, G., J. P. Bielawski, Z. Yang. 2006. Proposed standard nomenclature for the a- and b-globin gene families. Genes and Genetic Systems. 81:367-371. pdf

Aguileta, G., J. P. Bielawski, and Z. Yang. 2006. Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene 380: 21-29. pdf

Yang, Z., and B. Rannala. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution 23:212-226. abstract pdf

2005

Ren, F., H. Tanaka, and Z. Yang. 2005. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Systematic Biology 54: 808-818. abstract pdf

Zhang, J., R. Nielsen, and Z. Yang. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution 22:2472-2479. abstract pdf

Bielawski, J. P., and Z. Yang. 2005. Maximum likelihood methods for detecting adaptive protein evolution, in (R. Nielsen ed.) Statistical Methods in Molecular Evolution, Springer-Verlag, New York. Book at Springer

Yang, Z., and B. Rannala. 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology 54: 455-470. abstract pdf

Sainudiin, R., W.S.W. Wong, K. Yogeeswaran, J. Nasrallah, Z. Yang, and R. Nielsen. 2005. Detecting site-specific physicochemical selective pressures: applications to the class-I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. Journal of Molecular Evolution 60: 315-326. pdf

Yang, Z., W.S.W. Wong, and R. Nielsen. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution 22: 1107-1118. abstract pdf

Yang, Z. 2005. The power of phylogenetic comparison in revealing protein function. Proceedings of the National Academy of Sciences of U.S.A. 102:3179-3180. pdf

Yang, Z. 2005. Bayesian inference in molecular phylogenetics. Pp. 63-90 in O. Gascuel, ed. Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford. poor-quality pdf (9.5MB) and Book at OUP

2004

Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. 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. pdf

Anisimova, A. and Z. Yang. 2004. Molecular evolution of hepatitis delta virus antigen gene: recombination or positive selection? Journal of Molecular Evolution, 59: 815-826 pdf (alignment is at the EMBL nucleotide sequence database - accession number ALIGN_000712)

Aguileta, G., J. P. Bielawski and Z. Yang. 2004. Gene conversion and functional divergence in the ß-globin gene family. Journal of Molecular Evolution, 59:177-189. pdf.

Yang, Z. 2004. A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zoologica Sinica 50:645-656. (in English with a Chinese abstract) pdf

Yoder, A.D., and Z. Yang. 2004. Divergence dates for Malagasy lemurs estimated from multiple gene loci: fit with climatological events and speciation models. Molecular Ecology 13:757-773. pdf

Schein, M., Z. Yang, T. Mitchell-Olds, and K. J. Schmid. 2004. Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thalianaand closely related species. Molecular Biology and Evolution 21:659-669. pdf

Yang, J., H. Gu and Z. Yang. 2004. Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in the morning glories (Ipomoea). Journal of Molecular Evolution 58:54-63. pdf

Bielawski, J. P., and Z. Yang. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution 59:121-13. pdf

Yang, Z. 2004. A probabilist's account of modern molecular population genetics, Review of Probability Models for DNA Sequence Evolution (by Rick Durrett. Springer-Verlag, New York, 2002). Heredity, 92: 474. pdf

2003

Aris-Brosou, S., and Z. Yang. 2003. Bayesian models of episodic evolution support a late pre-cambrian explosive diversification of the Metazoa. Molecular Biology and Evolution 20: 1947-1954. pdf

Furlong, R. F., and Z. Yang. 2003. Comparative genomics coming of age. Heredity 91: 533-534. pdf

Yang, Z. 2003. Phylogenetics as applied mathematics. Review of Phylogenetics (by Charles Semple and Mike Steel. Oxford University Press, 2003). Trends in Ecology and Evolution 18:558-559. pdf

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

Yang, W., J. P. Bielawski and Z. Yang. 2003. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. Journal of Molecular Evolution. 57:212-221. pdf and Data (HIVdata.YBY.tar2003.gz)

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. Systematic Biology 52:705-716. pdf (Data files for the ML analysis are included in the paml release in the examples/MouseLemurs/ folder. Data files for the Bayesian analysis are in the T3 distribution in the MouseLemurs/ folder.)

Rannala, B. and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656. pdf (The pdf file has a page glued at the end giving a detailed derivation of the Hastings ratio of the rubber-band algorithm described in the Appendix.) (Data files are included in the MCMCcoal program)

Nielsen, R., and Z. Yang. 2003. Estimating the distribution of selection coefficients from phylogenetic data with applications to mtDNA. Molecular Biology and Evolution 20:1231-1239. pdf

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

Yang, Z., Stephens, D., Dawson, K. J., Drummond, A., Nicholls, G., Griffiths, R. C., Wilkinson-Herbots, H. M., Beaumont, M. A., Baird, S. J. E., Lascoux, M., Leblois, R., Estoup, A., Nielsen, R., Hey, J., Stumpf, M. P. H. & Wilkinson-Herbots, H. M. 2003. Inference from DNA data: population histories, evolutionary processes and forensic match probabilities: Discussion, Journal of Royal Statistical Society A. 166: 188-201. pdf

Bielawski, J. P., and Z. Yang. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of Structural and Functional Genomics 3:201-212. pdf

Bielawski, J. P., and Z. Yang. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. Pp. 201-212 in A. Meyer, and Y. Van De Peer (eds.). Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions. Kluwer Academic Publishers, Dordrecht. pdf (This is the same as the journal paper above.)

Yang, Z. 2003. Adaptive molecular evolution, Chapter 9 (pp. 229-254) in Handbook of statistical genetics, 2nd Edition, eds. by D. Balding, M. Bishop, and C. Cannings. Wiley, New York.

2002

Yang, Z. 2002 Inference of selection from multiple species alignments. Current Opinion in Genetics and Development 12: 688-694. pdf

Yang, J., J. Huang, H. Gu, Y. Zhong and Z. Yang. 2002. Duplication and adaptive evolution of chalcone synthase genes in the genus Dendranthema (Asteraceae). Molecular Biology and Evolution 19: 1752-1759. pdf

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

Yang, Z., 2002 Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics 162: 1811-1823. pdf (The Bayes MCMC method described in this paper is superseded by the Rannala & Yang 2003 algorithm, which is implemented in the MCMCcoal program. The ML program, Ne3sML, is available in the MCMCcoal release as well; it uses Mathematica.)

Jiggins, F.M., G.D.D. Hurst, and Z. Yang. 2002. Host-symbiont conflicts: positive selection on the outer membrane protein of parasite but not mutualistic Rickettsiaceae. Molecular Biology and Evolution 19: 1341-1349. pdf

Anisimova, M., J. P. Bielawski and Z. Yang. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Molecular Biology and Evolution 19: 950-958. pdf

Yang, Z., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19: 908-917. pdf

Yang, Z. 2002. Molecular clock. M. Pagel (eds). Oxford Encyclopedia of Evolution. Oxford University Press, Oxford. pp.747-750. pdf and Books at OUP (2 volumes)

Yang, Z., and W. J. Swanson. 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Molecular Biology and Evolution 19:49-57. pdf (Both the lysin and the MHC datasets are included in the paml release. Look at the folder examples/)

Clote, P., G.J.P. Naylor, and Z. Yang. 2002. Proteins: structure, function and evolution. Pacific Symposium on BioComputing 2002 pp. 548-551. pdf

2001

Jiggins, C.D., M. Linares, R.E. Naisbit, C. Salazar, Z. Yang, J. Mallet. 2001. Sex-linked hybrid sterility in a butterfly. Evolution. 55:1631-1638. pdf

Anisimova, M., J. P. Bielawski and Z. Yang. 2001. The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Molecular Biology and Evolution 18: 1585-1592. pdf

Bielawski, J.P. and Z. Yang. 2001. Positive and negative selection in the DAZ gene family. Molecular Biology and Evolution 18: 523-529. pdf

Swanson, W. J., Z. Yang, M. F. Wolfner and C. F. Aquadro. 2001. Positive Darwinian selection in the evolution of mammalian female reproductive proteins. Proceedings of the National Academy of Sciences of U.S.A. 98:2509-2514. (featured in New York Times 27 February 2001) pdf

Dunn, K. A., J. P. Bielawski and Z. Yang. 2001. Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 157: 317-330. pdf

Yang, Z. 2001. Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pacific Symposium on BioComputing 2001 pages 226-237. pdf

Yang, Z. 2001. Adaptive molecular evolution, in Handbook of statistical genetics, eds. D. Balding, M. Bishop, and C. Cannings. Chapter 12, pp. 327-350, Wiley, London. pdf

2000

Thomas, M. G., E. Hagelberg, H. B. Jones, Z. Yang, and A. Lister. 2000. Mammoths, molecules and morphology. Proceedings of Royal Society of London B: Biological Sciences 267:2493-2500. pdf

Yang, Z. 2000. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. Journal of Molecular Evolution 51: 423-432. pdf Alignment, and tree

Yang, Z., and B. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution 15: 496-503. pdf

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

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

Yoder, A. D., and Z. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution 17: 1081-1090. pdf (The local clock models here are superseded by the Yang & Yoder 2003 cute-looking paper.)

Yang, Z., R. Nielsen, N. Goldman, A.-M. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449. pdf
(Quite a few example data sets are included in the paml release to demonstrate methods implemented in this paper; look at the readme files in the folders lysin, lysozyme, HIVNSsites. Also the paper says on page 448 that the data and list of sites will be posted at an ftp site. The ftp site is now dead, but the files are in the archive here; save it into file name YNGP2000.tar.gz)

Holbrook, J. D., G. M. Birdsey, Z. Yang, M. W. Bruford, and C. J. Danpure. 2000. Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates. Molecular Biology and Evolution 17: 387-400. pdf

Yang, Z. 2000. Complexity of the simplest phylogenetic estimation problem. Proceedings of the Royal Society B: Biological Sciences 267: 109-116. pdf

Yang, Z. 2000. Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites. Pacific Symposium on Computational Biology 2000: 81-92. pdf

Yang, Z., and R. Nielsen. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 17: 32-43. pdf (This method is implemented in the yn00 program in paml.)

1999

Excoffier, L., and Z. Yang. 1999. Substitution rate variation among sites in the mitochondrial hypervariable region I of humans and chimpanzees. Molecular Biology and Evolution 16: 1357-1368. pdf

Yang, Z., and A. Yoder. 1999. Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution 48: 274-283. pdf

1998

Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Systematic Biology 47:702-709. pdf

Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution 15:1600-1611. pdf (Example data set included in the paml release in the examples/mtCDNA/ folder.)

Hasegawa, M., Y. Cao, and Z. Yang. 1998. Preponderance of slightly deleterious polymorphism in mitochondrial DNA: replacement/synonymous rate ratio is much higher within species than between species. Molecular Biology and Evolution 15:1499-1505. pdf

Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15: 568-573. pdf (Example data are included in the paml release in the folder examples/lysozyme/.)

Yang, Z. 1998. On the best evolutionary rate for phylogenetic analysis. Systematic Biology 47:125-133. pdf

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

Yang, Z., and R. Nielsen. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution, 46: 409-418. pdf

1997

Yang, Z. 1997. PAML: a program for package for phylogenetic analysis by maximum likelihood. CABIOS 15: 555-556. (http://abacus.gene.ucl.ac.uk/software/paml.html). pdf

Yang, Z. and N. Goldman 1997. Are big trees indeed easy? Trends in Ecology and Evolution 12:357. pdf

Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Molecular Biology and Evolution, 14:717-724. pdf

Yang, Z. 1997. On the estimation of ancestral population sizes of modern humans. Genetical Research Cambridge, 69:111-116. pdf

Huelsenbeck, J. P., B. Rannala, and Z. Yang. 1997. Satistical tests of host- parasite coevolution. Evolution 51:410-419. pdf

Yang, Z. 1997. How often do wrong models produce better phylogenies? Molecular Biology and Evolution 14:105-108. pdf

1996

Yang, Z. 1996. Statistical properties of a DNA sample under the finite-sites model. Genetics 144:1941-1950. pdf

Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43: 304-311. pdf

Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11:367-372. pdf

Yang, Z. 1996. Maximum likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution 42:587-596. pdf

Yang, Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. Journal of Molecular Evolution 42:294-307. pdf

Yang, Z., and S. Kumar. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Molecular Biology and Evolution 13:650-659. pdf (Implemented in the pamp program in the paml package.)

1995

Yang, Z., S. Kumar, and M. Nei. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650. pdf (Example data file included in the paml release as stewart.aa.)

Yang, Z., N. Goldman, and A. E. Friday. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Systematic Biology 44:384-399. pdf

Yang, Z., and D. Roberts. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Molecular Biology and Evolution 12:451-458. pdf

Yang, Z., I. J. Lauder, and H. J. Lin. 1995. Molecular evolution of the hepatitis B virus genome. Journal of Molecular Evolution 41:587-596. pdf

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

Yang, Z. 1995. On the general reversible Markov-process model of nucleotide substitution: a reply to Saccone et al. Journal of Molecular Evolution 41:254-255. pdf

Yang, Z. 1995. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. Journal of Molecular Evolution 40:689-697. pdf

Yang, Z. 1995. A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005. pdf (This describes the auto-discrete-gamma models.)

1994

Yang, Z. 1994. Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Systematic Biology 43:329-342. pdf

Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306-314. pdf (This is the discrete-gamma paper.)

Goldman, N., and Z. Yang. 1994. Models of DNA substitution and the discrimination of evolutionary parameters. In Proceedings of the XVIIth International Biometrics Conference, Vol. I: Invited Papers. International Biometrics Society, Hamilton, Ontario, Canada, pp. 407-420. pdf

Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11:725-736. pdf

Yang, Z., N. Goldman, and A. E. Friday. 1994. Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Molecular Biology and Evolution 11:316-324. pdf

Yang, Z. 1994. Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution 39:105-111. pdf

Yang, Z., and N. Goldman. 1994. Evaluation and extension of Markov process models for the evolution of DNA. Acta Genetica Sinica 21:17-23. (in Chinese with an English abstract) pdf

1993

Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 10:1396-1401. pdf (The continuous gamma model is implemented in the basemlg program in the paml release, not used often due to heavy computation involved.)