中国培养：首位当选英皇家科学院士的华人

　　

生物通综合： 来自中国驻英国大使馆的消息，6月20日中国华人学者杨子恒教授当选为2006年度英国皇家科学院院士，成为世界历史上，第一次中国培养的博士，在世界级科学院获得院士级称号。

成立于1660年的英国皇家科学院是世界上历史最悠久、最著名的学术团体之一，目前有1400多位院士，其中包括60多位诺贝尔奖得主，也拥有像牛顿、法拉第、麦克斯韦等这样科学巨擎。

我国优秀留英学者、伦敦大学教授杨子恒当选皇家学会有史以来第一位中国大陆出身的会员。以前香港人以英国庶民身份，曾经有人当选过皇家学会会员，但是从来没有中国大陆的人当选。杨子恒的博士也不是国外拿的，而是中国农业大学的硕士和博士，而且他一辈子没有在《自然》、《科学》、《细胞》等顶级杂志上发过一篇论文。在此次大使馆庆祝活动上，中国驻英大使查培新表示，杨子恒的当选，是所有旅英华人学者的骄傲，是中国科技工作者的骄傲，也是所有中国人的骄傲。中国教育部副部长章新胜代表教育部发来贺电，向杨子恒表示祝贺。

附：

杨子恒教授1964年出生于甘肃，1984年毕业于甘肃农业大学畜牧系，同年考入中国农大畜牧系动物遗传育种专业，在著名数量遗传学家吴仲贤教授指导下攻读硕士学位，其后又在吴常信院士指导下攻读博士学位。1992年在中国农大获得农学博士学位后留校任教，其间在英国、美国进行合作研究。1998年到英国伦敦大学学院任讲师，因业绩突出在2001年晋升为教授。

主要从事分子进化、分子系统学、以及群体遗传学等方面的研究工作，在动植物种类史DNA分析方法和蛋白质顺序构成研究方面取得突出成绩。他同其他专家一道开发了数理统计模式和计算机运算法则，应用这些模式重建物种发展史和理解进化过程的机制，通过研究DNA和蛋白质序列的进化比较，对于人们重新构建物种发展的历史以及理解分子进化的机制将产生重要影响。
目前他的研究主要包括物种发展和发散性的贝叶斯估计，遗传学密码子替换和可适应的分子进化探索的马尔可夫算法，群体遗传学合并模式下的马尔可夫系列算法，以及滤过性毒菌和哺乳动物的染色体组的对比分析。

Academic degrees
1992: Ph.D., Beijing Agricultural University, China
1987: M.Sc., Beijing Agricultural University, China
1984: B.Sc., Gansu Agricultural University, China
Professional experience
Professor of Statistical Genetics (2001-present), Reader of Evolutionary Genetics (2000-2001), Lecturer (1997-2000) at Department of Biology (Galton Laboratory), University College London
1995-1997: Research fellow at Department of Integrative Biology, University of California at Berkeley .
1994-1995: Research fellow at Institute of Molecular Evolutionary Genetics, Pennsylvania State University .
1992-1994: Research fellow at Departments of Zoology, University of Cambridge and Department of Zoology, The Natural History Museum (London).
1992-1997: Lecturer of genetics at Department of Animal Science, Beijing Agricultural University.
1987-1989: Teacher of biostatistics and genetics at Department of Animal Science, Gansu Agricultural University.

Service for Journals and Funding Agencies
Associate Editor of Genetics, since 2003.
Associate Editor of Systematic Biology, 2001-2004.
Associate Editor of Journal of Molecular Evolution, 1998-2002.
Referee for
Annals of Human Genetics, BBSRC, Bioinxxxxatics, Biological Reviews, Computer Application in BioSciences, Current Biology, Genetical Research, Genetics, Genome Research, Genomics, Joint Infrastructure Funds (JIF), Journal of Molecular Evolution, Journal of Theoretical Biology, Mathematical BioSciences, Molecular Biology and Evolution, Molecular Phylogenetics and Evolution, National Science Foundation (USA), Nature, NERC, Proceedings of National Academy of Sciences of USA, Proceedings of the Royal Society Series B, Systematic Biology, Trends in Genetics, Trends in Ecology and Evolution, Wellcome Trust Foundation.
Publications
2005

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

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

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

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. Mol. Biol. Evol. 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 (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. (This is not very different from the chapter in the 1st Edition [2001] of the book, for which the pdf file is provided.) Books at Wiley (2 volumes)

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 (The lysin data set is included in the paml release in the folder examples/lysin/. The MHC data are here: bigmhc.phy, bigmhc.trees, codeml.bigmhc.ctl)

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. xxxxuation 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. xxxxuation 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.)