Note 2: Some typos are corrected in the pdf files.
Note 3: Total citations = 81k. H = 104 (Google Scholar, September 2023). Profile at Google Scholar
Note 4: My wordcloud.
Books
Yang, Z. 2006. Computational Molecular Evolution. Oxford University Press, Oxford, England (ISBN: 978-0-19-856702-8). Book web siteYang, Z. 2014. Molecular Evolution: A Statistical Approach. Oxford University Press, Oxford, England (ISBN: 978-0-19-960261-2). Book web site
2024
Rannala B, Yang Z. 2025. Reading tree leaves: Inferring speciation and extinction processes using phylogenies. Phil Trans R Soc Lond: in press.Kornai D, Jiao X, Ji, Jiayi, Flouri T, Yang Z. 2025. Hierarchical heuristic species delimitation under the multispecies coalescent model with migration. Syst Biol. pdf SI (DOI: 10.1093/sysbio/syae050)
Moody ERR, Alvarez-Carretero S, Mahendrarajah TA, Clark JW, Betts HC, Dombrowski N, Szantho LL, Boyle RA, Daines S, Chen X, Lane, N., Yang, Z., Shields, G.A., Szollosi, G.J., Spang, A., Pisani, D., Williams, T.A., Lenton, T.M., Donoghue, P.C.J. 2024. The nature of the last universal common ancestor and its impact on the early Earth system. Nat. Ecol. Evol. 8: 1654-1666 pdf (DOI: 10.1038/s41559-024-02461-1)
Nagel AA, Flouri T, Yang Z, Rannala B. 2024. Bayesian inference under the multispecies coalescent with ancient DNA sequences. Syst Biol pdf SI (DOI: 10.1093/sysbio/syae047)
Pavon-Vazquez CJ, Rana Q, Farleigh K, Crispo E, Zeng M, Liliah J, Mulcahy D, Ascanio A, Jezkova T, Leache AD, Flouri T, Yang Z, Blair C. 2024. Gene flow and isolation in the arid Nearctic revealed by genomic analyses of desert spiny lizards. Systematic Biology 73:323-342. pdf (DOI: 10.1093/sysbio/syae001)
2023
Flouri T, Jiao X, Huang J, Rannala B, Yang Z. 2023. Efficient Bayesian inference under the multispecies coalescent with migration. Proc Nat Acad Sci USA 120:e2310708120. pdf, SI.Thawornwattana Y, Seixas FA, Yang Z, Mallet J. 2023. Major patterns in the introgression history of Heliconius butterflies. eLife, https://doi.org/10.7554/eLife.90656.1 pdf, SI
Thawornwattana Y, Huang J, Flour T, Mallet J, Yang Z. 2023. Inferring the direction of introgression using genomic sequence data. Molecular Biology and Evolution 40(8):msad178, pdf, SI (DOI: 10.1093/molbev/msad178)
Kapli P, Kotari I, Telford M, Goldman N, Yang Z. 2023. DNA sequences are as useful as protein sequences for inferring deep phylogenies. Systematic Biology, 10.1093/sysbio/syad036 pdf, SI (DOI: 10.1093/sysbio/syad036)
Tiley G.P., Flour T., Jiao, X., Poelstra J.P., Xu, B., Zhu, T., Rannala, B., Yoder A.D., Yang Z. 2023. Estimation of species divergence times in presence of cross-species gene flow. Systematic Biology 72(4):820-836. 10.1093/sysbio/syad015 pdf, SI (DOI: 10.1093/sysbio/syad015)
Alvarez-Carretero, S., Paschalia Kapli, P., and Yang, Z. 2023. Beginner's guide on the use of PAML to detect positive selection. Molecular Biology and Evolution, 40(4): msad041 pdf, SI (DOI: 10.1093/molbev/msad041)
Ji J, Jackson DJ, Leache AD, Yang Z. 2023. Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks. Systematic Biology 72(2):446-465 (DOI: 10.1093/sysbio/syac077) pdf, SI (DOI: 10.1093/sysbio/syac077)
Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. 2023. CNETML: maximum likelihood inference of phylogeny from copy number proles of multiple samples. Genome Biology 24:144. pdf, (DOI: 10.1186/s13059-023-02983-0)
2022
Huang J, Thawornwattana Y, Flour T, Mallet J, Yang Z. 2022. Inference of gene flow between species under misspecified models. Molecular Biology and Evolution 39(6): msac237 pdf, SI (DOI: 10.1093/sysbio/syac077)Flouri T, Huang J, Jiao X, Kapli P, Rannala B, Yang Z. 2022. Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent. Molecular Biology and Evolution 39(8): msac161 pdf, SI (DOI: 10.1093/molbev/msac161) https://doi.org/10.1093/molbev/msac246)
Thawornwattana Y, Seixas FA, Mallet J, Yang Z. 2022. Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies. Systematic Biology 71:1159-1177. pdf, SI (DOI: 10.1093/sysbio/syac009 ).
Poelstra J, Montero BK, Ludemann J, Yang Z, Rakotondranary SJ, Hohenlohe P, Stetter N, Ganzhorn JU, Yoder AD. 2022. RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Proc Roy Soc B Biol Sci. 289: 20220596. pdf (DOI: 10.1098/rspb.2022.0596)
Yang Z, Flouri T. 2022. Estimation of cross-species introgression rates using genomic data despite model unidentifiability. Molecular Biology and Evolution 39(5): msac083. pdf, SI (DOI: 10.1093/molbev/msac083)
Zhu T, Flour T, Yang Z. 2022. A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model. Molecular Ecology pdf (DOI: 10.1111/mec.16433)
Huang J, Bennett J, Flouri T, Yang Z. 2022. Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model. Systematic Biology 71:334-352. pdf, SI (DOI:10.1093/sysbio/syab047)
Finger N, Farleigh K, Bracken JT, Leache AD, Francois O, Yang Z, Flour T, Charran T, Jezkova T, Williams DA et al. 2021. Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central USA. Genome Biol Evol. 14(1): 10.1093/gbe/evab260. pdf, SI, 10.1093/gbe/evab260
Alvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ, dos Reis M. 2021. A species-level timeline of mammal evolution integrating phylogenomic data. Nature, 602, 263-267. (DOI: 10.1038/s41586-41021-04341-41581)
2021
Jiao X, Flouri T, Yang Z. 2021. Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow. National Science Review: 8: nwab127 pdf (DOI: 110.1093/nsr/nwab127)Zhu T and Z. Yang 2021. Complexity of the simplest species tree problem. Molecular Biology and Evolution 39: 3993-4009 pdf (doi.org/10.1093/molbev/msab009)
Huang J, Liu Y, Zhu T, Yang Z. 2021. The asymptotic behavior of bootstrap support values in molecular phylogenetics. Systematic Biology, 70: 774-785. pdf (doi: 10.1093/sysbio/syaa100/6055564)
Feng Yuanqing, Hongzhan Xu, Jinghao Liu, Ning Xie, Lei Gao, Yanyun He, Yuan Yao, Fengxiang Lv, Yan Zhang, Jian Lu, Wei Zhang, Chuan-Yun Li, Xinli Hu, Ziheng Yang, Rui-Ping Xiao, 2021. Functional and adaptive significance of promoter mutations that affect divergent myocardial expressions of TRIM72 in primates. Molecular Biology and Evolution, 38: 2930-2945 pdf (doi.org/10.1093/molbev/msab083)
Jiao X, Yang Z. 2021. Defining species when there is gene flow. Systematic Biology 70: 108-119 pdf (doi.org/10.1093/sysbio/syaa052)
2020
Huang J, Flouri T, Yang Z. 2020. A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model. Molecular Biology and Evolution 32: 3211-3224 pdf, SI (doi: 10.1093/molbev/msaa166)Tiley GP, Poelstra JP, dos Reis M, Yang Z, Yoder AD. 2020. Molecular clocks without rocks: new solutions for old problems. Trends in Genetics 36:845-856 pdf (DOI:https://doi.org/10.1016/j.tig.2020.06.002)
Kapli P, Telford M, Yang Z. 2020. Phylogenetic tree building in the genomic age, Nature Reviews Genetics 21: 428-444. pdf (doi: 10.1038/s41576-020-0233-0)
Weber C., Yang Z., Goldman N. 2020. Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space. Systematic Biology 70(1): 21-32 pdf
Flouri T, Rannala B, Yang Z. 2020. A tutorial on the use of BPP for species tree estimation and species delimitation. Pp. 5.6.1-16 in Scornavacca C, Delsuc F, and Galtier N, eds. Phylogenetics in the Genomic Era. No Commercial Publisher. pdf
Rannala B, Yang Z. 2020. Species delimitation. Pp. 5.5.1-18 in Galtier N, Delsuc F, and Scornavacca C, eds. Phylogenetics in the Genomic Era. No Commercial Publisher. pdf
Rannala B, Edwards SV, Leache AD, Yang Z. 2020. The multispecies coalescent model and species tree inference. Pp. 3.3:1-20 in Scornavacca C, Delsuc F, and Galtier N, eds. Phylogenetics in the Genomic Era. No Commercial Publisher. pdf
Jiao X, Flouri T, Rannala B, Yang Z. 2020. The impact of cross-species gene flow on species tree estimation. Systematic Biology 69(5):830-847. pdf (DOI:10.1093/sysbio/syaa001)
Flouri T, Jiao X, Rannala B, Yang Z. 2020. A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis. Molecular Biology and Evolution, 37(4):1211-1223 pdf SI (doi:10.1093/molbev/msz296)
2019
Yang, Z. 2019. Adaptive molecular evolution, pp.369-395 in Handbook of Statistical Genomics, 4th Edition, eds. by David J. Balding, Ida Moltke and John Marioni. Wiley, New York. pdfDos Reis M, Yang Z. 2019. Bayesian molecular clock dating using genome-scale datasets in Anisimova M, ed. Evolutionary Genomics: Volume 2, Statistical and Computational Methods. Springer, New York. pdf
Halliday TJD, Dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, Goswami A. 2019. Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proc Biol Sci 286:20182418. pdf
Alvarez-Carretero, S., A. Goswami, Z. Yang, and M. dos Reis. 2019. Bayesian estimation of species divergence times using correlated quantitative characters. Systematic Biology 68:967-986 DOI:10.1093/sysbio/syz015. pdf
Leache AD, Zhu T, Rannala B, Yang Z. 2019. The spectre of too many species. Systematic Biology 68: 168-181. pdf
Ostrander EA, Wang GD, et al. 2019. Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. National Science Review 6:810-824. pdf
2018
Morris JL, Puttick MN, Clark J, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. 2018. Accurate timetrees do indeed require accurate calibrations. Response to comment by Hedges et al. Proc Nat Acad Sci USA 115: E9512-E9513 pdfLiu Z, Chen G, Zhu T, Zeng Z, Lyu Z, Wang J, Messenger K, Greenberg AJ, Guo Z, Yang Z et al. 2018. Prevalence of cryptic species in morphologically uniform taxa - Fast speciation and evolutionary radiation in Asian frogs. Molecular Phylogenetics and Evolution 127:723-731. pdf
Flouris T, Jiao, X, Rannala B, Yang Z. 2018. Species tree inference with BPP using genomic sequences and the multispecies coalescent. Mol Biol Evol. 35 (10): 2585-2593. pdf metrics
Morris J.L., Puttick M.N., Clark J., Edwards D., Kenrick P., Pressel S., Wellman C.H., Yang Z., Schneider H., Donoghue P.C.J. 2018. The timescale of early land plant evolution. Proc Nat Acad Sci USA 115: E2274-E2283. pdf
Yang Z, Zhu T. 2018. Bayesian selection of misspecified models is
overconifdent and may cause spurious posterior probabilities for
phylogenetic trees. Proc Nat Acad Sci USA 115:1854-1859.
pdf
Yang Z, Zhu T. 2018. The good, the bad, and the ugly: Bayesian model
selection produces spurious posterior probabilities
for phylogenetic trees. (This is the version published at the arXive of the paper above.)
pdf
Yang, Ziheng. Molecular Phylogenetics. In Oxford Bibliographies in Evolutionary Biology. Ed. Karin Pfennig. New York: Oxford University Press.
Yang, Z. 2018. AWF Edwards and the origin of Bayesian phylogenetics, pp. 352-362 in AWF Edwards (R. G. Winther, ed.) Cambridge University Press, Cambridge, England. pdf
Thawornwattana Y, Dalquen DA, Yang Z. 2018. Coalescent analysis of phylogenomic data confidently resolves the species relationships in the Anopheles gambiae species complex. Mol Biol Evol 35:2512-2527. pdf and metrics
Thawornwattana Y, Dalquen DA, Yang Z. 2018. Designing simple and efficient Markov chain Monte Carlo proposal kernels. Bayesian Analysis 13:1033-1059. pdf.
dos Reis M., Gunnell G.F., Barba-Montoya J., Wilkins A., Yang Z., Yoder A.D. 2018. Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: Primates as a test case. Systematic Biology 67:594-615. pdf
Barba-Montoya J, dos Reisa M, Schneider H, Donoghue PCJ, Yang Z. 2018. Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous terrestrial revolution. New Phytologist 218: 819-834. pdf
Angelis K, Alvarez-Carretero S, dos Reis M, Yang Z. 2018. An evaluation of different partitioning strategies for Bayesian estimation of species divergence times. Systematic Biology 67:61-77. pdf (Publisher's award for best student paper)
Shi, C.-M., and Z. Yang. 2018. Coalescent-based analyses of genomic sequence data provide a robust resolution of phylogenetic relationships among major groups of gibbons. Mol. Biol. Evol. 35: 159-179. pdf metrics
2017
Zeng, L, et al. 2017. Evolution of a high altitude ecotype of Arabidopsis thaliana from the Himalayas. Sci. Bull. 62: 1628-1630. pdfBarba-Montoya, J., M. dos Reis, and Z. Yang. 2017. Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol. Phylogenet. Evol. 114: 386-400. pdf
Nascimento, F. F., M. dos Reis, and Z. Yang. 2017. A biologist's guide to Bayesian phylogenetic analysis. Nat. Ecol. Evol. 1: 1446-1454. pdf
Warnock, R. C., Z. Yang, and P. C. Donoghue. 2017. Testing the molecular clock using mechanistic models of both fossil preservation and molecular evolution. Proc. R. Soc. Lond. B. 284: 20170227 pdf
Rannala, B., and Z. Yang. 2017. Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology 66: 823-842. pdf
Yang, Z., and B. Rannala. 2017. Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Mol. Ecol. 26: 3028-3036. pdf
Dalquen, D., T. Zhu, and Z. Yang. 2017. Maximum likelihood implementation of an isolation-with-migration model for three species. Syst. Biol. 66:379-398 pdf
2016
Xu B, Yang Z. 2016. Challenges in species tree estimation under the multispecies coalescent model. Genetics 204: 1353-1368. pdfYang Z. 2016. Bayesian phylogenetic inference, in R. Kliman, ed. Encyclopedia of Evolutionary Biology. Elsevier. Volume 1, pp. 137-140 pdf
Donoghue, P. C., and Z. Yang. 2016. The evolution of methods for establishing evolutionary timescales. Phil. Trans. R. Soc. B: Biol. Sci. 371:20160020. pdf
Yang, Z., and P. C. Donoghue. 2016. Dating species divergences using rocks and clocks: An introduction. Phil. Trans. R. Soc. B: 371:20150126. pdf
dos Reis, M., P.C.J. Donoghue and Z. Yang, 2016. Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics 17:71-80 pdf
2015
dos Reis, M., Y. Thawornwattana, K. Angelis, M. J. Telford, P. C. J. Donoghue, and Z. Yang. 2015. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Current Biology 25:2939-2950 pdfYang, Z. 2015. The BPP program for species tree estimation and species delimitation. Current Zoology 61: 854-865 pdf
Matsumoto T, Akashi H, Yang Z. 2015. Evaluation of ancestral sequence reconstruction methods to infer nonstationary patterns of nucleotide substitution. Genetics 200:873-890. pdf
Liu J, Zhang D-X, Yang Z. 2015. A discrete-beta model for testing gene flow after speciation. Methods in Ecology and Evolution 10.1111/2041-210X.12356 pdf
Zhu T, dos Reis M, Yang Z. 2015. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Systematic Biology 64:267-280. pdf
2014
Wang Y, Yang Z. 2014. Priors in Bayesian Phylogenetics, pp.5-23 in Bayesian Phylogenetics: Methods, Algorithms, and Applications (M.-H. CHen, L. Kuo, and P. Lewis, eds). Chapman & Hall/CRC, London.Yang, Z., and B. Rannala. 2014. Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31:3125-3135. pdf
Zhang C, Rannala B, Yang Z. 2014. Bayesian species delimitation can be robust to guide tree inference errors. Systematic Biology 63:993-1004. 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: 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: 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
Leache 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. Rodriguez. 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. pdfChen 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. pdfFletcher 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. pdfGoldman, 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. 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 intensive computation involved.)
