Ji J, Jackson DJ, Leaché AD, Yang Z. (2022) 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, syac077. doi: 10.1093/sysbio/syac077
Huang J, Thawornwattana Y, Mallet J, Yang Z. (2022) Inference of gene flow between species under misspecified models. Molecular Biology and Evolution, 39(12):msac237. PDF Suppl. Mat. doi: 10.1093/molbev/msac237
Thawornwattana Y, Seixas FA, Yang Z, Mallet J. (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(5):1159–1177. PDF Suppl. Mat. doi: 10.1093/sysbio/syac009
Poelstra JW, Montero BK, Lüdemann 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. Proceedings of the Royal Society B, 289(1980):20220596. PDF doi: 10.1098/rspb.2022.0596
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 Suppl. Mat. doi: 10.1093/molbev/msac161
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 Suppl. Mat. doi: 10.1093/molbev/msac083
Zhu T, Flouri T, Yang Z. (2022) A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model. Molecular Ecology, 31(10):2814-2829. PDF doi: 10.1111/mec.16433
Huang J, Bennett J, Flouri T, Leaché AD, Yang Z. (2022) Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model. Systematic Biology, 71(2):334–352. PDF Suppl. Mat. doi: 10.1093/sysbio/syab047
Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ, dos Reis M. (2022) A species-level timeline of mammal evolution integrating phylogenomic data. Nature, 602:263–267. PDF Suppl. Mat. doi: 10.1038/s41586-021-04341-1
Finger N, Farleigh K, Bracken JT, Leaché AD, François O, Yang Z, Flouri T, Charran T, Jezkova T, Williams DA, Blair C. (2022) Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States. Genome Biology and Evolution, 14(1):evab260. PDF Suppl. Mat. doi: 10.1093/gbe/evab260
Jiao X, Fouri T, Yang Z. (2021) Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow. National Science Review, 8(12):nwab127. PDF doi: 10.1093/nsr/nwab127
Zhu T, Yang Z. (2021) Complexity of the simplest species tree problem. Molecular Biology and Evolution, 38(9):3993–4009. PDF doi: 10.1093/molbev/msab009
Feng Y, Xu H, Liu J, Xie N, Gao L, He Y, Yao Y, Lv F, Zhang Y, Lu J, Zhang W, Li C-Y, Hu X, Yang Z, Xiao R-P. (2021) Functional and adaptive significance of promoter mutations that affect divergent myocardial expressions of TRIM72 in primates. Molecular Biology and Evolution, 38(7):2930–2945. PDF doi: 10.1093/molbev/msab083
Huang J, Liu Y, Zhu T, Yang Z. (2021) The asymptotic behavior of bootstrap support values in molecular phylogenetics. Systematic Biology, 70(4):774–785. PDF doi: 10.1093/sysbio/syaa100
Weber C, Perron U, Casey D, Yang Z, Goldman N. (2021) Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space. Systematic Biology, 70(1):21-32. PDF doi: 10.1093/sysbio/syaa036
Jiao X, Yang Z. (2021) Defining species when there is gene flow. Systematic Biology, 70(1):108–119. PDF doi: 10.1093/sysbio/syaa052
Tiley GP, Poelstra JW, dos Reis M, Yang Z, Yoder AD. (2020) Molecular clocks without rocks: new solutions for old problems. Trends in Genetics, 36(11):845-846. PDF doi: 10.1016/j.tig.2020.06.002
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, 37(11):3211-3224. PDF Suppl. Mat. doi: 10.1093/molbev/msaa166
Kapli P, Yang Z, Telford M. (2020) Phylogenetic tree building in the genomic age. Nature Reviews Genetics, 21(7):428-444. doi: 10.1038/s41576-020-0233-0
Flouri T, Rannala B, Yang Z. (2020) A tutorial on the use of BPP for species tree estimation and species delimitation. Phylogenetics in the Genomic Era, 5.6:1–5.6:16. No commercial publisher | Authors open access book. PDF
Rannala B, Yang Z. (2020) Species delimitation. Phylogenetics in the Genomic Era, 5.5:15.5:18. No commercial publisher | Authors open access book. PDF
Rannala B, Edwards SV, Leaché AD, Yang Z. (2020) The multi-species coalescent model and species tree inference. Phylogenetics in the Genomic Era, 3.3:1–3.3:21. No commercial publisher | Authors open access book. 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 Suppl. Mat. doi: 10.1093/molbev/msz296
Yang Z. (2019) Adaptive molecular evolution. Handbook of Statistical Genomics, 4th Editions, 68(6):967-986. Wiley, New York. PDF doi: 10.1002/9781119487845.ch13
dos 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 doi: 10.1093/sysbio/syz015
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(1898):20182418. PDF doi: 10.1098/rspb.2018.2418
Álvarez-Carretero S, Goswami A, Yang Z, and dos Reis M. (2019) Bayesian estimation of species divergence times using correlated quantitative characters. Systematic Biology, 68(6):967-986. PDF doi: 10.1093/sysbio/syz015
Leaché AD, Zhu T, Rannala B, Yang Z. (2019) The spectre of too many species. Systematic Biology, 68(1):168-181. PDF doi: 10.1093/sysbio/syy051
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, 115(41):E9512-E9513. PDF doi: 10.1073/pnas.1812816115
Liu Z, Chen G, Zhu T, Zeng Z, Lyu Z, Wang J, Messenger K, Greenberg AJ, Guo Z, Yang Z. (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 doi: 10.1016/j.ympev.2018.06.020
Flouri T, Jiao X, Rannala B, Yang Z. (2018) Species tree inference with BPP using genomic sequences and the multispecies coalescent. Molecular Biology and Evolution, 35(10):2585-2593. PDF doi: 10.1093/molbev/msy147
Morris JL, Puttick MN, Clark J, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. (2018) The timescale of early land plant evolution. Proc Nat Acad Sci, 115(10):E2274-E2283. PDF doi: 10.1073/pnas.1719588115
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, 115(8):1854-1859. PDF doi: 10.1073/pnas.1712673115
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 Z. (2018) Molecular Phylogenetics. Oxford Bibliographies in Evolutionary Biology. Ed. Karin Pfennig. New York: Oxford University Press. doi: 10.1093/obo/9780199941728-0098
Yang Z. (2018) AWF Edwards and the origin of Bayesian phylogenetics. In AWF Edwards (R. G. Winther, ed.), 352-362. Cambridge University Press, Cambridge, England. PDF doi: 10.1017/9781316276259.035
Thawornwattana Y, Dalquen DA, Yang Z. (2018) Coalescent analysis of phylogenomic data confidently resolves the species relationships in the Anopheles gambiae species complex. Molecular Biology and Evolution, 35(10):2512-2527. PDF doi: 10.1093/molbev/msy158
Thawornwattana Y, Dalquen DA, Yang Z. (2018) Designing simple and efficient Markov chain Monte Carlo proposal kernels. Bayesian Analysis, 13(4):1037-1063. PDF doi: 10.1214/17-BA1084
dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD. (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(4):594-615. PDF doi: 10.1093/sysbio/syy001
Barba-Montoya J, dos Reis 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(2):819-834. PDF doi: 10.1111/nph.15011
Angelis K, Álvarez-Carretero S, dos Reis M, Yang Z. (2018) An evaluation of different partitioning strategies for Bayesian estimation of species divergence times. Systematic Biology, 67(1):61-77. PDF (Publisher’s award for best student paper) doi: 10.1093/sysbio/syx061
Shi CM, Yang Z. (2018) Coalescent-based analyses of genomic sequence data provide a robust resolution of phylogenetic relationships among major groups of gibbons. Molecular Biology and Evolution, 35(1):159-179. PDF doi: 10.1093/molbev/msx277
Zeng L, et al. (2017) Discovery of a high-altitude ecotype and ancient lineage of Arabidopsis thaliana from Tibet. Science Bulletin, 62(24):1628-1630. PDF doi: 10.1016/j.scib.2017.10.007
Barba-Montoya J, dos Reis M, Yang Z. (2017) Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Molecular Phylogenetics and Evolution, 114:386-400. PDF doi: 10.1016/j.ympev.2017.07.005
Nascimento FF, dos Reis M, Yang Z. (2017) A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology and Evolution, 1(10):1446-1454. PDF doi: 10.1038/s41559-017-0280-x
Warnock RC, Yang Z, Donoghue PCJ. (2017) Testing the molecular clock using mechanistic models of both fossil preservation and molecular evolution. Proc Biol Sci, 284(1857):20170227. PDF doi: 10.1098/rspb.2017.0227
Rannala B, Yang Z. (2017) Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology, 66(5):823-842. PDF doi: 10.1093/sysbio/syw119
Yang Z, Rannala B. (2017) Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Molecular Ecology, 26(11):3028-3036. PDF doi: 10.1111/mec.14093
Dalquen D, Zhu T, Yang Z. (2017) Maximum likelihood implementation of an isolation-with-migration model for three species. Systematic Biology, 66(3):379-398. PDF doi: 10.1093/sysbio/syw063
Xu B, Yang Z. (2016) Challenges in species tree estimation under the multispecies coalescent model. Genetics, 204(4):1353-1368. PDF doi: 10.1534/genetics.116.190173
Yang Z. (2016) Bayesian phylogenetic inference. Encyclopedia of Evolutionary Biology, 1:137-140. Elsevier. PDF doi: 10.1016/B978-0-12-800049-6.00208-0
Donoghue PCJ, Yang Z. (2016) The evolution of methods for establishing evolutionary timescales. Proc Biol Sci, 371(1699):20160020. PDF doi: 10.1098/rstb.2016.0020
Yang Z, Donoghue PCJ. (2016) Dating species divergences using rocks and clocks: An introduction. Proc Biol Sci, 371(1699):20160020. PDF doi: 10.1098/rstb.2015.0126
dos Reis M, Donoghue PCJ, Yang Z. (2016) Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics, 17(2):71-80. PDF doi: 10.1038/nrg.2015.8
dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PCJ, Yang Z. (2015) Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Current Biology, 25(22):2939-2950. PDF doi: 10.1016/j.cub.2015.09.066
Yang Z. (2015) The BPP program for species tree estimation and species delimitation. Current Zoology, 61(5):854-865. PDF doi: 10.1093/czoolo/61.5.854
Matsumoto T, Akashi H, Yang Z. (2015) Evaluation of ancestral sequence reconstruction methods to infer nonstationary patterns of nucleotide substitution. Genetics, 200(3):873-890. PDF doi: 10.1534/genetics.115.177386
Liu J, Zhang DX, Yang Z. (2015) A discrete-beta model for testing gene flow after speciation. Methods in Ecology and Evolution, 6(6):715-724. PDF doi: 10.1111/2041-210X.12356
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(2):267-280. PDF doi: 10.1093/sysbio/syu109
Wang Y, Yang Z. (2014) Priors in Bayesian Phylogenetics. Bayesian Phylogenetics: Methods, Algorithms and Applications, 5-23. Chapman & Hall/CRC, London.
Yang Z, Rannala B. (2014) Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31(12):3125-3135. PDF doi: 10.1093/molbev/msu279
Zhang C, Rannala B, Yang Z. (2014) Bayesian species delimitation can be robust to guide tree inference errors. Systematic Biology, 63(6):993-1004. PDF doi: 10.1093/sysbio/syu052
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 doi: 10.1093/molbev/msu142
dos Reis M, Zhu T, Yang Z. (2014) The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Systematic Biology, 63(4):555-565. PDF doi: 10.1093/sysbio/syu020
dos Reis M, Donoghue PCJ, Yang Z. (2014) Neither phylogenomic nor palaeontological data support a Paleogene origin of placental mammals. Biology Letters, 10(1):20131003. PDF doi: 10.1098/rsbl.2013.1003
Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasolarison R, Barrett M, Roos C, Kappeler P, Bielawski JP, Yang Z. (2014) Molecular evolutionary characterization of a V1R subfamily unique to Strepsirrhine primates. Genome Biology and Evolution, 6(1):213-227. PDF doi: 10.1093/gbe/evu006
Leaché AD, Harris RB, Rannala B, Yang Z. (2014) The influence of gene flow on species tree estimation: a simulation study. Systematic Biology, 63(1):17-30. PDF doi: 10.1093/sysbio/syt049
Yang Z, Rodriduez CE. (2013) Searching for efficient Markov chain Monte Carlo proposal kernels. Proceedings of the National Academy of Sciences, 110(48):19307-19312. PDF and an extended version of the proof of equation (11) doi: 10.1073/pnas.1311790110
Xu B, Yang Z. (2013) PamlX: A graphical user interface for PAML. Molecular Biology and Evolution, 30(12):2723-2724. PDF doi: 10.1093/molbev/mst179
Rannala B, Yang Z. (2013) Molecular clock dating. The Princeton Guide to Evolution, 67-74. Princeton University Press, New York. PDF
dos Reis M, Yang Z. (2013) Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?. Genetics, 195(1):195-204. PDF doi: 10.1534/genetics.113.152025
Stadler T, Yang Z. (2013) Dating phylogenies with sequentially sampled tips. Systematic Biology, 62(5):674-688. PDF doi: 10.1093/sysbio/syt030
Zou XH, 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(4):1155-1164. PDF doi: https://doi.org/10.1111/nph.12230
Rannala B, Yang Z. (2013) Improved reversible jump algorithms for Bayesian species delimitation. Genetics, 194(1):245-253. PDF doi: 10.1534/genetics.112.149039
dos Reis M, Yang Z. (2013) The unbearable uncertainty of Bayesian divergence time estimation. Journal of Systematics and Evolution, 51(1):30-43. PDF doi: 10.1111/j.1759-6831.2012.00236.x
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. IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 700-708. IEEE. doi: 10.1109/IPDPSW.2012.88
dos Reis M, Inoue J, Hasegawa M, Asher R, Donoghue PCJ, Yang Z. (2012) Phylogenomic data sets provide both precision and accuracy in estimating the timescale of placental mammal evolution. Proc Biol Sci, 279(1742):3491-3500. PDF Suppl. Mat. doi: 10.1098/rspb.2012.0683
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(10):2889-2893. PDF doi: 10.1093/molbev/mss104
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(3):379-398. PDF doi: 10.1093/sysbio/syw063
Zhang C, Rannala B, Yang Z. (2012) Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Systematic Biology, 61(5):779-784. PDF doi: 10.1093/sysbio/sys030
Yang Z, Rannala B. (2012) Molecular phylogenetics: principles and practice. Nature Review Genetics, 13(5):303-314. PDF doi: 10.1038/nrg3186
Parham J, Donoghue PCJ, 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, Benton M. (2012) Best Practices for Justifying Fossil Calibrations. Systematic Biology, 61(2):346-359. PDF doi: 10.1093/sysbio/syr107
Warnock RCM, Yang Z, Donoghue PCJ. (2012) Exploring uncertainty in the calibration of the molecular clock. Biology Letters, 8(1):156-159. PDF doi: 10.1098/rsbl.2011.0710
Rannala B, Zhu T, Yang Z. (2012) Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Molecular Biology and Evolution, 29(1):325-335. PDF doi: 10.1093/molbev/msr210
Zhang C, Zhang DX, Zhu T, Yang Z. (2011) Evaluation of a Bayesian coalescent method of species delimitation. Molecular Biology and Evolution, 60(6):747-761. PDF doi: 10.1093/sysbio/syr071
Brown RP, Yang Z. (2011) Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evolutionary Biology, 11:271. PDF doi: 10.1186/1471-2148-11-271
Zang LL, Zou XH, Zhang FM, Yang Z, Ge S. (2011) Phylogeny and species delimitation of the C-genome diploid species in Oryza. Journal of Systematics and Evolution, 49(5):386-395. PDF doi: 10.1111/j.1759-6831.2011.00145.x
Groussin M, Pawlowski J, Yang Z. (2011) Bayesian relaxed clock estimation of divergence times in Foraminifera. Molecular Phylogenetics and Evolution, 61(1):157-166. PDF doi: 10.1016/j.ympev.2011.06.008
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(4):e18630. doi: 10.1371/journal.pone.0018630
dos Reis M, Yang Z. (2011) Approximate likelihood calculation for Bayesian estimation of divergence times. Molecular Biology and Evolution, 28(7):2161-2172. PDF doi: 10.1093/molbev/msr045
Zhu T, Hu Y, Ma Z, Zhang DX, Li T, Yang Z. (2011) Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics, 27(6):837-843. PDF doi: 10.1093/bioinformatics/btr025
Yang Z, dos Reis M. (2011) Statistical properties of the branch-site test of positive selection. Molecular Biology and Evolution, 28(3):1217-1228. PDF doi: 10.1093/molbev/msq303
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(1):16-31. PDF doi: 10.1093/sysbio/syq054
Yang Z. (2010) The Timetree of Life. Quarterly Review of Biology, 85(3):360-361. PDF doi: 10.1086/655063
Chen MS, Liu X, Yang Z, Zhao H, Shukle R, Stuart J, Hulbert S. (2010) Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC Evolutionary Biology, 10:296. PDF doi: 10.1186/1471-2148-10-296
Fletcher W, Yang Z. (2010) The effect of insertions, deletions and alignment errors on the branch-site test of positive selection. Molecular Biology and Evolution, 27(10):2257-2267. PDF doi: 10.1093/molbev/msq115
Yang Z, Rannala B. (2010) Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, 107(20):9264-9269. PDF doi: 10.1073/pnas.0913022107
Yang Z. (2010) A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biology and Evolution, 2:200-211. PDF doi: 10.1093/gbe/evq011
Beaumont M, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson S, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet JM, Huelsenbeck J, Novembre J, Foll M, Yang Z, Rousset F, Balding D, Excoffier L. (2010) In defence of model-based inference in phylogeography. Molecular Ecology, 19(3):436-446. PDF doi: 10.1111/j.1365-294X.2009.04515.x
Brown RP, Yang Z. (2010) Bayesian dating of shallow phylogenies with a relaxed clock. Systematic Biology, 59(2):119-131. PDF doi: 10.1093/sysbio/syp082
Inoue J, Donoghue PCJ, Yang Z. (2010) The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology, 59(1):74-89. PDF doi: 10.1093/sysbio/syp078
Yang Z, Nielsen R, Goldman N. (2009) In defense of statistical methods for detecting positive selection. Proceedings of the National Academy of Sciences, 106(36):E95. PDF doi: 10.1073/pnas.0904550106
Fletcher W, Yang Z. (2009) INDELible: A flexible simulator of biological sequence evolution. Molecular Biology and Evolution, 26(8):1879-1888. PDF doi: 10.1093/molbev/msp098
Ren F, Tanaka H, Yang Z. (2009) A likelihood look at the supermatrix-supertree controversy. Gene, 441:119-125. PDF doi: 10.1016/j.gene.2008.04.002
Ren F, Tanaka H, Yang Z. (2009) MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Molecular Phylogenetics and Evolution, 52(1):268-272. PDF doi: 10.1016/j.ympev.2009.01.011
Schmid KJ, Yang Z. (2008) The trouble with sliding windows. PLOS One, 3(11):e3746. PDF doi: 10.1371/journal.pone.0003746
Goldman N, Yang Z. (2008) Statistical and computational challenges in molecular phylogenetics and evolution. Phil. Trans. R. Soc. B, 363(1512):3889-3892. PDF doi: 10.1098/rstb.2008.0182
Yang Z. (2008) Empirical evaluation of a prior for Bayesian phylogenetic inference. Phil. Trans. R. Soc. B, 363(1512):4031-4039. PDF doi: 10.1098/rstb.2008.0164
Vamathevan J, Hasan S, Emes R, Amrine-Madsen H, Rajagopalan D, Topp S, Kumar V, Word M, Simmons M, Foord S, Sanseau P, Yang Z, Holbrook J. (2008) The role of positive selection in determining the molecular cause of species differences in disease. BMC Evolutionary Biology, 8:273. PDF doi: 10.1186/1471-2148-8-273
Burgess R, Yang Z. (2008) Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution, 25(9):1979-1994. PDF doi: 10.1093/molbev/msn148
Rannala B, Yang Z. (2008) Phylogenetic inference using whole genomes. Annual Review of Genomics and Human Genetics, 9:217-231. PDF doi: 10.1146/annurev.genom.9.081307.164407
Emes RD, Yang Z. (2008) Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLOS One, 3(5):e2295. PDF doi: 10.1371/journal.pone.0002295
Furlong RF, Yang Z. (2008) Diversifying and purifying selection in the peptide binding region of DRB in mammals. Journal of Molecular Evolution, 66(4):384-394. PDF doi: 10.1007/s00239-008-9092-6
Yang Z, Nielsen R. (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular Biology and Evolution, 25(3):568-579. PDF doi: 10.1093/molbev/msm284
Zhou R, Zeng K, Wu W, Chen X, Yang Z, Shi S, Wu CI. (2007) Population genetics of speciation in nonmodel organisms. Molecular Biology and Evolution, 24(12):2746-2754. PDF doi: 10.1093/molbev/msm209
Anisimova M, Bielawski JP, Dunn K, Yang Z. (2007) Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evolutionary Biology, 7:154. PDF doi: 10.1186/1471-2148-7-154
Yang Z. (2007) Fair-balance paradox, star-tree paradox and Bayesian phylogenetics. Molecular Biology and Evolution, 24(8):1639-1655. PDF doi: 10.1093/molbev/msm081
Yang Z. (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8):1586-1591. PDF doi: 10.1093/molbev/msm088
Rannala B, Yang Z. (2007) Inferring speciation times under an episodic molecular clock. Systematic Biology, 56(3):453-466. PDF doi: 10.1080/10635150701420643
Anisimova M, Yang Z. (2007) Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Molecular Biology and Evolution, 24(5):1219-1228. PDF doi: 10.1093/molbev/msm042
Hurley IA, Mueller RL, Dunn KA, Schmidt RJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG, Coates MI. (2007) A new time-scale for ray-finned fish evolution. Proc. R. Soc. B, 274(1609):489-498. PDF Suppl. Mat. doi: 10.1098/rspb.2006.3749
Yang Z. (2007) Adaptive molecular evolution. Handbook of statistical genetics, 3rd Edition, 375-406. Wiley, New York. doi: 10.1002/9780470061619.ch12
Yang Z. (2006) On the varied pattern of evolution of two fungal genomes: a critique of Hughes and Friedman. Molecular Biology and Evolution, 23(12):2279-2282. PDF doi: 10.1093/molbev/msl122
Ren F, Tsubota A, Hirokawa T, Kumada H, Yang Z, Tanaka H. (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 doi: 10.1016/j.gene.2006.07.018
Aguileta G, Bielawski JP, Yang Z. (2006) Proposed standard nomenclature for the a- and b-globin gene families. Genes and Genetic Systems, 81(5):367-371. doi: 10.1266/ggs.81.367
Aguileta G, Bielawski JP, Yang Z. (2006) Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene, 380(1):21-29. doi: 10.1016/j.gene.2006.04.019
Yang Z, Rannala B. (2006) Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution, 23(1):212-226. PDF doi: 10.1093/molbev/msj024
Ren F, Tanaka H, Yang Z. (2005) An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Systematic Biology, 54(5):808-818. PDF doi: 10.1080/10635150500354688
Zhang J, Nielsen R, Yang Z. (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution, 22(12):2472-2479. PDF doi: 10.1093/molbev/msi237
Bielawski JP, Yang Z. (2005) Maximum likelihood methods for detecting adaptive protein evolution. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health, 103-124. Springer, New York, NY. doi: https://doi.org/10.1007/0-387-27733-1_5
Yang Z, Rannala B. (2005) Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology, 54(3):455-470. PDF doi: 10.1080/10635150590945313
Sainudiin R, Wong WSW, Yogeeswaran K, Nasrallah J, Yang Z, Nielsen R. (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(3):315-326. PDF doi: 10.1007/s00239-004-0153-1
Yang Z, Wong WSW, Nielsen R. (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution, 22(4):1107-1118. PDF doi: 10.1093/molbev/msi097
Yang Z. (2005) The power of phylogenetic comparison in revealing protein function. Proceedings of the National Academy of Sciences, 102(9):3179-3180. PDF doi: 10.1073/pnas.0500371102
Yang Z. (2005) Bayesian inference in molecular phylogenetics. Mathematics of Evolution and Phylogeny, 63-90. Oxford University Press, Oxford. poor-quality pdf (9.5MB) and book at OUP
Wong WSW, Yang Z, Goldman N, Nielsen R. (2004) Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics, 168(2):1041-1051. PDF doi: 10.1534/genetics.104.031153
Anisimova M, Yang Z. (2004) Molecular evolution of hepatitis delta virus antigen gene: recombination or positive selection?. Journal of Molecular Evolution, 59(6):815-826. PDF (alignment is at the EMBL nucleotide sequence database - accession number ALIGN_000712) doi: 10.1007/s00239-004-0112-x
Aguileta G, Bielawski JP, Yang Z. (2004) Gene conversion and functional divergence in the β-globin gene family. Journal of Molecular Evolution, 59(2):177-189. PDF doi: 10.1007/s00239-004-2612-0
Yang Z. (2004) A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Journal of Molecular Evolution, 50(4):645-656. PDF (in English with a Chinese abstract)
Yoder AD, Yang Z. (2004) Divergence dates for Malagasy lemurs estimated from multiple gene loci: fit with climatological events and speciation models. Molecular Ecology, 13(4):757-773. PDF doi: 10.1046/j.1365-294X.2004.02106.x
Schein M, Yang Z, Mitchell-Olds T, Schmid KJ. (2004) Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Molecular Biology and Evolution, 21(4):659-669. doi: 10.1093/molbev/msh059
Bielawski JP, Yang Z. (2004) Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in the morning glories (Ipomoea). Journal of Molecular Evolution, 59(1):121-132. PDF doi: 10.1007/s00239-004-2597-8
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 doi: 10.1038/sj.hdy.6800419
Aris-Brosou S, Yang Z. (2003) Bayesian models of episodic evolution support a late pre-cambrian explosive diversification of the Metazoa. Molecular Biology and Evolution, 20(12):1947-1954. PDF doi: 10.1093/molbev/msg226
Furlong RF, Yang Z. (2003) Comparative genomics coming of age. Heredity, 91(6):533-534. PDF doi: 10.1038/sj.hdy.6800372
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(11):558-559. PDF doi: 10.1016/S0169-5347(03)00194-0
Yang Z, Ro S, Rannala B. (2003) Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics, 165(2):695-705. PDF
Yang W, Bielawski JP, Yang Z. (2003) Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. Journal of Molecular Evolution, 57(2):212-221. PDF Data (HIVdata.YBY.tar2003.gz) doi: 10.1007/s00239-003-2467-9
Yang Z, Yoder AD. (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(5):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.) doi: 10.1080/10635150390235557
Rannala B, Yang Z. (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164(4):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, Yang Z. (2003) Estimating the distribution of selection coefficients from phylogenetic data with applications to mtDNA. Molecular Biology and Evolution, 20(8):1231-1239. PDF doi: 10.1093/molbev/msg147
Anisimova M, Nielsen R, Yang Z. (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics, 164(3):1229-1236. PDF
Yang Z, Stephens D, Dawson KJ, Drummond A, Nicholls G, Griffiths RC, Wilkinson-Herbots HM, Beaumont MA, Baird SJE, Lascoux M, Leblois R, Estoup A, Nielsen R, Hey J, Stumpf MPH. (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 JP, Yang Z. (2003) Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of Structural and Functional Genomics, 3(1-4):201-212. PDF
Bielawski JP, Yang Z. (2003) Maximum likelihood methods for detecting adaptive evolution after gene duplication. Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions, 201-212. Kluwer Academic Publishers, Dordrecht. PDF (This is the same as the journal paper above.)
Yang Z. (2003) Adaptive Molecular Evolution. Handbook of statistical genetics, 2nd Edition, 229-254. Wiley, New York.
Yang Z. (2002) Inference of selection from multiple species alignments. Current Opinion in Genetics and Development, 12(6):688-694. PDF doi: 10.1016/s0959-437x(02)00348-9
Yang J, Huang J, Gu H, Zhong Y, Yang Z. (2002) Duplication and adaptive evolution of chalcone synthase genes in the genus Dendranthema (Asteraceae). Molecular Biology and Evolution, 19(10):1752-1759. PDF doi: 10.1093/oxfordjournals.molbev.a003997
Aris-Brosou S, Yang Z. (2002) The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny. Systematic Biology, 51(5):703-714. PDF doi: 10.1080/10635150290102375
Yang Z. (2002) Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics, 162(4):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 FM, Hurst GDD, Yang Z. (2002) Host-symbiont conflicts: positive selection on the outer membrane protein of parasite but not mutualistic Rickettsiaceae. Molecular Biology and Evolution, 19(8):1341-1349. PDF doi: 10.1093/oxfordjournals.molbev.a004195
Anisimova M, Bielawski JP, Yang Z. (2002) Accuracy and power of Bayes prediction of amino acid sites under positive selection. Molecular Biology and Evolution, 19(6):950-958. PDF doi: 10.1093/oxfordjournals.molbev.a004152
Yang Z, Nielsen R. (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution, 19(6):908-917. PDF doi: 10.1093/oxfordjournals.molbev.a004148
Yang Z. (2002) Molecular clock. Oxford Encyclopedia of Evolution, 747-750. Oxford University Press, Oxford. PDF book at OUP (2 volumes)
Yang Z, Swanson WJ. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Molecular Biology and Evolution, 19(1):49-57. PDF doi: 10.1093/oxfordjournals.molbev.a003981
Clote P, Naylor GJP, Yang Z. (2002) Proteins: structure, function and evolution. Pacific Symposium on BioComputing, 19(1):548-551. PDF
Jiggins CD, Linares M, Naisbit RE, Salazar C, Yang Z, Mallet J. (2001) Sex-linked hybrid sterility in a butterfly. Evolution, 55(8):1631-1638. PDF doi: 10.1111/j.0014-3820.2001.tb00682.x
Anisimova M, Bielawski JP, Yang Z. (2001) Accuracy and power of likelihood ratio test in detecting adaptive molecular evolution. Molecular Biology and Evolution, 18(8):1585-1592. PDF doi: 10.1093/oxfordjournals.molbev.a003945
Bielawski JP, Yang Z. (2001) Positive and negative selection in the DAZ gene family. Molecular Biology and Evolution, 18(8):523-529. PDF doi: 10.1093/oxfordjournals.molbev.a003831
Swanson WJ, Yang Z, Wolfner MF, Aquadro CF. (2001) Positive Darwinian selection in the evolution of mammalian female reproductive proteins. Proceedings of the National Academy of Sciences, 98(5):2509-2512. PDF (featured in New York Times 27 February 2001) doi: 10.1073/pnas.051605998
Dunn KA, Bielawski JP, Yang Z. (2001) Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics, 157(1):317-330. PDF
Yang Z. (2001) Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pacific Symposium on BioComputing, 226-237. PDF
Yang Z. (2001) Adaptive molecular evolution. Handbook of statistical genetics, 327-350. Wiley, London. PDF
Thomas MG, Hagelberg E, Jones HB, Yang Z, Lister A. (2000) Molecular and morphological evidence on the phylogeny of the Elephantidae. Proc Biol Sci, 267(1461):2493-2500. PDF doi: 10.1098/rspb.2000.1310
Yang Z. (2000) Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. Journal of Molecular Evolution, 51(5):423-432. PDF alignment, and tree doi: 10.1007/s002390010105
Yang Z, Bielawski JP. (2000) Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution, 15(12):496-503. PDF doi: 10.1016/s0169-5347(00)01994-7
Bielawski JP, Dunn K, Yang Z. (2000) Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics, 156(3):1299-1308. PDF
Yang Z, Swanson WJ, Vacquier VD. (2000) Maximum likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Molecular Biology and Evolution, 17(10):1446-1455. PDF doi: 10.1093/oxfordjournals.molbev.a026245
Yoder AD, Yang Z. (2000) Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution, 17(7):1081-1090. PDF (The local clock models here are superseded by the Yang & Yoder 2003 cute-looking paper.) doi: 10.1093/oxfordjournals.molbev.a026389
Yang Z, Nielsen R, Goldman N, Pedersen AM. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 155(1):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 JD, Birdsey GM, Yang Z, Bruford MW, Danpure CJ. (2000) Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates. Molecular Biology and Evolution, 17(3):387-400. PDF doi: 10.1093/oxfordjournals.molbev.a026318
Yang Z. (2000) Complexity of the simplest phylogenetic estimation problem. Proc Biol Sci, 267(1439):109-116. PDF doi: 10.1098/rspb.2000.0974
Yang Z. (2000) Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites. Pacific Symposium on Computational Biology, 81-92. PDF
Yang Z, Nielsen R. (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution, 17(1):32-43. PDF (This method is implemented in the yn00 program in paml.) doi: 10.1093/oxfordjournals.molbev.a026236
Excoffier L, Yang Z. (1999) Substitution rate variation among sites in the mitochondrial hypervariable region I of humans and chimpanzees. Molecular Biology and Evolution, 16(10):1357-1368. PDF doi: 10.1093/oxfordjournals.molbev.a026046
Yang Z, Yoder AD. (1999) Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution, 48(3):274-283. PDF doi: 10.1007/pl00006470
Rannala B, Huelsenbeck JP, Yang Z, Nielsen R. (1998) Taxon sampling and the accuracy of large phylogenies. Systematic Biology, 47(4):702-709. PDF doi: 10.1080/106351598260680
Yang Z, Nielsen R, Hasegawa M. (1998) Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution, 15(12):1600-1611. PDF (Example data set included in the paml release in the examples/mtCDNA/ folder.) doi: 10.1093/oxfordjournals.molbev.a025888
Hasegawa M, Cao Y, Yang Z. (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(11):1499-1505. PDF doi: 10.1093/oxfordjournals.molbev.a025877
Yang Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution, 15(5):568-573. PDF (Example data are included in the paml release in the folder examples/lysozyme/.) doi: 10.1093/oxfordjournals.molbev.a025957
Yang Z. (1998) On the best evolutionary rate for phylogenetic analysis. Systematic Biology, 47(1):125-133. PDF doi: 10.1093/sysbio/syx051
Nielsen R, Yang Z. (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148(3):929-936. PDF
Yang Z, Nielsen R. (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution, 46(4):409-418. PDF doi: 10.1007/pl00006320
Yang Z. (1997) PAML: a program for package for phylogenetic analysis by maximum likelihood. CABIOS, 13(5):555-556. PDF Website doi: 10.1093/bioinformatics/13.5.555
Yang Z, Goldman N. (1997) Are big trees indeed easy?. Trends in Ecology and Evolution, 12(9):357. PDF doi: 10.1016/s0169-5347(97)83196-5
Yang Z, Rannala B. (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Molecular Biology and Evolution, 14(7):717-724. PDF doi: 10.1093/oxfordjournals.molbev.a025811
Yang Z. (1997) On the estimation of ancestral population sizes of modern humans. Genetical Research Cambridge, 69(2):111-116. PDF doi: 10.1017/s001667239700270x
Huelsenbeck JP, Rannala B, Yang Z. (1997) Satistical tests of host-parasite cospeciation. Evolution, 51(2):410-419. PDF doi: 10.1111/j.1558-5646.1997.tb02428.x
Yang Z. (1997) How often do wrong models produce better phylogenies?. Molecular Biology and Evolution, 14(1):105-108. PDF doi: 10.1093/oxfordjournals.molbev.a025695
Yang Z. (1996) Statistical properties of a DNA sample under the finite-sites model. Genetics, 144(4):1941-1950. PDF
Rannala B, Yang Z. (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution, 43(3):304-311. PDF doi: 10.1007/BF02338839
Yang Z. (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution, 11(9):367-372. PDF doi: 10.1016/0169-5347(96)10041-0
Yang Z. (1996) Maximum-Likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution, 42(5):587-596. PDF doi: 10.1007/BF02352289
Yang Z. (1996) Phylogenetic analysis using parsimony and likelihood methods. Journal of Molecular Evolution, 42(2):294-307. PDF doi: 10.1007/BF02198856
Yang Z, Kumar S. (1996) Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Molecular Biology and Evolution, 13(5):650-659. PDF (Implemented in the pamp program in the paml package.) doi: 10.1093/oxfordjournals.molbev.a025625
Yang Z, Kumar S, Nei M. (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics, 141(4):1641-1650. PDF (Example data file included in the paml release as stewart.aa.)
Yang Z, Goldman N, Friday AE. (1995) Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Systematic Biology, 44(3):384-399. PDF doi: 10.1093/sysbio/44.3.384
Yang Z, Roberts D. (1995) On the use of nucleic acid sequences to infer early branchings in the tree of life. Molecular Biology and Evolution, 12(3):451-458. PDF doi: 10.1093/oxfordjournals.molbev.a040220
Yang Z, Lauder IJ, Lin HJ. (1995) Molecular evolution of the hepatitis B virus genome. Journal of Molecular Evolution, 41(5):587-596. PDF doi: 10.1007/BF00175817
Yang Z, Wang T. (1995) Mixed model analysis of DNA sequence evolution. Biometrics, 51(2):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 doi: 10.1007/BF00170682
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 doi: 10.1007/BF00160518
Yang Z. (1995) A space-time process model for the evolution of DNA sequences. Genetics, 139(2):993-1005. PDF (This describes the auto-discrete-gamma models.) doi: 10.1007/BF00160518
Yang Z. (1994) Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Systematic Biology, 43(3):329-342. PDF doi: 10.1093/sysbio/43.3.329
Yang Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39(3):306-314. PDF (This is the discrete-gamma paper.) doi: 10.1007/BF00160154
Yang Z. (1994) Models of DNA substitution and the discrimination of evolutionary parameters. In Proceedings of the XVIIth International Biometrics Conference, Vol. I: Invited Papers, 407-420. International Biometrics Society, Hamilton, Ontario, Canada. PDF
Goldman N, Yang Z. (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11(5):725-736. PDF doi: 10.1093/oxfordjournals.molbev.a040153
Yang Z, Goldman N, Friday AE. (1994) Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Molecular Biology and Evolution, 11(2):316-324. PDF doi: 10.1093/oxfordjournals.molbev.a040112
Yang Z. (1994) Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution, 39(1):105-111. PDF doi: 10.1007/BF00178256
Yang Z, Goldman N. (1994) Evaluation and extension of Markov process models for the evolution of DNA. Acta Genetica Sinica, 21(1):17-23. (in Chinese with an English abstract) doi: 10.1007/BF00178256
Yang Z. (1993) Maximum-likelihood Estimation of Phylogeny From DNA Sequences When Substitution Rates Differ Over Sites. Molecular Biology and Evolution, 10(6):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.) doi: 10.1093/oxfordjournals.molbev.a040082
