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Population Genetics of Molecular Evolution

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References

  1. J. M. Akey, G. Zhang, K. Zhang, L. Jin, and M. D. Shriver. Interrogating a high-density SNP map for signatures of natural selection. Genome Res, 12(12):1805–1814, Dec 2002.

    Article  CAS  PubMed  Google Scholar 

  2. D. Bachtrog. Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nat Genet, 34(2):215–219, Jun 2003.

    Article  CAS  PubMed  Google Scholar 

  3. D. Bachtrog. Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics, 165(3):1221–1232, Nov 2003.

    CAS  PubMed  Google Scholar 

  4. M. Barrier, C. D. Bustamante, J. Yu, and M. D. Purugganan. Selection on rapidly evolving proteins in the Arabidopsis genome. Genetics,163(2):723–733, Feb 2003.

    CAS  PubMed  Google Scholar 

  5. A. J. Betancourt and D. C. Presgraves. Linkage limits the power of natural selection in Drosophila. Proc Natl Acad Sci USA, 99(21):13616–13620, Oct 2002.

    Article  CAS  PubMed  Google Scholar 

  6. N. Bierne and A. Eyre-Walker. The genomic rate of adaptive amino-acid substitution in Drosophila. Mol Biol Evol, Mar 2004.

    Google Scholar 

  7. C. W. Birky and J. B. Walsh. Effects of linkage on rates of molecular evolution. Proc Natl Acad Sci USA, 85(17):6414–6418, Sep 1988.

    CAS  PubMed  Google Scholar 

  8. C. D. Bustamante, R. Nielsen, S. A. Sawyer, K. M. Olsen, M. D. Purugganan, and D. L. Hartl. The cost of inbreeding in Arabidopsis. Nature, 416(6880):531–534, Apr 2002.

    Article  CAS  PubMed  Google Scholar 

  9. B. Charlesworth. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet Res, 63(3):213–227, Jun 1994.

    Article  CAS  PubMed  Google Scholar 

  10. B. Charlesworth, M. T. Morgan, and D. Charlesworth. The effect of deleterious mutations on neutral molecular variation. Genetics,134(4):1289–1303, Aug 1993.

    CAS  PubMed  Google Scholar 

  11. D. Charlesworth, B. Charlesworth, and M. T. Morgan. The pattern of neutral molecular variation under the background selection model. Genetics, 141(4):1619–1632, Dec 1995.

    CAS  PubMed  Google Scholar 

  12. M. Choisy, C. H. Woelk, J. F. Guegan, and D. L. Robertson. Comparative of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol, 78(4):1962–1970, Feb 2004.

    Article  CAS  PubMed  Google Scholar 

  13. A. G. Clark, S. Glanowski, R. Nielsen, P. D. Thomas, A. Kejariwal, M. A. Todd, D. M. Tanenbaum, D. Civello, F. Lu, B. Murphy, S. Ferriera, G. Wang, X. Zheng, T. J. White, J. J. Sninsky, M. D. Adams, and M. Cargill. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science, 302(5652):1960–1963, Dec 2003.

    Article  CAS  PubMed  Google Scholar 

  14. R. M. Clark, E. Linton, J. Messing, and J. F. Doebley. Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci USA, 101(3):700–707, Jan 2004.

    Article  CAS  PubMed  Google Scholar 

  15. J. M. Comeron and M. Kreitman. Population, evolutionary and genomic consequences of interference selection. Genetics, 161(1):389–410, May 2002.

    CAS  PubMed  Google Scholar 

  16. D. J. Cutler. Clustered mutations have no effect on the overdispersed molecular clock: A response to Huai and Woodruff. Genetics,149(1):463–464, May 1998.

    CAS  PubMed  Google Scholar 

  17. D. J. Cutler. The index of dispersion of molecular evolution: Slow fluctuations. Theor Popul Biol, 57(2):177–186, Mar 2000.

    MATH  CAS  PubMed  Google Scholar 

  18. D. J. Cutler. Understanding the overdispersed molecular clock. Genetics,154(3):1403–1417, Mar 2000.

    MathSciNet  CAS  PubMed  Google Scholar 

  19. J. da Silva. The evolutionary adaptation of HIV-1 to specific immunity. Curr HIV Res, 1(3):363–371, Jul 2003.

    Article  MATH  PubMed  Google Scholar 

  20. C. Darwin. The Origin of Species. Oxford University Press, Oxford, reissue edition, 1859.

    Google Scholar 

  21. W. J. Ewens. A note on the sampling theory for infinite alleles and infinite sites models. Theor Popul Biol, 6(2):143–148, Oct 1974.

    MATH  MathSciNet  CAS  PubMed  Google Scholar 

  22. W. J. Ewens. A note on the variance of the number of loci having a given gene frequency. Genetics, 801):221–222, May 1975.

    CAS  PubMed  Google Scholar 

  23. W. J. Ewens. Mathematical Population Genetics. Springer, New York, 2004.

    Google Scholar 

  24. J. C. Fay, G. J. Wyckoff., and C. I. Wu. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature, 415(6875):1024–1026, Feb 2002.

    Article  CAS  PubMed  Google Scholar 

  25. J. Felsenstein. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J Mol Evol, 53(4-5):447–455, Oct 2001.

    Article  CAS  PubMed  Google Scholar 

  26. J. Felsenstein and G. A. Churchill. A hidden Markov model approach to variation among site in rate of evolution. Mol Biol Evol, 13(1):93–104, Jan 1996.

    CAS  PubMed  Google Scholar 

  27. R. A. Fisher. On the dominance ratio. Proc Roy Soc Edinburgh, 42:321–341, 1922.

    Google Scholar 

  28. R. A. Fisher. The Genetical Theory of Natural Selection. Clarendon Press, Oxford, 1st edition, 1930.

    Google Scholar 

  29. Y. Gilad, C. D. Bustamante, D. Lancet, and S. Paabo. Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet, 73(3):489–501, Sep 2003.

    Article  CAS  PubMed  Google Scholar 

  30. J. H. Gillespie. A general model to account for enzyme variation in natural populations. v. the sas-cff model. Theor Popul Biol, 14:1–45, 1978.

    MATH  CAS  PubMed  Google Scholar 

  31. J. H. Gillespie. The Causes of Molecular Evolution. Oxford University Press, Oxford, 1991.

    Google Scholar 

  32. J. H. Gillespie. Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model. Genetics, 134:971–981, 1993.

    CAS  PubMed  Google Scholar 

  33. J. H. Gillespie. Substitution processes in molecular evolution. II. Exchangeable models from population genetics. Evolution, 48:1101–1113, 1994.

    Google Scholar 

  34. J. H. Gillespie. Substitution processes in molecular evolution. III. Deleterious alleles. Genetics, 138:943–952, 1994.

    CAS  PubMed  Google Scholar 

  35. J. H. Gillespie. The role of population size in molecular evolution. Theor Popul Biol, 55:145–156, 1999.

    MATH  CAS  PubMed  Google Scholar 

  36. J. H. Gillespie. Genetic drift in an infinite population. The pseudohitchhiking model. Genetics, 155(2):909–919, Jun 2000.

    MathSciNet  CAS  PubMed  Google Scholar 

  37. J. H. Gillespie. The neutral theory in an infinite population. Gene, 261(1):11–18, Dec 2000.

    Article  MathSciNet  CAS  PubMed  Google Scholar 

  38. S. Glinka, L. Ometto, S. Mousset, W. Stephan, and D. De Lorenzo. Demography and natural selection have shaped genetic variation in Drosophila melanogaster: A multi-locus approach. Genetics, 165(3):1269–1278, Nov 2003.

    PubMed  Google Scholar 

  39. N. Goldman and Z. Yang. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol, 11(5):725–736, Sep 1994.

    CAS  PubMed  Google Scholar 

  40. M. Hasegawa, H. Kishino, and T. Yano. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol, 22(2):160–174, 1985.

    Article  CAS  PubMed  Google Scholar 

  41. I. Hellmann, S. Zollner, W. Enard, I. Ebersberger, B. Nickel, and S. Paabo. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res, 13(5):831–837, May 2003.

    Article  CAS  PubMed  Google Scholar 

  42. W. G. Hill and A. Robertson. The effect of linkage on limits to artificial selection. Genet Res, 8(3):269–294, Dec 1966.

    CAS  PubMed  Google Scholar 

  43. J. L. Hubby and R. C. Lewontin. A molecular approach to the study of genic heterozygosity in natural populations. I. The number of alleles at different loci in Drosophila pseudoobscura. Genetics, 54(2):577–594, Aug 1966.

    CAS  PubMed  Google Scholar 

  44. R. R. Hudson. Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology 7, pages 1–44. Oxford University Press, Oxford, 1990.

    Google Scholar 

  45. J. P. Huelsenbeck and R. Nielsen. Effect of nonindependent substitution on phylogenetic accuracy. Syst Biol, 48(2):317–328, Jun 1999.

    CAS  PubMed  Google Scholar 

  46. G. A. Huttley, M. W. Smith, M. Carrington, and S. J. O’Brien. A scan for linkage disequilibrium across the human genome. Genetics, 152(4):1711–1722, Aug 1999.

    CAS  PubMed  Google Scholar 

  47. V. Jaenicke-Despres, E. S. Buckler, B. D. Smith, M. T. Gilbert, A. Cooper, J. Doebley, and S. Paabo. Early allelic selection in maize as revealed by ancient DNA. Science, 302(5648):1206–1208, Nov 2003.

    Article  CAS  PubMed  Google Scholar 

  48. T. H. Jukes and C. R. Cantor. Evolution of protein molecules. In Mammalian Protein Metabolism, pages 21–132. Academic Press, New York, 1969.

    Google Scholar 

  49. S. Karlin and H. M. Taylor. A Second Course in Stochastic Processes. Academic Press, New York, 1981.

    Google Scholar 

  50. M. Kayser, S. Brauer, and M. Stoneking. A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol, 20(6):893–900, Jun 2003.

    CAS  PubMed  Google Scholar 

  51. F. P. Kelly. Reversibility and Stochastic Networks. John Wiley & Sons, Chichester, 1979.

    Google Scholar 

  52. M. Kimura. Solution of a process of random genetic drift with a continuous model. Proc Natl Acad Sci USA, 41:114–150, 1955.

    Google Scholar 

  53. M. Kimura. On the probability of fixation of mutant genes in a population. Genetics, 47:713–719, 1962.

    CAS  PubMed  Google Scholar 

  54. M. Kimura. Diffusion models in population genetics. J Appl Probab, 1:177–232, 1964.

    MATH  Google Scholar 

  55. M. Kimura. Evolutionary rate at the molecular level. Nature, 217:624–626, 1968.

    CAS  PubMed  Google Scholar 

  56. M. Kimura. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61(4):893–903, Apr 1969.

    CAS  PubMed  Google Scholar 

  57. M. Kimura. The rate of molecular evolution considered from the standpoint of poulation genetics. Proc Natl Acad Sci USA, 63:1181–1188,1969.

    CAS  PubMed  Google Scholar 

  58. M. Kimura. Theoretical foundation of population genetics at the molecular level. Theor Popul Biol, 2(2):174–208, Jun 1971.

    MATH  CAS  PubMed  Google Scholar 

  59. M. Kimura. Models of effectively neutral mutations in which selective constraint is incorporated. Proc Nat Acad Sci USA, 76:3440–3444, 1979.

    MATH  PubMed  Google Scholar 

  60. M. Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol, 162):11–120, Dec 1980.

    Article  Google Scholar 

  61. M. Kimura. The Neutral Theory of Molecular Evolution. Cambridge University Press, Camebridge, 1983.

    Google Scholar 

  62. M. Kimura and T. Ohta. Protein polymorphism as a phase of molecular evolution. Nature, 29(5285):67–469, Feb 1971.

    Google Scholar 

  63. J. L. King and T. H. Jukes. Non-Darwinian evolution. Science, 164:88–798, 1969.

    Google Scholar 

  64. R. C. Lewontin. The Genetic Basis of Evolutionary Change. Columbia University Press, New York, 1974.

    Google Scholar 

  65. R. C. Lewontin and J. L. Hubby. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics, 54(2):595–609, Aug 1966.

    CAS  PubMed  Google Scholar 

  66. W. H. Li. Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics, 85(2):331–337, Feb 1977.

    CAS  PubMed  Google Scholar 

  67. T. Mitchell-Olds and M. J. Clauss. Plant evolutionary genomics. Curr Opin Plant Biol, 5(1):74–79, Feb 2002.

    Article  CAS  PubMed  Google Scholar 

  68. C. B. Moore, M. John, I. R. James, F. T. Christiansen, C. S. Witt, and S. A. Mallal. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science, 296(5572):1439–1443, May 2002.

    Article  CAS  PubMed  Google Scholar 

  69. S. V. Muse. Evolutionary analyses of DNA sequences subject to constraints of secondary structure. Genetics, 139(3):1429–1439, Mar 1995.

    CAS  PubMed  Google Scholar 

  70. S. V. Muse and B. S. Gaut. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol, 11(5):715–724, Sep 1994.

    CAS  PubMed  Google Scholar 

  71. R. Nielsen and J. Wakeley. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics, 158(2):885–896, Jun 2001.

    CAS  PubMed  Google Scholar 

  72. R. Nielsen and Z. Yang. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148(3):929–936, Mar 1998.

    CAS  PubMed  Google Scholar 

  73. R. Nielsen and Z. Yang. Estimating the distribution of selection coeficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol, 20(8):1231–1239, Aug 2003.

    CAS  PubMed  Google Scholar 

  74. J. R. Norris. Markov Chains. Cambridge University Press, Cambridge, 1997.

    Google Scholar 

  75. D. Nurminsky, D. D. Aguiar, C. D. Bustamante, and D. L. Hartl. Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Science, 291(5501):128–130, Jan 2001.

    Article  CAS  PubMed  Google Scholar 

  76. T. Ohta. Evolutionary rate of cistrons and DNA divergence. J Mol Evol, 1:150–157, 1972.

    CAS  Google Scholar 

  77. T. Ohta. Slightly deleterious mutant substitutions in evolution. Nature, 246:96–98, 1973.

    Article  CAS  PubMed  Google Scholar 

  78. T. Ohta. Mutational pressure as the main cause of molecular evolution and polymorphism. Nature, 252:351–354, 1974.

    Article  CAS  Google Scholar 

  79. T. Ohta. Extension of the neutral mutation drift hypothesis. In M. Kimura, editor, Molecular Evolution and Polymorphism, pages 148–167. National Institute of Genetics, Mishima, Japan, 1977.

    Google Scholar 

  80. T. Ohta. Near-neutrality in evolution of genes and gene regulation. ProcNatl Acad Sci USA, 99(25):16134–16137, Dec 2002.

    CAS  Google Scholar 

  81. T. Ohta and M. Kimura. On the constancy of the evolutionary rate of cistrons. J Mol Evol, 1:18–25, 1971.

    Article  CAS  Google Scholar 

  82. T. Ohta and H. Tachida. Theoretical study of nearly neutrality. I. Heterozygosity and rate of mutant substitution. Genetics, 126:219–229, 1990.

    CAS  PubMed  Google Scholar 

  83. B. A. Payseur, A. D. Cutter, and M. W. Nachman. Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol Biol Evol, 19(7):1143–1153, Jul 2002.

    CAS  PubMed  Google Scholar 

  84. D. M. Rand, D. M. Weinreich, and B. O. Cezairliyan. Neutrality tests of conservative-radical amino acid changes in nuclear-and mitochondrially-encoded proteins. Gene, 261(1):115–125, Dec 2000.

    Article  CAS  PubMed  Google Scholar 

  85. D. M. Robinson, D. T. Jones, H. Kishino, N. Goldman, and J. L. Thorne. Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol, 20(10):1692–1704, Oct 2003.

    CAS  PubMed  Google Scholar 

  86. N. A. Rosenberg. The probability of topological concordance of gene trees and species trees. Theor Popul Biol, 61(2):225–247, Mar 2002.

    Article  MATH  PubMed  Google Scholar 

  87. P. C. Sabeti, D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter, S. F. Scha.ner, S. B. Gabriel, J. V. Platko, N. J. Patterson, G. J. Mc-Donald, H. C. Ackerman, S. J. Campbell, D. Altshuler, R. Cooper, D. Kwiatkowski, R. Ward, and E. S. Lander. Detecting recent positive selection in the human genome from haplotype structure. Nature, 419(6909):832–837, Oct 2002.

    Article  CAS  PubMed  Google Scholar 

  88. S. A. Sawyer. On the past history of an allele now known to have frequency p. J Appl Probab, 14:439–450, 1977.

    MATH  MathSciNet  Google Scholar 

  89. S. A. Sawyer and D. L. Hartl. Population genetics of polymorphism and divergence. Genetics, 132(4):1161–1176, Dec 1992.

    CAS  PubMed  Google Scholar 

  90. S. A. Sawyer, R. J. Kulathinal, C. D. Bustamante, and D. L. Hartl. Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J Mol Evol, 57(Suppl 1):S154–S164, 2003.

    CAS  PubMed  Google Scholar 

  91. K. J. Schmid, L. Nigro, C. F. Aquadro, and D. Tautz. Large number of replacement polymorphisms in rapidly evolving genes of Drosophila: Implications for genome-wide surveys of DNA polymorphism. Genetics, 153(4):1717–1729, Dec 1999.

    CAS  PubMed  Google Scholar 

  92. M. Schoniger and A. von Haeseler. A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol, 3(3):240–247, Sep 1994.

    CAS  PubMed  Google Scholar 

  93. L. A. Sheldahl, D. M. Weinreich, and D. M. Rand. Recombination, dominance and selection on amino acid polymorphism in the Drosophila genome: Contrasting patterns on the x and fourth chromosomes. Genetics, 165(3):1195–1208, Nov 2003.

    CAS  PubMed  Google Scholar 

  94. A. Siepel and D. Haussler. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol Biol Evol, 21(3):468–488, Mar 2004.

    CAS  PubMed  Google Scholar 

  95. N. G. Smith and A. Eyre-Walker. Adaptive protein evolution in Drosophila. Nature, 415(6875):1022–1024, Feb 2002.

    Article  CAS  PubMed  Google Scholar 

  96. J. F. Storz and M. W. Nachman. Natural selection on protein polymorphism in the rodent genus Peromyscus: Evidence from interlocus contrasts. Evol Int J Org Evol, 57(11):2628–2635, Nov 2003.

    CAS  Google Scholar 

  97. S. Sunyaev, F. A. Kondrashov, P. Bork, and V. Ramensky. Impact of selection, mutation rate and genetic drift on human genetic variation. Hum Mol Genet 12(24):3325–3330, Dec 2003.

    Article  CAS  PubMed  Google Scholar 

  98. W. J. Swanson, A. G. Clark, H. M. Waldrip-Dail, M. F. Wolfner, and C. F. Aquadro. Evolutionary EST analysis identities rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA, 98(13):7375–7379, Jun 2001.

    Article  CAS  PubMed  Google Scholar 

  99. N. Takahata. Population Genetics, Molecular Evolution, and the Neutral Theory. University of Chicago Press, Chicago, 1994.

    Google Scholar 

  100. N. Takahata, K. Ishii, and H. Matsuda. Effects of temporal fluctuation of selection coefficient on gene frequency in a population. Proc Natl Acad Sci USA, 72:4541–4545, 1975.

    CAS  PubMed  Google Scholar 

  101. N. Takahata and M. Nei. Gene genealogy and variance of interpopulational nucleotide differences. Genetics, 110(2):325–344, Jun 1985.

    CAS  PubMed  Google Scholar 

  102. N. Takahata, Y. Satta, and J. Klein. Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol, 48(2):198–221, Oct 1995.

    CAS  PubMed  Google Scholar 

  103. M. I. Tenaillon, M. C. Sawkins, L. K. Anderson, S. M. Stack, J. Doebley, and B. S. Gaut. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays L. ssp.). Genetics, 162(3):1401–1413, Nov 2002.

    CAS  PubMed  Google Scholar 

  104. J. L. Thorne. Models of protein sequence evolution and their applications. Curr Opin Genet Dev, 10(6):602–605, Dec 2000.

    Article  CAS  PubMed  Google Scholar 

  105. J. Wakeley and J. Hey. Estimating ancestral population parameters. Genetics, 145(3):847–855, Mar 1997.

    CAS  PubMed  Google Scholar 

  106. J. D. Wall. Estimating ancestral population sizes and divergence times. Genetics, 163(1):395–404, Jan 2003.

    CAS  PubMed  Google Scholar 

  107. G. A. Watterson. On the number of segregating sites in genetical models without recombination. Theor Popul Biol, 7(2):256–276, Apr 1975.

    MATH  MathSciNet  CAS  PubMed  Google Scholar 

  108. G. A. Watterson. Mutant substitutions at linked nucleotide sites. Adv Appl Probab, 14:206–224, 1982.

    MATH  MathSciNet  Google Scholar 

  109. G. A. Watterson. Substitution times for a mutant nucleotide. J Appl Probab, 19A:59–70, 1984.

    MathSciNet  Google Scholar 

  110. C. Weinig, L. A. Dorn, N. C. Kane, Z. M. German, S. S. Halldorsdottir, M. C. Ungerer, Y. Toyonaga, T. F. Mackay, M. D. Purugganan, and J. Schmitt. Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics, 165(1):321–329, Sep 2003.

    CAS  PubMed  Google Scholar 

  111. D. M. Weinreich. The rates of molecular evolution in rodent and primate mitochondrial DNA. J Mol Evol, 52(1):40–50, Jan 2001.

    MathSciNet  CAS  PubMed  Google Scholar 

  112. D. M. Weinreich and D. M. Rand. Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics, 156(1):385–399, Sep 2000.

    CAS  PubMed  Google Scholar 

  113. S. Whelan, P. Lio, and N. Goldman. Molecular phylogenetics: state-ofthe-art methods for looking into the past. Trends Genet, 17(5):262–272, May 2001.

    Article  CAS  PubMed  Google Scholar 

  114. D. E. Wildman, M. Uddin, G. Liu, L. I. Grossman, and M. Goodman. Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo. Proc Natl Acad Sci USA, 100(12):7181–7188, Jun 2003.

    Article  CAS  PubMed  Google Scholar 

  115. S. Williamson. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol, 20(8):1318–1325, Aug 2003.

    CAS  PubMed  Google Scholar 

  116. S. Wright. Evolution in mendelian populations. Genetics, 160:97–159,1931.

    Google Scholar 

  117. S. Wright. The distribution of gene frequencies under irreversible mutation. Proc Natl Acad Sci USA, 24:253–259, 1938.

    MATH  CAS  PubMed  Google Scholar 

  118. W. Yang, J. P. Bielawski, and Z. Yang. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol, 57(2):212–221, Aug 2003.

    CAS  Google Scholar 

  119. Z. Yang. Estimating the pattern of nucleotide substitution. J Mol Evol,39(1):105–111, Jul 1994.

    Article  PubMed  Google Scholar 

  120. Z. Yang. A space-time process model for the evolution of DNA sequences. Genetics, 139(2):993–1005, Feb 1995.

    CAS  PubMed  Google Scholar 

  121. Z. Yang. Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. In Pacific Symposium on Biocomputing, pages 226–237. World Scientific, Singapore, 2001.

    Google Scholar 

  122. Z. Yang. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics, 162(4):1811–1823, Dec 2002.

    PubMed  Google Scholar 

  123. Z. Yang and R. Nielsen. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol, 19(6):908–917, Jun 2002.

    CAS  PubMed  Google Scholar 

  124. Z. Yang, R. Nielsen, N. Goldman, and A. M. Pedersen. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 155(1):431–449, May 2000.

    CAS  PubMed  Google Scholar 

  125. E. Yuste, A. Moya, and C. Lopez-Galindez. Frequency-dependent selection in human immunodeficiency virus type 1. J Gen Virol, 83(Pt 1):103–106, Jan 2002.

    CAS  PubMed  Google Scholar 

  126. E. Zuckerkandl and L. Pauling. Evolutionary divergence and convergence in proteins. In V. Bryson and H. Voge, editors, Evolving Genes and Proteins, pages 97–166. Academic Press, New York, 1965.

    Google Scholar 

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Bustamante, C.D. (2005). Population Genetics of Molecular Evolution. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health. Springer, New York, NY. https://doi.org/10.1007/0-387-27733-1_4

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