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References
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.
D. Bachtrog. Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nat Genet, 34(2):215–219, Jun 2003.
D. Bachtrog. Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics, 165(3):1221–1232, Nov 2003.
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.
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.
N. Bierne and A. Eyre-Walker. The genomic rate of adaptive amino-acid substitution in Drosophila. Mol Biol Evol, Mar 2004.
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.
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.
B. Charlesworth. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet Res, 63(3):213–227, Jun 1994.
B. Charlesworth, M. T. Morgan, and D. Charlesworth. The effect of deleterious mutations on neutral molecular variation. Genetics,134(4):1289–1303, Aug 1993.
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.
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.
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.
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.
J. M. Comeron and M. Kreitman. Population, evolutionary and genomic consequences of interference selection. Genetics, 161(1):389–410, May 2002.
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.
D. J. Cutler. The index of dispersion of molecular evolution: Slow fluctuations. Theor Popul Biol, 57(2):177–186, Mar 2000.
D. J. Cutler. Understanding the overdispersed molecular clock. Genetics,154(3):1403–1417, Mar 2000.
J. da Silva. The evolutionary adaptation of HIV-1 to specific immunity. Curr HIV Res, 1(3):363–371, Jul 2003.
C. Darwin. The Origin of Species. Oxford University Press, Oxford, reissue edition, 1859.
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.
W. J. Ewens. A note on the variance of the number of loci having a given gene frequency. Genetics, 801):221–222, May 1975.
W. J. Ewens. Mathematical Population Genetics. Springer, New York, 2004.
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.
J. Felsenstein. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J Mol Evol, 53(4-5):447–455, Oct 2001.
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.
R. A. Fisher. On the dominance ratio. Proc Roy Soc Edinburgh, 42:321–341, 1922.
R. A. Fisher. The Genetical Theory of Natural Selection. Clarendon Press, Oxford, 1st edition, 1930.
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.
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.
J. H. Gillespie. The Causes of Molecular Evolution. Oxford University Press, Oxford, 1991.
J. H. Gillespie. Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model. Genetics, 134:971–981, 1993.
J. H. Gillespie. Substitution processes in molecular evolution. II. Exchangeable models from population genetics. Evolution, 48:1101–1113, 1994.
J. H. Gillespie. Substitution processes in molecular evolution. III. Deleterious alleles. Genetics, 138:943–952, 1994.
J. H. Gillespie. The role of population size in molecular evolution. Theor Popul Biol, 55:145–156, 1999.
J. H. Gillespie. Genetic drift in an infinite population. The pseudohitchhiking model. Genetics, 155(2):909–919, Jun 2000.
J. H. Gillespie. The neutral theory in an infinite population. Gene, 261(1):11–18, Dec 2000.
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.
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.
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.
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.
W. G. Hill and A. Robertson. The effect of linkage on limits to artificial selection. Genet Res, 8(3):269–294, Dec 1966.
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.
R. R. Hudson. Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology 7, pages 1–44. Oxford University Press, Oxford, 1990.
J. P. Huelsenbeck and R. Nielsen. Effect of nonindependent substitution on phylogenetic accuracy. Syst Biol, 48(2):317–328, Jun 1999.
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.
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.
T. H. Jukes and C. R. Cantor. Evolution of protein molecules. In Mammalian Protein Metabolism, pages 21–132. Academic Press, New York, 1969.
S. Karlin and H. M. Taylor. A Second Course in Stochastic Processes. Academic Press, New York, 1981.
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.
F. P. Kelly. Reversibility and Stochastic Networks. John Wiley & Sons, Chichester, 1979.
M. Kimura. Solution of a process of random genetic drift with a continuous model. Proc Natl Acad Sci USA, 41:114–150, 1955.
M. Kimura. On the probability of fixation of mutant genes in a population. Genetics, 47:713–719, 1962.
M. Kimura. Diffusion models in population genetics. J Appl Probab, 1:177–232, 1964.
M. Kimura. Evolutionary rate at the molecular level. Nature, 217:624–626, 1968.
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.
M. Kimura. The rate of molecular evolution considered from the standpoint of poulation genetics. Proc Natl Acad Sci USA, 63:1181–1188,1969.
M. Kimura. Theoretical foundation of population genetics at the molecular level. Theor Popul Biol, 2(2):174–208, Jun 1971.
M. Kimura. Models of effectively neutral mutations in which selective constraint is incorporated. Proc Nat Acad Sci USA, 76:3440–3444, 1979.
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.
M. Kimura. The Neutral Theory of Molecular Evolution. Cambridge University Press, Camebridge, 1983.
M. Kimura and T. Ohta. Protein polymorphism as a phase of molecular evolution. Nature, 29(5285):67–469, Feb 1971.
J. L. King and T. H. Jukes. Non-Darwinian evolution. Science, 164:88–798, 1969.
R. C. Lewontin. The Genetic Basis of Evolutionary Change. Columbia University Press, New York, 1974.
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.
W. H. Li. Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics, 85(2):331–337, Feb 1977.
T. Mitchell-Olds and M. J. Clauss. Plant evolutionary genomics. Curr Opin Plant Biol, 5(1):74–79, Feb 2002.
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.
S. V. Muse. Evolutionary analyses of DNA sequences subject to constraints of secondary structure. Genetics, 139(3):1429–1439, Mar 1995.
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.
R. Nielsen and J. Wakeley. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics, 158(2):885–896, Jun 2001.
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.
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.
J. R. Norris. Markov Chains. Cambridge University Press, Cambridge, 1997.
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.
T. Ohta. Evolutionary rate of cistrons and DNA divergence. J Mol Evol, 1:150–157, 1972.
T. Ohta. Slightly deleterious mutant substitutions in evolution. Nature, 246:96–98, 1973.
T. Ohta. Mutational pressure as the main cause of molecular evolution and polymorphism. Nature, 252:351–354, 1974.
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.
T. Ohta. Near-neutrality in evolution of genes and gene regulation. ProcNatl Acad Sci USA, 99(25):16134–16137, Dec 2002.
T. Ohta and M. Kimura. On the constancy of the evolutionary rate of cistrons. J Mol Evol, 1:18–25, 1971.
T. Ohta and H. Tachida. Theoretical study of nearly neutrality. I. Heterozygosity and rate of mutant substitution. Genetics, 126:219–229, 1990.
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.
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.
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.
N. A. Rosenberg. The probability of topological concordance of gene trees and species trees. Theor Popul Biol, 61(2):225–247, Mar 2002.
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.
S. A. Sawyer. On the past history of an allele now known to have frequency p. J Appl Probab, 14:439–450, 1977.
S. A. Sawyer and D. L. Hartl. Population genetics of polymorphism and divergence. Genetics, 132(4):1161–1176, Dec 1992.
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.
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.
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.
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.
A. Siepel and D. Haussler. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol Biol Evol, 21(3):468–488, Mar 2004.
N. G. Smith and A. Eyre-Walker. Adaptive protein evolution in Drosophila. Nature, 415(6875):1022–1024, Feb 2002.
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.
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.
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.
N. Takahata. Population Genetics, Molecular Evolution, and the Neutral Theory. University of Chicago Press, Chicago, 1994.
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.
N. Takahata and M. Nei. Gene genealogy and variance of interpopulational nucleotide differences. Genetics, 110(2):325–344, Jun 1985.
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.
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.
J. L. Thorne. Models of protein sequence evolution and their applications. Curr Opin Genet Dev, 10(6):602–605, Dec 2000.
J. Wakeley and J. Hey. Estimating ancestral population parameters. Genetics, 145(3):847–855, Mar 1997.
J. D. Wall. Estimating ancestral population sizes and divergence times. Genetics, 163(1):395–404, Jan 2003.
G. A. Watterson. On the number of segregating sites in genetical models without recombination. Theor Popul Biol, 7(2):256–276, Apr 1975.
G. A. Watterson. Mutant substitutions at linked nucleotide sites. Adv Appl Probab, 14:206–224, 1982.
G. A. Watterson. Substitution times for a mutant nucleotide. J Appl Probab, 19A:59–70, 1984.
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.
D. M. Weinreich. The rates of molecular evolution in rodent and primate mitochondrial DNA. J Mol Evol, 52(1):40–50, Jan 2001.
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.
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.
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.
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.
S. Wright. Evolution in mendelian populations. Genetics, 160:97–159,1931.
S. Wright. The distribution of gene frequencies under irreversible mutation. Proc Natl Acad Sci USA, 24:253–259, 1938.
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.
Z. Yang. Estimating the pattern of nucleotide substitution. J Mol Evol,39(1):105–111, Jul 1994.
Z. Yang. A space-time process model for the evolution of DNA sequences. Genetics, 139(2):993–1005, Feb 1995.
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.
Z. Yang. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics, 162(4):1811–1823, Dec 2002.
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.
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.
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.
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.
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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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