Detecting and understanding natural selection

Codon Evolution: Mechanisms and Models

Volumn , Issue , 2012, Pages

  Anisimova, Maria ^a   Liberles, David A ^b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF WYOMING   (United States)

Author keywords

Codon models; Evolutionary medicine; Genome; Natural selection; Phenotypic variation; Statistical methods

Indexed keywords

EID: 84938534717     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1093/acprof:osobl/9780199601165.003.0006     Document Type: Chapter

References (212)

1. Abhiman, S. and E.L. Sonnhammer (2005a). FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res 33: D197-200.
2. Abhiman, S. and E.L. Sonnhammer (2005b). Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins 60: 758-768.
3. Adzhubei, I.A., S. Schmidt, L. Peshkin, V.E. Ramensky, A. Gerasimova et al. (2010). A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
4. Akaike, H. (1974). A new look at the statistical model identification. Automatic Control, IEEE Transactions on Automatic Control 19: 716-723.
5. Akashi, H. (1995). Inferring weak selection from patterns of polymorphism and divergence at 'silent' sites in Drosophila DNA. Genetics 139: 1067-1076.
6. Akashi, H. (1999a). Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics 151: 221-238.
7. Akashi, H. (1999b). Within-and between-species DNA sequence variation and the 'footprint' of natural selection. Gene 238: 39-51.
8. Akashi, H. (2001). Gene expression and molecular evolution. Curr Opin Genet Dev 11: 660-666.
9. Akashi, H. and A. Eyre-Walker (1998). Translational selection and molecular evolution. Curr Opin Genet Dev 8:688-693.
10. Akey, J.M. (2009). Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 19: 711-722.
11. Andolfatto, P., J.D. Wall, and M. Kreitman (1999). Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
12. Anisimova, M. (2003). Detecting positive selection in protein coding genes. PhD thesis. University College London, London.
13. Anisimova, M. and D.A. Liberles (2007). The quest for positive election in the era of comparative genomics. Heredity 99: 567-579.
14. Anisimova, M. and Z. Yang (2007). Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol 24: 1219-1228.
15. Anisimova, M., J.P. Bielawski, and Z. Yang (2001). Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18: 1585-1592.
16. Anisimova, M., J.P. Bielawski, and Z. Yang (2002). Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol 19: 950-958.
17. 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.
18. Anisimova, M., J. Bielawski, K. Dunn, and Z. Yang (2007). Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol 7: 154.
19. Ardawatia, H. and D.A. Liberles (2007). A systematic analysis of lineage-specific evolution in metabolic pathways. Gene 387: 67-74.
20. Ashley, E.A., A.J. Butte, M.T. Wheeler, R. Chen, T.E. Klein et al. (2010). Clinical assessment incorporating a personal genome. The Lancet 375: 1525-1535.
21. Baudry, E. and F. Depaulis (2003). Effect of misoriented sites on neutrality tests with outgroup. Genetics 165:1619-1622.
22. Beaumont, M. (2002). Flavouring composition prepared by fermentation with Bacillus spp. Int J Food Microbiol 75: 189-196.
23. Beaumont, M.A. and D.J. Balding (2004). Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13: 969-980.
24. Beaumont, M.A., R. Nielsen, C. Robert, J. Hey, O. Gaggiotti et al. (2010). In defence of modelbased inference in phylogeography. Molecular Ecology 19: 436-446.
25. Benjamini, Y. and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statist Soc Ser B 57: 289-300.
26. Benner, S., N. Trabesinger, and D. Schreiber (1998). Post-genomic science: converting primary structure into physiological function. Adv Enzyme Regul 38: 155-180.
27. Biswas, S. and J.M. Akey (2006). Genomic insights into positive selection. Trends Genet 22: 437-446.
28. Blekhman, R., O. Man, L. Herrmann, A.R. Boyko, A. Indap et al. (2008). Natural selection on genes that underlie human disease susceptibility. Curr Biol 18: 883-889.
29. Blouin, C., Y. Boucher, and A.J. Roger (2003). Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res 31: 790-797.
30. Box, G.E. P. (1979). Robustness in the strategy of scientific model building in Robustness in statistics, edited by R.L. Launer and G.N. Wilkinson. Academic Press, New York.
31. Boyko, A.R., S.H. Williamson, A.R. Indap, J.D. Degenhardt, R.D. Hernandez et al. (2008). Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083.
32. Bustamante, C.D., J. Wakeley, S. Sawyer and D.L. Hartl (2001). Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
33. Bustamante, C.D., A. Fledel-Alon, S. Williamson, R. Nielsen, M.T. Hubisz et al. (2005). Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
34. Cannarozzi, G., N.N. Schraudolph, M. Faty, P. von Rohr, M. Friberg et al. (2010). A role for codon order in translation dynamics. Cell 141: 355-367.
35. Carlini, D.B. and J.E. Genut (2006). Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J Mol Evol 62: 89-98.
36. Cartegni, L., J. Wang, Z. Zhu, M.Q. Zhang, and A.R. Krainer (2003). ESE finder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res 31: 3568-3571.
37. Cavalli-Sforza, L.L. (1966). Population structure and human evolution. Proc R Soc Lond B Biol Sci 164: 362-379.
38. Chamary, J.V., J.L. Parmley, and L.D. Hurst (2006). Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7: 98-108.
39. Chen, C.H., T.J. Chuang, B.Y. Liao, and F.C. Chen (2009). Scanning for the signatures of positive selection for human-specific insertions and deletions. Genome Biol Evol 1: 415-419.
40. Chen, H., N. Patterson, and D. Reich (2010). Population differentiation as a test for selective sweeps. Genome Res 20: 393-402.
41. Cho, S., Z.Y. Huang, D.R. Green, D.R. Smith, and J. Zhang (2006). Evolution of the complementary sex-determination gene of honey bees: balancing selection and transspecies polymorphisms. Genome Res 16: 1366-1375.
42. Chun, S. and J.C. Fay (2009). Identification of deleterious mutations within three human genomes. Genome Res 19: 1553-1561.
43. Clark, N.L. and C.F. Aquadro (2010). A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins. Mol Biol Evol 27: 1152-1161.
44. Clark, A.G., S. Glanowski, R. Nielsen, P.D. Thomas, A. Kejariwal et al. (2003). Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
45. Copley, S.D. (2009). Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat Chem Biol 5: 559-566.
46. Corona, E., J.T. Dudley, and A.J. Butte (2010). Extreme evolutionary disparities seen in positive selection across seven complex diseases. PLoS ONE 5.
47. de la Chaux, N., P.W. Messer, and P.F. Arndt (2007). DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. BMC Evol Biol 7: 191.
48. Depaulis, F. and M. Veuille (1998). Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol Biol Evol 15: 1788-1790.
49. DePristo, M.A., D.M. Weinreich, and D.L. Hartl (2005). Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 6: 678-687.
50. Di Rienzo, A. (2006). Population genetics models of common diseases. Curr Opin Genet Dev 16: 630-636.
51. Di Rienzo, A. and R.R. Hudson (2005). An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet 21: 596-601.
52. Dimitrieva, S. and M. Anisimova (2010). PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources. Trends Evol Biol 2: e1.
53. Ding, K. and I.J. Kullo (2009). Evolutionary genetics of coronary heart disease. Circulation 119: 459-467.
54. Dirksen, W.P., X. Li, A. Mayeda, A.R. Krainer and F.M. Rottman (2000). Mapping the SF2/ASF binding sites in the bovine growth hormone exonic splicing enhancer. J Biol Chem 275: 29170-29177.
55. Dorman, K.S. (2007). Identifying dramatic selection shifts in phylogenetic trees. BMC Evol Biol 7 Suppl 1: S10.
56. Drummond, D.A. and C.O. Wilke (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352.
57. Duret, L. (2002). Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12: 640-649.
58. Elena, S.F., C.O. Wilke, C. Ofria, and R.E. Lenski (2007). Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61:666-674.
59. Eyre-Walker, A. (2002). Changing effective population size and the McDonald-Kreitman test. Genetics 162:2017-2024.
60. Fay, J.C. and C.I. Wu (2000). Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
61. Fisher, R.A. (1930). The genetical theory of natural selection. Dover Press, New York.
62. Fletcher, W. and Z. Yang (2010). The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 27: 2257-2267.
63. Forster, R., C. Adami, and C.O. Wilke (2006). Selection for mutational robustness in finite populations. J Theor Biol 243: 181-190.
64. Fu, Y.X. and W.H. Li (1993). Statistical tests of neutrality of mutations. Genetics 133: 693-709.
65. Fukami-Kobayashi, K., D.R. Schreiber, and S.A. Benner (2002). Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J Mol Biol 319: 729-743.
66. Galtier, N. (2001). Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol 18: 866-873.
67. Galtier, N. and A. Jean-Marie (2004). Markov-modulated Markov chains and the covarion process of molecular evolution. J Comput Biol 11: 727-733.
68. Gaucher, E.A., X. Gu, M.M. Miyamoto, and S.A. Benner (2002). Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci 27: 315-321.
69. Gillespie, J.H. (2000a). Genetic drift in an infinite population. The pseudohitchhiking model. Genetics 155:909-919.
70. Gillespie, J.H. (2000b). The neutral theory in an infinite population. Gene 261: 11-18.
71. Gillespie, J.H. (2001). Is the population size of a species relevant to its evolution? Evolution 55: 2161-2169.
72. Goode, M., S. Guindon, and A. Rodrigo (2008). Modelling the evolution of protein coding sequences sampled from Measurably Evolving Populations. Genome Inform 21:150-164.
73. Gould, S.J. and R.C. Lewontin (1979). The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205: 581-598.
74. Gu, X. (2001). Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 18: 453-464.
75. Gu, X. (2006). A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol 23: 1937-1945.
76. Hahn, M.W. (2008). Toward a selection theory of molecular evolution. Evolution 62: 255-265.
77. Hancock, A.M., D.B. Witonsky, A.S. Gordon, G. Eshel, J.K. Pritchard et al. (2008). Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet 4: e32.
78. Hartl, D.L., E.N. Moriyama, and S.A. Sawyer (1994). Selection intensity for codon bias. Genetics 138: 227-234.
79. Hilser, V.J. and E.B. Thompson (2007). Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc Natl Acad Sci USA 104: 8311-8315.
80. Hirsh, A.E., H.B. Fraser, and D.P. Wall (2005). Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 22: 174-177.
81. Holder, M.T., P.O. Lewis, and D.L. Swofford (2010). The akaike information criterion will not choose the no common mechanism model. Syst Biol 59: 477-485.
82. Horowitz, N.H. (1945). On the evolution of biochemical syntheses. Proc Natl Acad Sci USA 31: 153-157.
83. Hudson, R.R., M. Kreitman, and M. Aguade (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
84. Hudson, R.R., M. Slatkin, and W.P. Maddison (1992). Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
85. Hudson, R.R., K. Bailey, D. Skarecky, J. Kwiatowski, and F.J. Ayala (1994). Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136: 1329-1340.
86. Huelsenbeck, J.P. (2002). Testing a covariotide model of DNA substitution. Mol Biol Evol 19: 698-707.
87. Hughes, A.L. and M. Nei (1988). Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
88. Hughes, T., D. Ekman, H. Ardawatia, A. Elofsson, and D.A. Liberles (2007). Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol 8: 213.
89. Jensen, R.A. (1976). Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
90. Kamneva, O., D.A. Liberles, and N. Ward (2010). Genomewide analysis of insertion and deletion substitutions in organisms of the PVC superphylum. Genome Biol Evol 2: 870-886.
91. Kim, Y. and R. Nielsen (2004). Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
92. Kim, Y. and W. Stephan (2002). Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
93. Kimchi-Sarfaty, C., J.M. Oh, I.W. Kim, Z.E. Sauna, A.M. Calcagno et al. (2007). A 'silent' polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528.
94. Kimura, M. (1962). On the probability of fixation of mutant genes in a population. Genetics 47: 713-719.
95. Kimura, R., A. Fujimoto, K. Tokunaga, and J. Ohashi (2007). A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS ONE 2: e286.
96. Kleinman, C.L., N. Rodrigue, N. Lartillot, and H. Philippe (2010). Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol 27: 1546-1560.
97. Komar, A.A. (2007). Genetics. SNPs, silent but not invisible. Science 315: 466-467.
98. Komar, A.A. (2009). A pause for thought along the co-translational folding pathway. Trends Biochem Sci 34: 16-24.
99. Kosakovsky Pond, S.L., S.D. Frost, Z. Grossman, M.B. Gravenor, D.D. Richman et al. (2006). Adaptation to different human populations by HIV-1 revealed by codon based analyses. PLoS Comput Biol 2: e62.
100. Kosakovsky Pond, S.L., K. Scheffler, M.B. Gravenor, A.F. Poon, and S.D. Frost (2010). Evolutionary finger printing of genes. Mol Biol Evol 27: 520-536.
101. Kosiol, C., T. Vinar, R.R. da Fonseca, M.J. Hubisz, C.D. Bustamante et al. (2008). Patterns of positive selection in six Mammalian genomes. PLoS Genet 4: e1000144.
102. Kreitman, M. and Akashi H. 1995 Molecular evidence for natural selection. Annu Rev Ecol Syst 26: 403-422.
103. Krishnamurthy, N., D.P. Brown, D. Kirshner, and K. Sjolander (2006). PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biol 7: R83.
104. Kryazhimskiy, S. and J.B. Plotkin (2008). The population genetics of dN/dS. PLoS Genet 4: e1000304.
105. Kwiatkowski, D.P. (2005). How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Genet 77: 171-192.
106. Landau, M., I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz et al. (2005). ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-302.
107. Lewontin, R.C. and J. Krakauer (1973). Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
108. Liberles, D.A. (2001). Evaluation of methods for determination of a reconstructed history of gene sequence evolution. Mol Biol Evol 18: 2040-2047.
109. Liberles, D.A., D.R. Schreiber, S. Govindarajan, S.G. Chamberlin, and S.A. Benner (2001). The adaptive evolution database (TAED). Genome Biol 2: RESEARCH0028.
110. Liberles, D.A., G. Kolesov, and K. Dittmar (2010). Joining biochemistry and population genetics to understand gene duplication in Evolution after gene duplication, edited by K. Dittmar and D.A. Liberles. Wiley, New York.
111. Liberles, D.A., M.D. Tisdell and J.A. Grahnen (2011). Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy. Proc Biol Sci B 278(1714): 1930-1935.
112. Light, S. and P. Kraulis (2004). Network analysis of metabolic enzyme evolution in Escherichia coli. BMC Bioinformatics 5: 15.
113. Liu, H.X., M. Zhang, and A.R. Krainer (1998). Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev 12: 1998-2012.
114. Lockhart, P.J., M.A. Steel, A.C. Barbrook, D.H. Huson, M.A. Charleston et al. (1998). A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol Biol Evol 15: 1183-1188.
115. Lunter, G., C.P. Ponting, and J. Hein (2006). Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2: e5.
116. MacCallum, C. and E. Hill (2006). Being positive about selection. PLoS Biol 4: e87.
117. Mallick, S., S. Gnerre, P. Muller, and D. Reich D (2009). The difficulty of avoiding false positives in genome scans for natural selection. Genome Res 19(5): 922-933.
118. Manly, K.F., D. Nettleton, and J.T. G. Hwang (2006). Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Res 14: 997-1001.
119. Manolio, T.A., F.S. Collins, N.J. Cox, D.B. Goldstein, L.A. Hindorff et al. (2009). Finding the missing heritability of complex diseases. Nature 461: 747-753.
120. McClellan, D.A. and D.D. Ellison (2010). Assessing and improving the accuracy of detecting protein adaptation with the Tree SAAP analytical software. Int J Bioinform Res Appl 6: 120-133.
121. McDonald, J.H. and M. Kreitman (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
122. Miller, R.G. J. (1981). Simultaneous statistical inference. Springer-Verlag, New York.
123. Miyamoto, M.M. and W.M. Fitch (1995). Testing the covarion hypothesis of molecular evolution. Mol Biol Evol 12: 503-513.
124. Moran, P.A. P. (1962). The statistical processes of evolutionary theory. Clarendon Press, Oxford.
125. Neel, J.V. (1962). Diabetes mellitus: a 'thrifty' genotype rendered detrimental by 'progress'? Am J Hum Genet 14: 353-362.
126. Ng, P.C. and S. Henikoff (2001). Predicting deleterious amino acid substitutions. Genome Res 11: 863-874.
127. Nielsen, R. (2001). Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
128. Nielsen, R. (2009). Adaptionism-30 years after Gould and Lewontin. Evolution 63: 2487-2490.
129. Nielsen, R. and Z. Yang (2003). Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol 20: 1231-1239.
130. Nielsen, R., S. Williamson, Y. Kim, M.J. Hubisz, A.G. Clark et al. (2005). Genomic scans for selective sweeps using SNP data. Genome Res 15: 1566-1575.
131. Nielsen, R., I. Hellmann, M. Hubisz, C. Bustamante, and A.G. Clark (2007). Recent and ongoing selection in the human genome. Nat Rev Genet 8: 857-868.
132. Nielsen, R., M.J. Hubisz, I. Hellmann, D. Torgerson, A.M. Andres et al. (2009). Darwinian and demographic forces affecting human protein coding genes. Genome Res 19: 838-849.
133. Nozawa, M., Y. Suzuki, and M. Nei (2009). Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA 106: 6700-6705.
134. Ohta, T. (1992). Theoretical study of near neutrality. II. Effect of subdivided population structure with local extinction and recolonization. Genetics 130: 917-923.
135. Ohta, T. (2002). Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci USA 99:16134-16137.
136. Parmley, J.L., J.V. Chamary, and L.D. Hurst (2006). Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23: 301-309.
137. Pechmann, S., E.D. Levy, G.G. Tartaglia, and M. Vendruscolo (2009). Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins. Proc Natl Acad Sci USA 106: 10159-10164.
138. Penn, O., A. Stern, N.D. Rubinstein, J. Dutheil, E. Bacharach et al. (2008). Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol 4: e1000214.
139. Penny, D., B.J. McComish, M.A. Charleston, and M.D. Hendy (2001). Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J Mol Evol 53: 711-723.
140. Perry, G.H., N.J. Dominy, K.G. Claw, A.S. Lee, H. Fiegler et al. (2007). Diet and the evolution of human amylase gene copy number variation. Nat Genet 39: 1256-1260.
141. Philippe, H., D. Casane, S. Gribaldo, P. Lopez, and J. Meunier (2003). Heterotachy and functional shift in protein evolution. IUBMB Life 55: 257-265.
142. Pie, M.R. and L.E. Alvares (2006). Evolution of myostatin in vertebrates: is there evidence for positive selection? Mol Phylogenet Evol 41: 730-734.
143. Podlaha, O., and J. Zhang (2003). Positive selection on protein-length in the evolution of a primate sperm ion channel. Proc Natl Acad Sci USA 100: 12241-12246.
144. Pollard, A.J., A.R. Krainer, S.C. Robson, and G.N. Europe-Finner (2002). Alternative splicing of the adenylyl cyclase stimulatory G-protein G alpha(s) is regulated by SF2/ASF and heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and involves the use of an unusual TG 3′-splice Site. J Biol Chem 277: 15241-15251.
145. Proux, E., R.A. Studer, S. Moretti, and M. Robinson-Rechavi (2009). Selectome: a database of positive selection. Nucleic Acids Res 37: D404-407.
146. Pupko, T. and N. Galtier (2002). A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc Biol Sci 269: 1313-1316.
147. Ramensky, V., P. Bork, and S. Sunyaev (2002). Human nonsynonymous SNPs: server and survey. Nucleic Acids Res 30: 3894-3900.
148. Rannala, B., T. Zhu, and Z. Yang, in press. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol Biol Evol.
149. Rastogi, S., N. Reuter and D.A. Liberles (2006). Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophys Chem 124: 134-144.
150. Resch, A.M., L. Carmel, L. Marino-Ramirez, A.Y. Ogurtsov, S.A. Shabalina et al. (2007). Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol 24: 1821-1831.
151. Rivas, E. (2005). Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics 6: 63.
152. Rivas, E. and S.R. Eddy (2008). Probabilistic phylogenetic inference with insertions and deletions. PLoS Comput Biol 4: e1000172.
153. Robinson, D.M., D.T. Jones, H. Kishino, N. Goldman, and J.L. Thorne (2003). Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol 20: 1692-1704.
154. Rocha, E.P. (2004). Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res 14: 2279-2286.
155. Rodrigue, N., H. Philippe, and N. Lartillot (2010). Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci USA 107: 4629-4634.
156. Rogers, A.R., D. Iltis, and S. Wooding (2004). Genetic variation at the MCIR locus and the time since loss of human body hair. Current Anthropology 45: 105-108.
157. Rom, D.M. (1990). A sequentially rejective test procedure based on a modified Bonferroni inequality. Biometrika 77: 663-665.
158. Rooke, N., V. Markovtsov, E. Cagavi, and D.L. Black (2003). Roles for SR proteins and hnRNP A1 in the regulation of c-src exon N1. Mol Cell Biol 23: 1874-1884.
159. Roth, C., M.J. Betts, P. Steffansson, G. Saelensminde, and D.A. Liberles (2005). The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. Nucleic Acids Res 33: D495-497.
160. Roth, C., S. Rastogi, L. Arvestad, K. Dittmar, S. Light et al. (2007). Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. J Exp Zool B Mol Dev Evol 308: 58-73.
161. Rubinstein, N.D., A. Doron-Faigenboim, I. Mayrose, and T. Pupko, 2011. Evolutionary models accounting for layers of selection in protein coding genes and their impact on the inference of positive selection. Mol Biol Evol.
162. Sabath, N. and D. Graur (2010). Detection of functional overlapping genes: simulation and case studies. J Mol Evol 71: 308-316.
163. Sabath, N., G. Landan, and D. Graur (2008). A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS ONE 3: e3996.
164. Sabeti, P.C., D.E. Reich, J.M. Higgins, H.Z. Levine, D.J. Richter et al. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
165. Sabeti, P.C., P. Varilly, B. Fry, J. Lohmueller, E. Hostetter et al. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
166. Sawyer, S.A. and D.L. Hartl (1992). Population genetics of polymorphism and divergence. Genetics 132:1161-1176.
167. Schneider, A., A. Souvorov, N. Sabath, G. Landan, G.H. Gonnet, and D. Graur (2009). Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol 1: 114-118.
168. Schwarz, G. (1978). Estimating the dimension of a model. Ann. Statist. 6: 461-464.
169. Seo, T.K. and H. Kishino (2008). Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins. Syst Biol 57: 367-377.
170. Seo, T.K. and H. Kishino (2009). Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences. Syst Biol 58: 199-210.
171. Shriver, M.D., G.C. Kennedy, E.J. Parra, H.A. Lawson, V. Sonpar et al. (2004). The genomic distribution of population substructure in four populations using 8,525 auto-somal SNPs. Hum Genomics 1: 274-286.
172. Siltberg, J. and D.A. Liberles (2002). A simple covarion based approach to analyse nucleotide substitution rates. Journal of Evolutionary Biology 15: 588-594.
173. Smith, N.G. and A. Eyre-Walker (2002). Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
174. Soyer, O.S. and S. Bonhoeffer (2006). Evolution of complexity in signaling pathways. Proc Natl Acad Sci USA 103: 16337-16342.
175. Spiegelhalter, D.J., N.G. Best, B.P. Carlin, and A. Van Der Linde (2002). Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64: 583-639.
176. Stern, A. and T. Pupko (2006). An evolutionary space-time model with varying among-site dependencies. Mol Biol Evol 23: 392-400.
177. Studer, R.A. and M. Robinson-Rechavi (2010). Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. Mol Biol Evol 27: 2618-2627.
178. Suchard, M.A. and B.D. Redelings (2006). BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22: 2047-2048.
179. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
180. Tang, K., K.R. Thornton, and M. Stoneking (2007). A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5: e171.
181. Tellgren, A., A.C. Berglund, P. Savolainen, C.M. Janis, and D.A. Liberles (2004). Myostatin rapid sequence evolution in ruminants predates domestication. Mol Phylogenet Evol 33: 782-790.
182. Tellgren-Roth, A., K. Dittmar, S.E. Massey, C. Kemi, C. Tellgren-Roth et al. (2009). Keeping the blood flowing-plasminogen activator genes and feeding behavior in vampire bats. Naturwissenschaften 96: 39-47.
183. Templeton, A.R. (1996). Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 144: 1263-1270.
184. Teufel, A.I., J.A. Grahnen, and D.A. Liberles (2012). Modeling proteins at the interface of structure, evolution, and population genetics in Computational modeling of biological systems: from molecules to pathways, edited by Dokholyan. Springer-Verlag, New York.
185. Thornton, K. and P. Andolfatto (2006). Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
186. Thornton, K.R., J.D. Jensen, C. Becquet, and P. Andolfatto (2007). Progress and prospects in mapping recent selection in the genome. Heredity 98: 340-348.
187. Tishkoff, S.A., F.A. Reed, A. Ranciaro, B.F. Voight, C.C. Babbitt et al. (2007). Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 39: 31-40.
188. Tsai, C.J., Z.E. Sauna, C. Kimchi-Sarfaty, S.V. Ambudkar, M.M. Gottesman et al. (2008). Synonymous mutations and ribosome stalling can lead to altered folding path-ways and distinct minima. J Mol Biol 383: 281-291.
189. Tuffley, C. and M. Steel (1998). Modeling the covarion hypothesis of nucleotide substitution. Math Biosci 147: 63-91.
190. Van der Hoorn, R.A., P.J. De Wit, and M.H. Joosten (2002). Balancing selection favors guarding resistance proteins. Trends Plant Sci 7: 67-71.
191. Voight, B.F., S. Kudaravalli, X. Wen, and J.K. Pritchard (2006). A map of recent positive selection in the human genome. PLoS Biol 4: e72.
192. Wagner, A. (2010). On the energy and material cost of gene duplication in Evolution after gene duplication, edited by K. Dittmar and D.A. Liberles. Wiley, New York.
193. Wang, E.T., G. Kodama, P. Baldi, and R.K. Moyzis (2006). Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci USA 103: 135-140.
194. Wang, H.C., M. Spencer, E. Susko, and A.J. Roger (2007). Testing for covarion-like evolution in protein sequences. Mol Biol Evol 24: 294-305.
195. Weir, B.S., L.R. Cardon, A.D. Anderson, D.M. Nielsen, and W.G. Hill (2005). Measures of human population structure show heterogeneity among genomic regions. Genome Res 15: 1468-1476.
196. Wichman, H.A., J. Millstein, and J.J. Bull (2005). Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170: 19-31.
197. Wilke, C.O. and D.A. Drummond (2010). Signatures of protein biophysics in coding sequence evolution. Curr Opin Struct Biol 20: 385-389.
198. Williams, P.D., D.D. Pollock, and R.A. Goldstein (2001). Evolution of functionality in lattice proteins. J Mol Graph Model 19: 150-156.
199. Williamson, S.H., M.J. Hubisz, A.G. Clark, B.A. Payseur, C.D. Bustamante et al. (2007). Localizing recent adaptive evolution in the human genome. PLoS Genet 3: e90.
200. Wong, W.S., 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.
201. Woolley, S., J. Johnson, M.J. Smith, K.A. Crandall, and D.A. McClellan (2003). TreeSAAP: selection on aminoacid properties using phylogenetic trees. Bioinformatics 19: 671-672.
202. Xing, Y. and C. Lee (2006). Can RNA selection pressure distort the measurement of Ka/Ks? Gene 370: 1-5.
203. Yang, Z. (2006). Computational molecular evolution. Oxford University Press, Oxford.
204. Yang, Z. and R. Nielsen (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
205. Yang, Z. and R. Nielsen (2008). Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25: 568-579.
206. Yang, Z., R. Nielsen, and N. Goldman (2009). In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA 106: E95; author reply E96.
207. Yap, V.B., H. Lindsay, S. Easteal, and G. Huttley (2010). Estimates of the effect of natural selection on proteincoding content. Mol Biol Evol 27: 726-734.
208. Zhang, L. and W.H. Li (2004). Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 21: 236-239.
209. Zhang, P., S. Mueller, M.C. Morais, C.M. Bator, V.D. Bowman et al. (2008). Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses. Proc Natl Acad Sci USA 105: 18284-18289.
210. Zhou, T., D.A. Drummond, and C.O. Wilke (2008). Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol 66: 395-404.
211. Zhou, T., W. Gu, and C.O. Wilke (2010). Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol 27: 1912-1922.
212. Zhu, L., and C.D. Bustamante (2005). A composite-likelihood approach for detecting directional selection from DNA sequence data. Genetics 170: 1411-1421.