Erratum: Nonadaptive processes in primate and human evolution (Yearbook of Physical Anthropology (2010) 53 (13-45) DOI: 10.1002/ajpa.21439);Nonadaptive processes in primate and human evolution

American Journal of Physical Anthropology

Volumn 143, Issue SUPPL. 51, 2010, Pages 13-45

  Harris, Eugene E ^a  

^a QUEENSBOROUGH COMMUNITY COLLEGE   (United States)

Author keywords

compensatory substitution; effective population size; gene duplication; genetic drift; neutral theory; positive selection; purifying selection; selective constraint

Indexed keywords

MITOCHONDRIAL DNA;

CRANIOFACIAL MORPHOLOGY; EFFECTIVE POPULATION SIZE; EVOLUTION; EVOLUTIONARY ADAPTATION; EVOLUTIONARY RATE; GENE DUPLICATION; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENETIC DRIFT; GENETIC SELECTION; HUMAN; NATURAL SELECTION; NEUTRAL GENE THEORY; NONHUMAN; PRIMATE; REVIEW;

EID: 78649667359     PISSN: 00029483     EISSN: 10968644     Source Type: Journal    
DOI: 10.1002/ajpa.21654     Document Type: Erratum

References (293)

1. Ackermann RR, Cheverud JM,. 2004. Detecting genetic drift versus selection in human evolution. Proc Natl Acad Sci USA 101: 17946-17951.
2. Aguade M, Miyashita N, Langley CH,. 1989. Reduced variation in the Yellow-Achaete-Scute Region in natural populations of Drosophila melanogaster. Genetics 122: 607-615.
3. Akey JM,. 2009. Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 19: 711-722.
4. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD,. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12: 1805-1814.
5. Arbiza L, Dopazo J, Dopazo H,. 2006. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol 2: e38.
6. Arcos-Burgos M, Muenke M,. 2002. Genetics of population isolates. Clin Genet 61: 233-247.
7. Bailey JA, Liu G, Eichler EE,. 2003. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 73: 823-834.
8. Bakewell MA, Shi P, Zhang J,. 2007. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104: 7489-7494.
9. Bamshad M, Wooding SP,. 2003. Signatures of natural selection in the human genome. Nat Rev Genet 4: 99-111.
10. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L,. 2008. Natural selection has driven population differentiation in modern humans. Nat Genet 40: 340-345.
11. Bazin E, Glémin S, Galtier N,. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 312: 570-572.
12. Beaumont MA, Balding DJ,. 2004. Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13: 969-980.
13. Begun DJ, Aquadro CF,. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
14. Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH,. 2007. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol 5: e310.
15. Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN,. 2004. Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74: 1111-1120.
16. Betti L, Balloux F, Amos W, Hanihara T, Manica A,. 2009. Distance from Africa, not climate, explains within-population phenotypic diversity in humans. Proc Biol Sci 276: 809-814.
17. Bierne N, Eyre-Walker A,. 2004. The genomic rate of adaptive amino acid substitution in Drosophila. Mol Biol Evol 21: 1350-1360.
18. Birky CW Jr, Walsh JB,. 1988. Effects of linkage on rates of molecular evolution. Proc Natl Acad Sci USA 85: 6414-6418.
19. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD,. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083.
20. Bramble DM, Lieberman DE,. 2004. Endurance running and the evolution of Homo. Nature 432: 345-352.
21. Bromham L, Woolfit M,. 2004. Explosive radiations and the reliability of molecular clocks: island endemic radiations as a test case. Syst Biol 53: 758-766.
22. Brosius J,. 1991. Retroposons-seeds of evolution. Science 251: 753.
23. Brosius J, Gould SJ,. 1992. On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA." Proc Natl Acad Sci USA 89: 10706-10710.
24. Burch CL, Chao L,. 1999. Evolution by small steps and rugged landscapes in the RNA virus φ6. Genetics 151: 921-927.
25. Burgess R, Yang Z,. 2008. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25: 1979-1994.
26. Burton OJ, Travis JM,. 2008. The frequency of fitness peak shifts is increased at expanding range margins due to mutation surfing. Genetics 179: 941-950.
27. Bush EC, Lahn BT,. 2005. Selective constraint on noncoding regions of hominid genomes. PLoS Comput Biol 1: e73.
28. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG,. 2005. Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
29. Cai JJ, Macpherson JM, Sella G, Petrov DA,. 2009. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5: e1000336.
30. Camps M, Herman A, Loh E, Loeb LA,. 2007. Genetic constraints on protein evolution. Crit Rev Biochem Mol Biol 42: 313-326.
31. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A, Chen Z, Chu J, Carcassi C, Contu L, Du R, Excoffier L, Ferrara GB, Friedlaender JS, Groot H, Gurwitz D, Jenkins T, Herrera RJ, Huang X, Kidd J, Kidd KK, Langaney A, Lin AA, Mehdi SQ, Parham P, Piazza A, Pistillo MP, Qian Y, Shu Q, Xu J, Zhu S, Weber JL, Greely HT, Feldman MW, Thomas G, Dausset J, Cavalli-Sforza LL,. 2002. A human genome diversity cell line panel. Science 296: 261-262.
32. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES,. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22: 231-238.
33. Carroll SB,. 2003. Genetics and the making of Homo sapiens. Nature 422: 849-857.
34. Caswell JL, Mallick S, Richter DJ, Neubauer J, Schirmer C, Gnerre S, Reich D,. 2008. Analysis of chimpanzee history based on genome sequence alignments. PLoS Genet 4: e1000057.
35. Cavalli-Sforza LL,. 1966. Population structure and human evolution. Proc R Soc Lond B Biol Sci 164: 362-379.
36. Cavalli-Sforza LL,. 1994. The history and geography of human genes. Princeton, NJ: Princeton University Press.
37. Cavalli-Sforza LL, Menozzi P, Piazza A,. 1993. Demic expansions and human evolution. Science 259: 639-646.
38. Chakroborty R, Nei M,. 1982. Genetic differentiation of quantitative characters between populations or species. I. Mutation and random genetic drift. Genet Res 39: 303-214.
39. Charlesworth B,. 1994. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet Res 63: 213-227.
40. Charlesworth B, Morgan MT, Charlesworth D,. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
41. Charlesworth J, Eyre-Walker A,. 2006. The rate of adaptive evolution in enteric bacteria. Mol Biol Evol 23: 1348-1356. (Pubitemid 43992336)
42. Charlesworth J, Eyre-Walker A,. 2007. The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proc Natl Acad Sci USA 104: 16992-16997.
43. Charlesworth J, Eyre-Walker A,. 2008. The McDonald-Kreitman test and slightly deleterious mutations. Mol Biol Evol 25: 1007-1015.
44. Chen FC, Li WH,. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet 68: 444-456.
45. Chen XH, Shi H, Liu XL, Su B,. 2006. The testis-specific apoptosis related gene TTL.6 underwent adaptive evolution in the lineage leading to humans. Gene 370: 58-63.
46. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Paabo S, Rocchi M, Eichler EE,. 2005. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437: 88-93.
47. Chiaroni J, Underhill PA, Cavalli-Sforza LL,. 2009. Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci USA 106: 20174-20179.
48. Clarimon J, Andres AM, Bertranpetit J, Comas D,. 2004. Comparative analysis of Alu insertion sequences in the APP 5′ flanking region in humans and other primates. J Mol Evol 58: 722-731.
49. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M,. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
50. Clegg SM, Degnan SM, Moritz C, Estoup A, Kikkawa J, Owens IP,. 2002. Microevolution in island forms: the roles of drift and directional selection in morphological divergence of a passerine bird. Evolution 56: 2090-2099.
51. Crow J,. 2008. Mid-century controversies in population genetics. Ann Rev Genet 42: 1-16.
52. Currat M, Excoffier L, Maddison W, Otto SP, Ray N, Whitlock MC, Yeaman S,. 2006. Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens" and "Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans." Science 313: 172; author reply 172.
53. Davis BH, Poon AF, Whitlock MC,. 2009. Compensatory mutations are repeatable and clustered within proteins. Proc Biol Sci 276: 1823-1827.
54. DeGiorgio M, Jakobsson M, Rosenberg NA,. 2009. Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci USA 106: 16057-16062.
55. Deshpande O, Batzoglou S, Feldman MW, Cavalli-Sforza LL,. 2009. A serial founder effect model for human settlement out of Africa. Proc Biol Sci 276: 291-300.
56. Demuth JP, Hahn MW,. 2009. The life and death of gene families. Bioessays 31: 29-39.
57. DePristo MA, Weinreich DM, Hartl DL,. 2005. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 6: 678-687.
58. Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM,. 2007. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res 17: 1266-1277.
59. Edmonds CA, Lillie AS, Cavalli-Sforza LL,. 2004. Mutations arising in the wave front of an expanding population. Proc Natl Acad Sci USA 101: 975-979.
60. Ellegren H,. 2009. A selection model of molecular evolution incorporating the effective population size. Evolution 63: 301-305.
61. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P, Nieselt-Struwe K, Muchmore E, Varki A, Ravid R, Doxiadis GM, Bontrop RE, Paabo S,. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
62. Endler JA,. 1973. Gene flow and population differentiation. Science 179: 243-250.
63. Eory L, Halligan DL, Keightley PD,. 2010. Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol 1: 177-192.
64. Estes S, Lynch M,. 2003. Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans. Evolution 57: 1022-1030.
65. Eswaran V,. 2002. A diffusion wave out of Africa: the mechanism of the modern human revolution? Curr Anthropol 43: 749-774.
66. Eswaran V, Harpending H, Rogers AR,. 2005. Genomics refutes an exclusively African origin of humans. J Hum Evol 49: 1-18.
67. Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, Vaez-Azizi LM, Tishkoff SA, Hudson RR, Lahn BT,. 2005. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 309: 1717-1720.
68. Excoffier L, Hofer T, Foll M,. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103: 285-298.
69. Excoffier L, Ray N,. 2008. Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol Evol 23: 347-351.
70. Eyre-Walker A,. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics 162: 2017-2024.
71. Eyre-Walker A,. 2006a. The genomic rate of adaptive evolution. Trends Ecol Evol 21: 569-575.
72. Eyre-Walker A,. 2006b. Size does not matter for mitochondrial DNA. Science 312: 537-538.
73. Eyre-Walker A, Keightley PD,. 1999. High genomic deleterious mutation rates in hominids. Nature 397: 344-347.
74. Eyre-Walker A, Keightley PD,. 2007. The distribution of fitness effects of new mutations. Nat Rev Genet 8: 610-618.
75. Eyre-Walker A, Keightley PD,. 2009. Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol 26: 2097-2108.
76. Eyre-Walker A, Keightley PD, Smith NG, Gaffney D,. 2002. Quantifying the slightly deleterious mutation model of molecular evolution. Mol Biol Evol 19: 2142-2149.
77. Eyre-Walker A, Woolfit M, Phelps T,. 2006. The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173: 891-900.
78. Fay JC, Wyckoff GJ, Wu CI,. 2001. Positive and negative selection on the human genome. Genetics 158: 1227-1234.
79. Felsenstein J,. 1974. The evolutionary advantage of recombination. Genetics 78: 737-756.
80. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J,. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
81. Ford EB,. 1964. Ecological genetics. New York: John Wiley.
82. François O, Currat M, Ray N, Han E, Excoffier L, Novembre J,. 2010. Principal component analysis under population genetic models of range expansion and admixture. Mol Biol Evol 27: 1257-1268.
83. Fu YX,. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
84. Gaffney DJ, Blekhman R, Majewski J,. 2008. Selective constraints in experimentally defined primate regulatory regions. PLoS Genet 4: e1000157.
85. Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N,. 2007. Population bottlenecks as a potential major shaping force of human genome architecture. PLoS Genet 3: e119.
86. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS,. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234. (Pubitemid 46633091)
87. Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP,. 2006. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
88. Gillespie JH,. 1991. The causes of molecular evolution. Oxford: Oxford University Press.
89. Gillespie JH,. 2000a. The neutral theory in an infinite population. Gene 261: 11-18.
90. Gillespie JH,. 2000b. Genetic drift in an infinite population. The pseudohitchhiking model. Genetics 155: 909-919.
91. Gillespie JH,. 2001. Is the population size of a species relevant to its evolution? Evolution 55: 2161-2169.
92. Gojobori J, Tang H, Akey JM, Wu CI,. 2007. Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution. Proc Natl Acad Sci USA 104: 3907-3912.
93. Gould SJ, Lewontin RC,. 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.
94. Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC,. 2010. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327: 883-886.
95. Hahn MW,. 2008. Toward a selection theory of molecular evolution. Evolution 62: 255-265.
96. Hahn MW, Demuth JP, Han SG,. 2007. Accelerated rate of gene gain and loss in primates. Genetics 177: 1941-1949.
97. Hallatschek O, Nelson DR,. 2008. Gene surfing in expanding populations. Theor Popul Biol 73: 158-170.
98. Hallatschek O, Nelson DR,. 2009. Life at the front of an expanding population. Evolution 64: 193-206.
99. Halligan DL, Oliver F, Eyre-Walker A, Harr B, Keightley PD,. 2010. Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet 6: 1-9.
100. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, Weder A, Cooper R, Lipshutz R, Chakravarti A,. 1999. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22: 239-247.
101. Hamblin MT, DiRienzo A,. 2000. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet 66: 1669-1679.
102. Hamblin MT, Thompson EE, DiRienzo A,. 2002. Complex signatures of natural selection at the Duffy blood group locus. Am J Hum Genet 70: 369-383.
103. Hamdi HK, Nishio H, Tavis J, Zielinski R, Dugaiczyk A,. 2000. Alu-mediated phylogenetic novelties in gene regulation and development. J Mol Biol 299: 931-939.
104. Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW,. 2009. Adaptive evolution of young gene duplicates in mammals. Genome Res 19: 859-867.
105. Handley LJ, Manica A, Goudet J, Balloux F,. 2007. Going the distance: human population genetics in a clinal world. Trends Genet 23: 432-439.
106. Harris EE, Hey J,. 1999. X chromosome evidence for ancient human histories. Proc Natl Acad Sci USA 96: 3320-3324.
107. Harris EE, Hey J,. 2001. Human populations show reduced DNA sequence variation at the factor IX locus. Curr Biol 11: 774-748.
108. Harris EE, Meyer D,. 2006. The molecular signature of selection underlying human adaptations. Am J Phys Anthropol Suppl 43: 89-130.
109. Hartl DL, Taubes CH,. 1996. Compensatory nearly neutral mutations: selection without adaptation. J Theor Biol 182: 303-309.
110. Hawks J, Wang ET, Cochran GM, Harpending HC, Moyzis RK,. 2007. Recent acceleration of human adaptive evolution. Proc Natl Acad Sci USA 104: 20753-20758.
111. Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA,. 2007. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet 39: 1140-1144.
112. Hazkani-Covo E, Graur D,. 2007. A comparative analysis of numt evolution in human and chimpanzee. Mol Biol Evol 24: 13-18.
113. He X, Zhang J,. 2005. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164.
114. Heger A, Ponting CP,. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res 17: 1837-1849.
115. Hellmann I, Mang Y, Gu Z, Li P, de la Vega FM, Clark AG, Nielsen R,. 2008. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res 18: 1020-1029.
116. Hellmann I, Prüfer K, Ji H, Zody MC, Pääbo S, Ptak SE,. 2005. Why do human diversity levels vary at a megabase scale? Genome Res 15: 1222-1231.
117. Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD,. 2007. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 316: 240-243.
118. Hey J,. 1999. The neutralist, the fly and the selectionist. Trends Ecol Evol 14: 35-38.
119. Hill WG, Robertson A,. 1966. The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.
120. Hofer T, Ray N, Wegmann D, Excoffier L,. 2009. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann Hum Genet 73: 95-108.
121. Hughes AL,. 1994. The evolution of functionally novel proteins after gene duplication. Proc Biol Sci 256: 119-124.
122. Hughes AL,. 2007. Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364-373.
123. Hughes AL,. 2008. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann N Y Acad Sci 1133: 162-179.
124. Hughes AL,. 2009. Evolution in the post-genome era. Perspect Biol Med 52: 332-337.
125. Hughes AL, Friedman R,. 2009. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene 440: 50-56.
126. Hughes AL, Nei M,. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
127. Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M,. 2003. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc Natl Acad Sci USA 100: 15754-15757.
128. Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M,. 2005. Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding loci. Genetics 170: 1181-1187.
129. Hunley KL, Healy ME, Long JC,. 2009. The global pattern of gene identity variation reveals a history of long-range migrations, bottlenecks, and local mate exchange: implications for biological race. Am J Phys Anthropol 139: 35-46.
130. Hunt G,. 2007. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proc Natl Acad Sci USA 104: 18404-18408.
131. International Human Genome Sequencing Consortium. 2004 Finishing the euchromatic sequence of the human genome. Nature. 431 (7011): 931-945.
132. Jensen-Seaman MI, Wildschutte JH, Soto-Calderon ID, Anthony NM,. 2009. A comparative approach shows differences in patterns of numt insertion during hominoid evolution. J Mol Evol 68: 688-699.
133. Kayser M, Brauer S, Stoneking M,. 2003. A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol 20: 893-900.
134. Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ,. 2005a. Evolutionary constraints in conserved nongenic sequences of mammals. Genome Res 15: 1373-1378.
135. Keightley PD, Lercher MJ, Eyre-Walker A,. 2005b. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol 3: e42.
136. Keightley PD, Lercher MJ, Eyre-Walker A,. 2006. Understanding the degradation of hominid gene control. PLoS Comput Biol 2: e19; author reply e26.
137. Khaitovich P, Enard W, Lachmann M, Paabo S,. 2006. Evolution of primate gene expression. Nat Rev Genet 7: 693-702.
138. Khaitovich P, Paabo S, Weiss G,. 2005. Toward a neutral evolutionary model of gene expression. Genetics 170: 929-939.
139. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, Wirkner U, Ansorge W, Paabo S,. 2004. A neutral model of transcriptome evolution. PLoS Biol 2: e132.
140. Kim SY, Pritchard JK,. 2007. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet 3: 1572-1586.
141. Kimura M,. 1968. Evolutionary rate at the molecular level. Nature 217: 624-626.
142. Kimura M,. 1969. The rate of molecular evolution considered from the standpoint of population genetics. Proc Natl Acad Sci USA 63: 1181-1188.
143. Kimura M,. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
144. Kimura M,. 1991. Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics. Proc Natl Acad Sci USA 88: 5969-5973.
145. King JL, Jukes TH,. 1969. Non-Darwinian evolution. Science 164: 788-798.
146. King MC, Wilson AC,. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
147. Klopfstein S, Currat M, Excoffier L,. 2006. The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol 23: 482-490.
148. Kondrashov AS,. 1995. Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? J Theor Biol 175: 583-594.
149. Kondrashov AS, Sunyaev S, Kondrashov FA,. 2002. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci USA 99: 14878-14883.
150. Kondrashov FA, Kondrashov AS,. 2006. Role of selection in fixation of gene duplications. J Theor Biol 239: 141-151.
151. Kondrashov FA, Koonin EV,. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet 20: 287-290.
152. Koonin EV,. 2004. A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man. Cell Cycle 3: 280-285.
153. Koonin EV,. 2009a. Darwinian evolution in the light of genomics. Nucleic Acids Res 37: 1011-1034.
154. Koonin EV,. 2009b. Evolution of genome architecture. Int J Biochem Cell Biol 41: 298-306.
155. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A,. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet 4: e1000144.
156. Kreitman M,. 1996. The neutral theory is dead. Long live the neutral theory. Bioessays 18: 678-683; discussion 683.
157. Krull M, Brosius J, Schmitz J,. 2005. Alu-SINE exonization: en route to protein-coding function. Mol Biol Evol 22: 1702-1711.
158. Kryukov GV, Schmidt S, Sunyaev S,. 2005. Small fitness effect of mutations in highly conserved non-coding regions. Hum Mol Genet 14: 2221-2229.
159. Kulathinal RJ, Bettencourt BR, Hartl DL,. 2004. Compensated deleterious mutations in insect genomes. Science 306: 1553-1554.
160. Lande R,. 1976. Natural selection and random genetic drift in phenotypic evolution. Evolution 30: 314-334.
161. Lande R,. 1979. Quantitative genetic analysis of multivariate evolution, applied to brain: body size, allometry. Evolution 33: 402-416.
162. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
163. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B,. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet Res 52: 223-235.
164. Lee J, Han K, Meyer TJ, Kim HS, Batzer MA,. 2008. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLoS One 3: e4047.
165. Lemos B, Meiklejohn CD, Caceres M, Hartl DL,. 2005. Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories. Evolution 59: 126-137.
166. Lenski RE, Travisano M,. 1994. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci USA 91: 6808-6814.
167. Lev-Maor G, Ram O, Kim E, Sela N, Goren A, Levanon EY, Ast G,. 2008. Intronic Alus influence alternative splicing. PLoS Genet 4: e1000204.
168. Lev-Maor G, Sorek R, Shomron N, Ast G,. 2003. The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 300: 1288-1291.
169. Lewontin RC,. 1974. The genetic basis of evolutionary change. New York: Columbia University Press.
170. Lewontin RC, Krakauer J,. 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
171. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM,. 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: 1100-1104.
172. Lin L, Jiang P, Shen S, Sato S, Davidson BL, Xing Y,. 2009. Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes. Hum Mol Genet 18: 2204-2214.
173. Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y,. 2008. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet 4: e1000225.
174. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
175. Liu G, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE,. 2003. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res 13: 358-368.
176. Liu H, Prugnolle F, Manica A, Balloux F,. 2006. A geographically explicit genetic model of worldwide human-settlement history. Am J Hum Genet 79: 230-237.
177. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD,. 2008. Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994-997.
178. Ludwig MZ, Bergman C, Patel NH, Kreitman M,. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
179. Lynch M,. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. Am Nat 136: 727-741.
180. Lynch M,. 2007a. The origins of genome architecture. Sunderland, MA: Sinauer Associates, Inc.
181. Lynch M,. 2007b. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104 (Suppl 1): 8597-8604.
182. Lynch M, Conery JS,. 2003. The origins of genome complexity. Science 302: 1401-1404.
183. Lynch M, Conery JS,. 2004. Testing genome complexity. Science 304: 389-390.
184. Lynch M, Force A,. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
185. Lynch M, Hill W,. 1986. Phenotypic evolution by neutral mutation. Evolution 40: 915-935.
186. Makalowski W,. 2003. Genomics. Not junk after all. Science 300: 1246-1247.
187. Mallick S, Gnerre S, Muller P, Reich D,. 2009. The difficulty of avoiding false positives in genome scans for natural selection. Genome Res 19: 922-933.
188. Marques-Bonet T, Girirajan S, Eichler EE,. 2009a. The origins and impact of primate segmental duplications. Trends Genet 25: 443-454.
189. Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Alkan C, Aksay G, Girirajan S, Siswara P, Chen L, Cardone MF, Navarro A, Mardis ER, Wilson RK, Eichler EE,. 2009b. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877-881.
190. Marroig G, Cheverud JM,. 2004. Did natural selection or genetic drift produce the cranial diversification of neotropical monkeys? Am Nat 163: 417-428.
191. Maslin MA, Christensen B,. 2007. Tectonics, orbital forcing, global climate change, and human evolution in Africa: introduction to the African paleoclimate special volume. J Hum Evol 53: 443-464.
192. Maynard Smith J, Haigh J,. 1974. The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
193. McDonald JH, Kreitman M,. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
194. McVicker G, Gordon D, Davis C, Green P,. 2009. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: e1000471.
195. Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT,. 2005. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 309: 1720-1722.
196. Mikkelsen TS, Hillier LW, Eichler EE, et al. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
197. Millien V,. 2006. Morphological evolution is accelerated among island mammals. PLoS Biol 4: e321.
198. Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE,. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet 78: 671-679.
199. Miyata T, Miyazawa S, Yasunaga T,. 1979. Two types of amino acid substitutions in protein evolution. J Mol Evol 12: 219-236.
200. Modrek B, Lee CJ,. 2003. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet 34: 177-180.
201. Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M,. 2008. Identification and analysis of genomic regions with large between-population differentiation in humans. Ann Hum Genet 72: 99-110.
202. Nachman MW, Bauer VL, Crowell SL, Aquadro CF,. 1998. DNA variability and recombination rates at X-linked loci in humans. Genetics 150: 1133-1141.
203. Nei M,. 2005. Selectionism and neutralism in molecular evolution. Mol Biol Evol 22: 2318-2342.
204. Nei M, Niimura Y, Nozawa M,. 2008. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 9: 951-963.
205. Nei M, Rooney AP,. 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39: 121-152.
206. Nguyen DQ, Webber C, Hehir-Kwa J, Pfundt R, Veltman J, Ponting CP,. 2008. Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res 18: 1711-1723.
207. Nielsen R,. 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86 (Pt 6): 641-647.
208. Nielsen R,. 2005. Molecular signatures of natural selection. Annu Rev Genet 39: 197-218.
209. Nielsen R, Yang Z,. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
210. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, Sninsky JJ, Adams MD, Cargill M,. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170.
211. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG,. 2007. Recent and ongoing selection in the human genome. Nat Rev Genet 8: 857-868. (Pubitemid 47609088)
212. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM,. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113-1118. (Pubitemid 44789035)
213. Novembre J, DiRienzo A,. 2009. Spatial patterns of variation due to natural selection in humans. Nat Rev Genet 10: 745-755.
214. Nozawa M, Kawahara Y, Nei M,. 2007. Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci USA 140: 20421-20426.
215. Nozawa M, Nei M,. 2008. Genomic drift and copy number variation of chemosensory receptor genes in humans and mice. Cytogenet Genome Res 123: 263-269.
216. Ohno S,. 1970. Evolution by gene duplication. Berlin: Springer-Verlag.
217. Ohta T,. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246: 96-98.
218. Ohta T,. 1974. Mutational pressure as the main cause of molecular evolution and polymorphism. Nature 246: 96-98.
219. Ohta T,. 2002. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci USA 99: 16134-16137.
220. Ohta T,. 2003. Origin of the neutral and nearly neutral theories of evolution. J Biosci 28: 371-377.
221. Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D,. 2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103-1108.
222. Pérez-Claros JA, Aledo JC,. 2007. Comment on "Morphological evolution is accelerated among island mammals." PLoS Biol 5: e180; author reply e176.
223. Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC,. 2007. Diet and the evolution of human amylase gene copy number variation. Nat Genet 39: 1256-1260. (Pubitemid 47482688)
224. Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R,. 2008. Copy number variation and evolution in humans and chimpanzees. Genome Res 18: 1698-1710.
225. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK,. 2009. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19: 826-837.
226. Ponting CP, Lunter G,. 2006. Signatures of adaptive evolution within human non-coding sequence. Hum Mol Genet 15 (Spec No 2): R170-175.
227. Pool JE, Hellmann I, Jensen JD, Nielsen R,. 2010. Population genetic inference from genomic sequence variation. Genome Res 20: 291-300.
228. Poon A, Davis BH, Chao L,. 2005. The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood. Genetics 170: 1323-1332.
229. Poon A, Otto SP,. 2000. Compensating for our load of mutations: freezing the meltdown of small populations. Evolution 54: 1467-1479.
230. Powers SK, Jackson MJ,. 2008. Exercise-induced oxidative stress: cellular mechanisms and impact on muscle force production. Physiol Rev 88: 1243-1276.
231. Premo LS, Hublin JJ,. 2009. Culture, population structure, and low genetic diversity in Pleistocene hominins. Proc Natl Acad Sci USA 106: 33-37.
232. Prud'homme B, Gompel N, Carroll SB,. 2007. Emerging principles of regulatory evolution. Proc Natl Acad Sci USA 104 (Suppl 1): 8605-8612.
233. Prugnolle F, Manica A, Balloux F,. 2005. Geography predicts neutral genetic diversity of human populations. Curr Biol 15: R159-R160.
234. Przeworski M, Hudson RR, DiRienzo A,. 2000. Adjusting the focus on human variation. Trends Genet 16: 296-302.
235. Qian W, Zhang J,. 2008. Gene dosage and gene duplicability. Genetics 179: 2319-2324.
236. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL,. 2005. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA 102: 15942-15947.
237. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME,. 2006. Global variation in copy number in the human genome. Nature 444: 444-454. (Pubitemid 44809057)
238. Reed FA, Akey JM, Aquadro CF,. 2005. Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes. Genome Res 15: 1211-1221.
239. Reed FA, Aquadro CF,. 2006. Mutation, selection and the future of human evolution. Trends Genet 22: 479-484.
240. Relethford JH,. 1994. Craniometric variation among modern human populations. Am J Phys Anthropol 95: 53-62.
241. Relethford JH,. 2002. Apportionment of global human genetic diversity based on craniometrics and skin color. Am J Phys Anthropol 118: 393-398.
242. Risch N, Tang H, Katzenstein H, Ekstein J,. 2003. Geographic distribution of disease mutations in the Ashkenazi Jewish population supports genetic drift over selection. Am J Hum Genet 72: 812-822.
243. Roseman CC,. 2004. Detecting interregionally diversifying natural selection on modern human cranial form by using matched molecular and morphometric data. Proc Natl Acad Sci USA 101: 12824-12829.
244. Roseman CC, Weaver TD,. 2007. Molecules versus morphology? Not for the human cranium. Bioessays 29: 1185-1188.
245. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES,. 2006. Positive natural selection in the human lineage. Science 312: 1614-1620.
246. Sawyer SA, Parsch J, Zhang Z, Hartl DL,. 2007. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci USA 104: 6504-6510.
247. Schultz ST, Lynch M,. 1997. Deleterious mutation and extinction: effects of variable mutational effects, synergistic epistasis, beneficial mutations, and degree of outcrossing. Evolution 51: 1363-1371.
248. Sella G, Petrov DA, Przeworski M, Andolfatto P,. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet 5: e1000495.
249. Siepel A,. 2009. Phylogenomics of primates and their ancestral populations. Genome Res 19: 1929-1941.
250. Slatkin M,. 2004. A population-genetic test of founder effects and implications for Ashkenazi Jewish diseases. Am J Hum Genet 75: 282-293.
251. Smith NG, Eyre-Walker A,. 2002. Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
252. Smouse PE, Vitzthum VJ, Neel JV,. 1981. The impact of random and lineal fission of the genetic divergence of small human groups: a case study among the Yanomama. Genetics 98: 179-197.
253. Sokal RR, Smouse PE, Neel JV,. 1986. The genetic structure of a tribal population, the Yanomama Indians. XV. Patterns inferred by autocorrelation analysis. Genetics 114: 259-287.
254. Soranzo N, Bufe B, Sabeti PC, Wilson JF, Weale ME, Marguerie R, Meyerhof W, Goldstein DB,. 2005. Positive selection on a high-sensitivity allele of the human bitter-taste receptor TAS2R16. Curr Biol 15: 1257-1265.
255. Sorrentino S, Libonati M,. 1997. Structure-function relationships in human ribonucleases: main distinctive features of the major RNase types. FEBS Lett 404: 1-5.
256. Steiper ME, Young NM,. 2006. Primate molecular divergence dates. Mol Phylogenet Evol 41: 384-394.
257. Stoltzfus A,. 1999. On the possibility of constructive neutral evolution. J Mol Evol 49: 169-181.
258. Stoltzfus A,. 2006. Mutationism and the dual causation of evolutionary change. Evol Dev 8: 304-317.
259. Stoltzfus A, Yampolsky LY,. 2009. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered 100: 637-647.
260. Tang K, Thornton KR, Stoneking M,. 2007. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5: e171.
261. Taylor JS, Raes J,. 2004. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38: 615-643.
262. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA,. 2006. Heterotachy in mammalian promoter evolution. PLoS Genet 2: e30.
263. Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM,. 2007. Recent human effective population size estimated from linkage disequilibrium. Genome Res 17: 520-526.
264. Thornburg BG, Gotea V, Makalowski W,. 2006. Transposable elements as a significant source of transcription regulating signals. Gene 365: 104-110.
265. Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, Deloukas P,. 2007. Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 39: 31-40.
266. Trauth MH, Larrasoana JC, Mudelsee M,. 2009. Trends, rhythms and events in Plio-Pleistocene African climate. Quart Sci Rev 28: 399-411.
267. Trauth MH, Maslin MA, Deino A, Strecker MR,. 2005. Late Cenozoic moisture history of East Africa. Science 309: 2051-2053.
268. Trauth MH, Maslin MA, Deino AL, Strecker MR, Bergner AG, Duhnforth M,. 2007. High- and low-latitude forcing of Plio-Pleistocene East African climate and human evolution. J Hum Evol 53: 475-486.
269. Travis JM, Munkemuller T, Burton OJ, Best A, Dytham C, Johst K,. 2007. Deleterious mutations can surf to high densities on the wave front of an expanding population. Mol Biol Evol 24: 2334-2343.
270. Vinogradov AE,. 2004. Testing genome complexity. Science 304: 389-390; author reply 389-390.
271. Voight BF, Kudaravalli S, Wen X, Pritchard JK,. 2006. A map of recent positive selection in the human genome. PLoS Biol 4: e72.
272. Wall JD,. 2003. Estimating ancestral population sizes and divergence times. Genetics 163: 395-404.
273. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, et al. 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175-183.
274. Weaver TD,. 2009. Out of Africa: modern human origins special feature: the meaning of Neandertal skeletal morphology. Proc Natl Acad Sci USA 106: 16028-16033.
275. Weaver TD, Roseman CC, Stringer CB,. 2007. Were Neandertal and modern human cranial differences produced by natural selection or genetic drift? J Hum Evol 53: 135-145.
276. Weber MJ,. 2006. Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet 2: e205.
277. Welch JJ,. 2006. Estimating the genomewide rate of adaptive protein evolution in Drosophila. Genetics 173: 821-837.
278. Whitehead A, Crawford DL,. 2006. Variation within and among species in gene expression: raw material for evolution. Mol Ecol 15: 1197-1211.
279. Whitlock MC,. 2000. Fixation of new alleles and the extinction of small populations: drift load, beneficial alleles, and sexual selection. Evolution 54: 1855-1861.
280. Whitlock MC,. 2003. Fixation probability and time in subdivided populations. Genetics 164: 767-779.
281. Williford A, Comeron JM,. 2010. Local effects of limited recombination: historical perspective and consequences for population estimates of adaptive evolution. J Hered 101 (Suppl 1): S127-S34.
282. Wong WS, Nielsen R,. 2004. Detecting selection in noncoding regions of nucleotide sequences. Genetics 167: 949-958.
283. Woolfit M, Bromham L,. 2005. Population size and molecular evolution on islands. Proc Biol Sci 272: 2277-2282.
284. Wray GA,. 2007. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206-216.
285. Wright S,. 1951. The genetical structure of populations. Ann Eugen 15: 323-354.
286. Xue Y, Daly A, Yngvadottir B, Liu M, Coop G, Kim Y, Sabeti P, Chen Y, Stalker J, Huckle E, Burton J, Leonard S, Rogers J, Tyler-Smith C,. 2006. Spread of an inactive form of caspase-12 in humans is due to recent positive selection. Am J Hum Genet 78: 659-670.
287. Yang Z, Nielsen R,. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19: 908-917.
288. Yi S, Streelman JT,. 2005. Genome size is negatively correlated with effective population size in ray-finned fish. Trends Genet 21: 643-646.
289. Yu N, Zhao Z, Fu YX, Sambuughin N, Ramsay M, Jenkins T, Leskinen E, Patthy L, Jorde LB, Kuromori T, Li WH,. 2001. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol 18: 214-222. (Pubitemid 32118866)
290. Zhang J,. 2006. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nat Genet 38: 819-823.
291. Zhang J,. 2007. The drifting human genome. Proc Natl Acad Sci USA 104: 20147-20148.
292. Zhang J, Zhang YP, Rosenberg HF,. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet 30: 411-415.
293. Zhang L, Li WH,. 2005. Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol 22: 2504-2507.