Great ape genomics

ILAR Journal

Volumn 54, Issue 2, 2013, Pages 82-90

  Wall, Jeffrey D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Conservation genetics; Demography; Evolution; Great apes; Natural selection; Population size

Indexed keywords

ANIMAL; ARTICLE; CHROMOSOME; CONSERVATION GENETICS; DEMOGRAPHY; EVOLUTION; GENETIC VARIABILITY; GENETICS; GENOMICS; GREAT APES; HOMINID; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; NATURAL SELECTION; POPULATION SIZE;

CONSERVATION GENETICS; DEMOGRAPHY; EVOLUTION; GREAT APES; NATURAL SELECTION; POPULATION SIZE;

ANIMALS; BIOLOGICAL EVOLUTION; CHROMOSOMES; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOMICS; HOMINIDAE; HUMANS; MUTATION;

EID: 84887094704     PISSN: 10842020     EISSN: 19306180     Source Type: Journal    
DOI: 10.1093/ilar/ilt048     Document Type: Article

References (115)

1. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. 2009. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41:1061-1067.
2. Arnold ML, Meyer A. 2006. Natural hybridization in primates: One evolutionary mechanism. Zoology (Jena) 109:261-276.
3. Auton A, Fledel-Alon A, Pfeifer S, Venn O, Segurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G. 2012. A fine-scale chimpanzee genetic map from population sequencing. Science 336:193-198.
4. Ayala FJ. 1995. The myth of Eve: Molecular biology and human origins. Science 270:1930-1936.
5. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, Przeworski M, Coop G, de Massy B. 2010. PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327:836-840.
6. 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.
7. Berg IL, Neumann R, Lam KW, Sarbajna S, Odenthal-Hesse L, May CA, Jeffreys AJ. 2010. PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans. Nat Genet 42:859-863.
8. Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. 2008. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet 4:e1000271.
9. Bowden R, MacFie TS, Myers S, Hellenthal G, Nerrienet E, Bontrop RE, Freeman C, Donnelly P, Mundy NI. 2012. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population. PLoS Genet 8:e1002504.
10. Britten RJ. 2002. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci U S A 99:13633-13635.
11. Buhl AM, Jurlander J, Jorgensen FS, Ottesen AM, Cowland JB, Gjerdrum LM, Hansen BV, Leffers H. 2006. Identification of a gene on chromosome 12q22 uniquely overexpressed in chronic lymphocytic leukemia. Blood 107:2904-2911.
12. 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.
13. 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.
14. Caballero A. 1994. Developments in the prediction of effective population size. Heredity (Edinb) 73 (Pt 6):657-679.
15. Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, Geschwind DH, Lockhart DJ, Preuss TM, Barlow C. 2003. Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A 100:13030-13035.
16. Campbell G, Kuehl H, N'Goran Kouame P, Boesch C. 2008. Alarming decline of West African chimpanzees in Cote d'Ivoire. Curr Biol 18: R903-904.
17. 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.
18. 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.
19. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
20. Coop G, Bullaughey K, Luca F, Przeworski M. 2008. The timing of selection at the human FOXP2 gene. Mol Biol Evol 25:1257-1259.
21. Cooper G, Rubinsztein DC, Amos W. 1998. Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Hum Mol Genet 7:1425-1429.
22. Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF. 2010. Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun 1:131.
23. Curnoe D, Xueping J, Herries AI, Kanning B, Tacon PS, Zhende B, Fink D, Yunsheng Z, Hellstrom J, Yun L, Cassis G, Bing S, Wroe S, Shi H, Parr WC, Shengmin H, Rogers N. 2012. Human remains from the Pleistocene-Holocene transition of southwest China suggest a complex evolutionary history for East Asians. PLoS One 7:e31918.
24. Darwin C. 1871. The Descent of Man, and Selection in Relation to Sex. London, England: John Murray.
25. Dorus S, Evans PD, Wyckoff GJ, Choi SS, Lahn BT. 2004. Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Nat Genet 36:1326-1329.
26. Dreszer TR, Wall GD, Haussler D, Pollard KS. 2007. Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion. Genome Res 17:1420-1430.
27. 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.
28. Enard W, Przeworski M, Fisher SE, Lai CS,Wiebe V, Kitano T, Monaco AP, Paabo S. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-872.
29. Fischer A, Pollack J, Thalmann O, Nickel B, Paabo S. 2006. Demographic history and genetic differentiation in apes. Curr Biol 16:1133-1138.
30. Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour- Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM. 2004. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2:E207.
31. Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A. 2001. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet 69:831-843.
32. Galtier N, Duret L. 2007. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet 23:273-277.
33. 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.
34. Goidts V, Armengol L, Schempp W, Conroy J, Nowak N, Muller S, Cooper DN, Estivill X, Enard W, Szamalek JM, Hameister H, Kehrer- Sawatzki H. 2006. Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum Genet 119:185-198.
35. Goodman M. 1996. Epilogue: A personal account of the origins of a new paradigm. Mol Phylogenet Evol 5:269-285.
36. Goossens B, Chikhi L, Ancrenaz M, Lackman-Ancrenaz I, Andau P, Bruford MW. 2006. Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biol 4:e25.
37. Groves CP. 2006. Order Primates. In: DE Wilson, DM Reeder, editors. Mammal Species of the World. Baltimore: Johns Hopkins University Press. p. 111-184.
38. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5:e1000695.
39. Hammer MF, Mendez FL, Cox MP,Woerner AE, Wall JD. 2008. Sex-biased evolutionary forces shape genomic patterns of human diversity. PLoS Genet 4:e1000202.
40. Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, Wall JD. 2010. The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nat Genet 42:830-831.
41. Harcourt AH, Harvey PH, Larson SG, Short RV. 1981. Testis weight, body weight and breeding system in primates. Nature 293:55-57.
42. Harding RM, Fullerton SM, Griffiths RC, Clegg JB. 1997. A gene tree for beta-globin sequences from Melanesia. JMol Evol 44 Suppl 1:pS133-138.
43. Harvati K, Stringer C, Grun R, Aubert M, Allsworth-Jones P, Folorunso CA. 2011. The Later Stone Age calvaria from Iwo Eleru, Nigeria: Morphology and chronology. PLoS One 6:e24024.
44. Hedrick PW. 2011. Population genetics of malaria resistance in humans. Heredity (Edinb) 107:283-304.
45. Hu HY, He L, Fominykh K, Yan Z, Guo S, Zhang X, Taylor MS, Tang L, Li J, Liu J,Wang W, Yu H, Khaitovich P. 2012. Evolution of the humanspecific microRNA miR-941. Nat Commun 3:1145.
46. Huet T, Cheynier R, Meyerhans A, Roelants G, Wain-Hobson S. 1990. Genetic organization of a chimpanzee lentivirus related to HIV-1. Nature 345:356-359.
47. Huxley TH. 1863. Evidence as to Man's Place in Nature. London England: Williams and Norgate.
48. IUCN. 2012. International Union for Conservation of Nature Red List.
49. Jolly CJ. 2001. A proper study for mankind: Analogies from the Papionin monkeys and their implications for human evolution. Am J Phys Anthropol Suppl 33:177-204.
50. Junker J, Blake S, Boesch C, Campbell G, du Toit L, Duvall C, Ekobo A, Etoga G, Galat-Luong A, Gamys J, Ganas-Swaray J, Gatti S, Ghiurghi A, Granier N, Hart J, Head J, Herbinger I, Hicks TC, Huijbregts B, Imong IS, Kuempel N, Lahm S, Lindsell J, Maisels F, McLennan M, Martinez L, Morgan B, Morgan D, Mulindahabi F, Mundry R, N'Goran KP, Normand E, Ntongho A, Okon DT, Petre CA, Plumptre A, Rainey H, Regnaut S, Sanz C, Stokes E, Tondossama A, Tranquilli S, Sunderland-Groves J, Walsh P, Warren Y, Williamson EA, Kuehl HS. 2012. Recent decline in suitable environmental conditions for African great apes. Diversity and Distributions 18:1077-1091.
51. Kaessmann H, Wiebe V, Weiss G, Paabo S. 2001. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat Genet 27:155-156.
52. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. 2010. GC-biased evolution near human accelerated regions. PLoS Genet 6:e1000960.
53. Keele BF, Van Heuverswyn F, Li Y, Bailes E, Takehisa J, Santiago ML, Bibollet- Ruche F, Chen Y, Wain LV, Liegeois F, Loul S, Ngole EM, Bienvenue Y, Delaporte E, Brookfield JF, Sharp PM, Shaw GM, Peeters M, Hahn BH. 2006. Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science 313:523-526.
54. Keinan A, Mullikin JC, Patterson N, Reich D. 2009. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet 41:66-70.
55. Kim HL, Igawa T, Kawashima A, Satta Y, Takahata N. 2010. Divergence, demography and gene loss along the human lineage. Philos Trans R Soc Lond B Biol Sci 365:2451-2457.
56. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge, United Kingdom: Cambridge University Press.
57. King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
58. Klein J, Satta Y, Takahata N, O'hUigin C. 1993. Trans-specific Mhc polymorphism and the origin of species in primates. J Med Primatol 22:57-64.
59. Knowles DG, McLysaght A. 2009. Recent de novo origin of human proteincoding genes. Genome Res 19:1752-1759.
60. Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin JJ, Hanni C, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Paabo S. 2007. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17:1908-1912.
61. Leffler EM, Gao Z, Pfeifer S, Segurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G, Donnelly P, McVean G, Przeworski M. 2013. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339:1578-1582.
62. 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.
63. Li WH, Sadler LA. 1991. Low nucleotide diversity in man. Genetics 129:513-523.
64. Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ. 2005. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437:94-100.
65. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G,Mauceli E,Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, RasmussenMD, Robinson J, Stark A, Vilella AJ,Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S,Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER,Weinstock GM,Wilson RK, Genome Institute atWashington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Keller M. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478:476-482.
66. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469:529-533.
67. Maricic T, Gunther V, Georgiev O, Gehre S, Curlin M, Schreiweis C, Naumann R, Burbano HA, Meyer M, Lalueza-Fox C, de la Rasilla M, Rosas A, Gajovic S, Kelso J, Enard W, Schaffner W, Pääbo S. 2013. A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene. Mol Biol Evol 4:844-852.
68. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
69. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF. 2008. Runs of homozygosity in European populations. Am J Hum Genet 83:359-372.
70. Morwood MJ, Brown P, Jatmiko, Sutikna T, Saptomo EW, Westaway KE, Due RA, Roberts RG, Maeda T, Wasisto S, Djubiantono T. 2005. Further evidence for small-bodied hominins from the Late Pleistocene of Flores, Indonesia. Nature 437:1012-1017.
71. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. 2005. A fine-scale map of recombination rates and hotspots across the human genome. Science 310:321-324.
72. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, MacFie TS, McVean G, Donnelly P. 2010. Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327:876-879.
73. Nater A, Arora N, Greminger MP, van Schaik CP, Singleton I, Wich SA, Fredriksson G, Perwitasari-Farajallah D, Pamungkas J, Krutzen M. 2013. Marked population structure and recent migration in the critically endangered Sumatran orangutan (Pongo abelii). J Hered 104:2-13.
74. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zöllner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V. 2012. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337:100-104.
75. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, J Sninsky J, Adams MD, Cargill M. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3:e170.
76. Nowick K, Gernat T, Almaas E, Stubbs L. 2009. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A 106:22358-22363.
77. O'hUigin C, Satta Y, Takahata N, Klein J. 2002. Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol Biol Evol 19:1501-1513.
78. Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS, Ponting CP. 2009. Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet 5:e1000753.
79. Olson MV. 1999. When less is more: Gene loss as an engine of evolutionary change. Am J Hum Genet 64:18-23.
80. Pluzhnikov A, Di Rienzo A, Hudson RR. 2002. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics 161:1209-1218.
81. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. 2006. Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2:e168.
82. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167-172.
83. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente- Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. 2013. Great ape genetic diversity and population history. Nature 449:471-475.
84. Prufer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486:527-531.
85. Ptak SE, Enard W, Wiebe V, Hellmann I, Krause J, Lachmann M, Paabo S. 2009. Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol 26:2181-2184.
86. Ptak SE, Roeder AE, Stephens M, Gilad Y, Paabo S, Przeworski M. 2004. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol 2:e155.
87. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques- Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.
88. Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
89. Rifkin SA, Houle D, Kim J, White KP. 2005. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 438:220-223.
90. Romero IG, Ruvinsky I, Gilad Y. 2012. Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet 13:505-516.
91. Satta Y, Klein J, Takahata N. 2000. DNA archives and our nearest relative: The trichotomy problem revisited. Mol Phylogenet Evol 14:259-275.
92. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175.
93. Segurel L, Thompson EE, Flutre T, Lovstad J, Venkat A, Margulis SW, Moyse J, Ross S, Gamble K, Sella G, Ober C, Przeworski M. 2012. The ABO blood group is a trans-species polymorphism in primates. Proc Natl Acad Sci U S A 109:18493-18498.
94. Sharp PM, Hahn BH. 2011. Origins of HIVand the AIDS pandemic. Cold Spring Harb Perspect Med 1:a006841.
95. Sibley CG, Ahlquist JE. 1987. DNA hybridization evidence of hominoid phylogeny: Results from an expanded data set. J Mol Evol 26:99-121.
96. Siepel A, Pollard KS, Haussler D. 2006. New methods for detecting lineage-specific selection. Research in Computational Molecular Biology, Proceedings 3909:190-205.
97. Somel M, Franz H, Yan Z, Lorenc A, Guo S, Giger T, Kelso J, Nickel B, Dannemann M, Bahn S, Webster MJ, Weickert CS, Lachmann M, Pääbo S, Khaitovich P. 2009. Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A 106:5743-5748.
98. Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J. 1999. Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400:667-671.
99. Stedman HH, Kozyak BW, Nelson A, Thesier DM, Su LT, Low DW, Bridges CR, Shrager JB, Minugh-Purvis N, Mitchell MA. 2004. Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 428:415-418.
100. Takahata N. 1993. Allelic genealogy and human evolution. Mol Biol Evol 10:2-22.
101. Takahata N, Satta Y. 1997. Evolution of the primate lineage leading to modern humans: Phylogenetic and demographic inferences from DNA sequences. Proc Natl Acad Sci U S A 94:4811-4815.
102. Ventura M, Catacchio CR, Sajjadian S, Vives L, Sudmant PH, Marques-Bonet T, Graves TA,Wilson RK, Eichler EE. 2012. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome Res 22:1036-1049.
103. Voight BF, Adams AM, Frisse LA, Qian Y, Hudson RR, Di Rienzo A. 2005. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci U S A 102:18508-18513.
104. Wall JD. 2003. Estimating ancestral population sizes and divergence times. Genetics 163:395-404.
105. Wall JD, Cox MP, Mendez FL, Woerner A, Severson T, Hammer MF. 2008. A novel DNA sequence database for analyzing human demographic history. Genome Res 18:1354-1361.
106. Wall JD, Frisse LA, Hudson RR, Di Rienzo A. 2003. Comparative linkagedisequilibrium analysis of the beta-globin hotspot in primates. Am J Hum Genet 73:1330-1340.
107. Wall JD, Slatkin M. 2012. Paleopopulation genetics. Annu Rev Genet 46:635-649.
108. Wilson GM, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG, Holt RA. 2006. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res 16:173-181.
109. Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GA, Gabriel SB, Reich D, Donnelly P, Altshuler D. 2005. Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308:107-111.
110. Wise CA, Sraml M, Rubinsztein DC, Easteal S. 1997. Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees. Mol Biol Evol 14:707-716.
111. Wu DD, Irwin DD, Zhang YP. 2011. De novo origin of human proteincoding genes. PLoS Genet 7:e1002379.
112. Xu AG, He L, Li Z, Xu Y, Li M, Fu X, Yan Z, Yuan Y, Menzel C, Li N, Somel M, Hu H, Chen W, Pääbo S, Khaitovich P. 2010. Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol 6:e1000843.
113. Xu X, Arnason U. 1996. The mitochondrial DNA molecule of Sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan. J Mol Evol 43:431-437.
114. 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.
115. Yunis JJ, Prakash O. 1982. The origin of man: A chromosomal pictorial legacy. Science 215:1525-1530.