Comparative primate genomics

Annual Review of Genomics and Human Genetics

Volumn 5, Issue , 2004, Pages 351-378

  Enard, Wolfgang ^a   Pääbo, Svante ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

Apes; Chimpanzee; Gene expression; Molecular evolution; Selection

Indexed keywords

APE; CHIMPANZEE; CHROMOSOME REARRANGEMENT; DNA SEQUENCE; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION; GENE INSERTION; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOMICS; HUMAN; HUMAN GENOME; INTERSPECIFIC RELATIONSHIP; KARYOTYPE; LONG INTERSPERSED REPEAT; MAMMAL; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIMATE; REVIEW; SHORT INTERSPERSED REPEAT; TANDEM REPEAT;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; EVOLUTION, MOLECULAR; GENOMICS; PHYLOGENY; PRIMATES; SPECIES SPECIFICITY;

ALOCASIA MACRORRHIZOS; INSERTION SEQUENCES; MAMMALIA; PAN TROGLODYTES; PRIMATES;

EID: 5444231736     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.5.061903.180040     Document Type: Review

References (154)

1. Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, et al. 2003. Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc. Natl. Acad. Sci. USA 100:7708-13
2. Arnason U, Gullberg A, Burguete AS, Janke A. 2000. Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133:217-28
3. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. 2002. Recent segmental duplications in the human genome. Science 297:1003-7
4. Bailey JA, Liu G, Eichler EE. 2003. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73:823-34
5. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. 2001. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11:1005-17
6. Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, et al. 2002. Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70:83-100
7. Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE. 2004. Analysis of segmental duplications and genome assembly in the mouse. Genome Res. 14: 789-801
8. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3:370-79
9. Bischoff JL, Shamp DD. 2003. The Sima de los Huesos hominids date to beyond U/Th equilibrium (>350 kyr) and perhaps to 400-500 kyr: new radiometric dates. J. Archaeol. Sci. 30:275-80
10. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, et al. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299:1391-94
11. Britten RJ. 2002. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Natl. Acad. Sci. USA 99:13633-35
12. Brosius J. 1999. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107: 209-38
13. Brosius J. 2003. The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118:99-116
14. Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, et al. 2003. Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl. Acad. Sci. USA 100:13030-35
15. Carroll SB. 2003. Genetics and the making of Homo sapiens. Nature 422:849-57
16. Chen F-C, Li W-H. 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. 68:444-56
17. Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, et al. 2003. Recent segmental and gene duplications in the mouse genome. Genome Biol. 4:R47
18. Chou HH, Takematsu H, Diaz S, Iber J, Nickerson E, et al. 1998. A mutation in human CMP-sialic acid hydroxylase occurred after the Homo-Pan divergence. Proc. Natl. Acad. Sci. USA 95:11751-56
19. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-63
20. Cooper GM, Sidow A. 2003. Genomic regulatory regions: insights from comparative sequence analysis. Curr. Opin. Genet. Dev. 13:604-10
21. Deinard A, Kidd K. 1999. Evolution of a HOXB6 intergenic region within the great apes and humans. J. Hum. Evol. 36: 687-703
22. Deinard AS, Kidd K. 2000. Identifying conservation units within captive chimpanzee populations. Am. J. Phys. Anthropol. 111:25-44
23. Deininger PL, Batzer MA. 1999. Alu repeats and human disease. Mol. Genet. Metab. 67:183-93
24. Deininger PL, Moran JV, Batzer MA, Kazazian HH Jr. 2003. Mobile elements and mammalian genome evolution. Curr. Opin. Genet. Dev. 13:651-58
25. Ebersberger I, Metzler D, Schwarz C, Paabo S. 2002. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70:1490-97
26. Eichler EE, DeJong PJ. 2002. Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resource. Genome Res. 12:673-78
27. Ellegren H, Primmer CR, Sheldon BC. 1995. Microsatellite 'evolution': directionality or bias? Nat. Genet. 11:360-62
28. Ellegren H, Smith NG, Webster MT. 2003. Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Dev. 13:562-68
29. Enard W, Fassbender A, Model F, Adorjan P, Paabo S, Olek A. 2004. Differences in DNA methylation patterns between humans and chimpanzees. Curr. Biol. 14:R148-49
30. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, et al. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 296:340-43
31. Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, et al. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-72
32. Excoffier L. 2002. Human demographic history: refining the recent African origin model. Curr. Opin. Genet. Dev. 12:675-82
33. Fan Y, Linardopoulou E, Friedman C, Williams E, Trask BJ. 2002. Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes. Genome Res. 12:1651-62
34. Fan Y, Newman T, Linardopoulou E, Trask BJ. 2002. Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions. Genome Res. 12:1663-72
35. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-13
36. Fay JC, Wu CI. 2003. Sequence divergence, functional constraint, and selection in protein evolution. Annu. Rev. Genomics Hum. Genet. 4:213-35
37. Fay JC, Wyckoff GJ, Wu CI. 2001. Positive and negative selection on the human genome. Genetics 158:1227-34
38. Fischer A, Wiebe V, Paabo S, Przeworski M. 2004. Evidence for a complex demographic history of chimpanzees. Mol. Biol. Evol. 21:799-808
39. Fleagle JG. 1999. Primate Adaptation and Evolution. San Diego: Academic
40. Frazer KA, Chen X, Hinds DA, Pant PV, Patil N, Cox DR. 2003. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 13:341-46
41. Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, et al. 2002. Construction and analysis of a human-chimpanzee comparative clone map. Science 295:131-34
42. Gagneux P, Amess B, Diaz S, Moore S, Patel T, et al. 2001. Proteomic comparison of human and great ape blood plasma reveals conserved glycosylation and differences in thyroid hormone metabolism. Am. J. Phys. Anthropol. 115:99-109
43. Gagneux P, Varki A. 2001. Genetic differences between humans and great apes. Mol. Phylogenet. Evol. 18:2-13
44. Gagneux P, Wills C, Gerloff U, Tautz D, Morin PA, et al. 1999. Mitochondrial sequences show diverse evolutionary histories of African hominoids. Proc. Natl. Acad. Sci. USA 96:5077-82
45. Deleted in proof
46. Gilad Y, Bustamante CD, Lancet D, Paabo S. 2003. Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am. J. Hum. Genet. 73:489-501
47. Glazko GV, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol. Biol. Evol. 20:424-34
48. Goldstein D, Schlotterer C. 1999. Microsatellites: Evolution and Applications. Oxford: Oxford Univ. Press
49. Goodman M. 1999. The genomic record of Humankind's evolutionary roots. Am. J. Hum. Genet. 64:31-39
50. Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, et al. 1998. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 9:585-98
51. Grubb P, Butynski TM, Oates JF, Bearder SK, Disotell TR, et al. 2003. Assessment of the diversity of African primates. Int. J. Primatol. 24:1301-57
52. Gu J, Gu X. 2003. Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 19:63-65
53. Hacia JG. 2001. Genome of the apes. Trends Genet. 17:637-45
54. Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST. 1998. Genetic traces of ancient demography. Proc. Natl. Acad. Sci. USA 95:1961-67
55. Hayakawa T, Satta Y, Gagneux P, Varki A, Takahata N. 2001. Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene. Proc. Natl. Acad. Sci. USA 98:11399-404
56. Hellmann I, Ebersberger I, Ptak SE, Paabo S, Przeworski M. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72:1527-35
57. Hellmann I, Zollner S, Enard W, Ebersberger I, Nickel B, Paabo S. 2003. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13:831-37
58. Hsieh WP, Chu TM, Wolfmger RD, Gibson G. 2003. Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165:747-57
59. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-59
60. Huxley TH. 1863. Evidence as to Man's Place in Nature. New York: D. Appleton
61. Irie A, Koyama S, Kozutsumi Y, Kawasaki T, Suzuki A. 1998. The molecular basis for the absence of N-glycolylneuraminic acid in humans. J. Biol. Chem. 273:15866-71
62. Jeffreys AJ, Kauppi L, Neumann R. 2001. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29:217-22
63. Jeffreys AJ, Neumann R. 2002. Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot. Nat. Genet. 31:267-71
64. Jensen-Seaman MI, Deinard AS, Kidd KK. 2001. Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas. J. Hered. 92:475-80
65. Kaessmann H, Pääbo S. 2002. The genetical history of humans and the great apes. J. Intern. Med. 251:1-18
66. Kaessmann H, Wiebe V, Paabo S. 1999. Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-62
67. Kaessmann H, Wiebe V, Weiss G, Paabo S. 2001. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet. 27:155-56
68. Karaman MW, Houck ML, Chemnick LG, Nagpal S, Chawannakul D, et al. 2003. Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts. Genome Res. 13:1619-30
69. Kehrer-Sawatzki H, Schreiner B, Tanzer S, Platzer M, Muller S, Hameister H. 2002. Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17. Am. J. Hum. Genet. 71:375-88
70. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, et al. 2004. A neutral model of transcriptome evolution. PLoS Biol. 2:E132
71. Kim Y, Stephan W. 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160:765-77
72. Kitano T, Schwarz C, Nickel B, Paabo S. 2003. Gene diversity patterns at 10 X-chromosomal loci in humans and chimpanzees. Mol. Biol. Evol. 20:1281-89
73. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, et al. 2002. A high-resolution recombination map of the human genome. Nat. Genet. 31:241-47
74. Kreitman M. 2000. Methods to detect selection in populations with applications to the human. Annu. Rev. Genomics Hum. Genet. 1:539-59
75. Krings M, Capelli C, Tschentscher F, Geisert H, Meyer S, et al. 2000. A view of Neandertal genetic diversity. Nat. Genet. 26:144-46
76. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Paabo S. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90: 19-30
77. Kumar S, Subramanian S. 2002. Mutation rates in mammalian genomes. Proc. Nad. Acad. Sci. USA 99:803-8
78. Lai CSL, Fisher SE, Hurst JA, Vargha-Khadem F, Monaco AP. 2001. A forkhead-domain gene is mutated in a severe speech and language disorder. Nature 413:519-23
79. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
80. Lawn RM, Boonmark NW, Schwartz K, Lindahl GE, Wade DP, et al. 1995. The recurring evolution of lipoprotein(a). Insights from cloning of hedgehog apolipoprotein(a). J. Biol. Chem. 270:24004-9
81. Lercher MJ, Williams EJ, Hurst LD. 2001. Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias. Mol. Biol. Evol. 18:2032-39
82. Li W-H. 1997. Molecular Evolution. Sunderland, MA: Sinauer
83. Li WH, Ellsworth DL, Krushkal J, Chang BH, Hewett-Emmett D. 1996. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5:182-87
84. Liu G, Zhao S, Bailey JA, Sahinalp SC, Alkan C, et al. 2003. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res. 13:358-68
85. Locke DP, Archidiacono N, Misceo D, Cardone MF, Deschamps S, et al. 2003. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol. 4:R50
86. Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, et al. 2003. Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res. 13:347-57
87. Long M, Betran E, Thornton K, Wang W. 2003. The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4:865-75
88. Lu J, Li WH, Wu CI. 2003. Comment on "chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes." Science 302: 988
89. Makova KD, Li WH. 2002. Strong male-driven evolution of DNA sequences in humans and apes. Nature 416:624-26
90. Maynard Smith J, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23:23-35
91. McConkey EH, Goodman M. 1997. A human genome evolution project is needed. Trends Genet. 13:350-51
92. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-54
93. McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR, Donnelly P. 2004. The fine-scale structure of recombination rate variation in the human genome. Science 304:581-84
94. Moran JV, DeBerardinis RJ, Kazazian HH Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283:1530-34
95. Muller S, Wienberg J. 2001. "Barcoding" primate chromosomes: molecular cytogenetic screening for the ancestral hominoid karyotype. Hum. Genet. 109:85-94
96. Murphy WJ, Stanyon R, O'Brien SJ. 2001. Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol. 2: REVIEWS0005.1-8
97. Nagpal S, Karaman MW, Timmerman MM, Ho VV, Pike BL, Hacia JG. 2004. Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks. Nucleic Acids Res. 32:e51
98. Navarre A, Barton NH. 2003. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution 57:447-59
99. Navarro A, Barton NH. 2003. Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 300: 321-24
100. Nei M, Kumar AM. 2000. Molecular Evolution and Phylogenetics. pp. 75-77. Oxford: Oxford Univ. Press
101. Nekrutenko A, Li WH. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17:619-21
102. Nielsen R. 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86:641-47
103. O'Brien SJ, Stanyon R. 1999. Phylogenomics. Ancestral primate viewed. Nature 402:365-66
104. Ohta T. 1993. An examination of the generation-time effect on molecular evolution. Proc. Natl. Acad. Sci. USA 90: 10676-80
105. Olson MV, Varki A. 2003. Sequencing the chimpanzee genome: insights into human evolution and disease. Nat. Rev. Genet. 4:20-28
106. Ovchinnikov IV, Gotherstrom A, Romanova GP, Kharitonov VM, Liden K, Goodwin W. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404:490-93
107. Page SL, Goodman M. 2001. Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade. Mol. Phylogenet. Evol. 18:14-25
108. Prak ET, Kazazian HH Jr. 2000. Mobile elements and the human genome. Nat. Rev. Genet. 1:134-44
109. Przeworski M. 2002. The signature of positive selection at randomly chosen loci. Genetics 160:1179-89
110. Przeworski M. 2003. Estimating the time since the fixation of a beneficial allele. Genetics 164:1667-76
111. Ptak SE, Roeder AD, Stephens M, Gilad Y, Paabo S, Przeworski M. 2004. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol. In press
112. Rieseberg LH. 2001. Chromosomal rearrangements and speciation. Trends Ecol. Evol. 16:351-58
113. Rogers J, Mahaney MC, Witte SM, Nair S, Newman D, et al. 2000. A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms. Genomics 67:237-47
114. Rosenberg HF, Feldmann MW. 2002. The Relationship Between Coalescence Times and Population Divergence Times. Oxford: Oxford Univ. Press
115. Rosenberg NA, Nordborg M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:380-90
116. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, et al. 2003. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423:873-76
117. Rubinsztein DC, Amos W, Leggo J, Goodburn S, Jain S, et al. 1995. Microsatellite evolution-evidence for directionality and variation in rate between species. Nat. Genet. 10:337-43
118. Ruvolo M. 1997. Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets. Mol. Biol. Evol. 14:248-65
119. Samonte RV, Eichler EE. 2002. Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3:65-72
120. Saunders IW, Tavare S, Watterson GA. 1984. On the genealogy of nested subsamples from a haploid population. Adv. Appl. Prob. 16:471-91
121. Schmilz J, Ohme M, Zischler H. 2001. SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157:777-84
122. Schmitz RW, Serre D, Bonani G, Feine S, Hillgruber F, et al. 2002. The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from lhe Neander Valley, Germany. Proc. Natl. Acad. Sci. USA 99:13342-47
123. Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, et al. 2004. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol. 2:E57
124. Springer MS, Murphy WJ, Eizirik E, O'Brien SJ. 2003. Placenlal mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. USA 100:1056-61
125. Slankiewicz P, Lupski JR. 2002. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18:74-82
126. Slone AC, Griffilhs RC, Zegura SL, Hammer MF. 2002. High levels of Y-chromosome nucleotide diversity in the genus Pan. Proc. Natl. Acad. Sci. USA 99:43-48
127. Subramanian S, Kumar S. 2003. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13:838-44
128. Szabo Z, Levi-Minzi SA, Christiano AM, Struminger C, Stoneking M, et al. 1999. Sequential loss of Iwo neighboring exons of the tropoelastin gene during primate evolution. J. Mol. Evol. 49:664-71
129. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-95
130. Tuzun E, Bailey JA, Eichler EE. 2004. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res. 14:493-506
131. Varki A. 2000. A chimpanzee genome project is a biomedical imperative. Genome Res. 10:1065-70
132. Varki A, Wills C, Perlmutter D, Woodruff D, Gage F, et al. 1998. Great ape phenome project? Science 282:239-40
133. Vigilant L, Hofreiter M, Siedel H, Boesch C. 2001. Paternity and relatedness in wild chimpanzee communities. Proc. Natl. Acad. Sci. USA 98:12890-95
134. Wall JD. 2003. Estimating ancestral population sizes and divergence times. Genetics 163:395-404
135. Wall JD, Prisse LA, Hudson RR, Di Rienzo A. 2003. Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates. Am. J. Hum. Genet. 73:1330-40
136. Walsh PD, Abernethy KA, Bermejo M, Beyers R, De Wachter P, et al. 2003. Catastrophic ape decline in western equatorial Africa. Nature 422:611-14
137. Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, et al. 2004. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 429:382-88
138. Watase K, Zoghbi HY. 2003. Modelling brain diseases in mice: the challenges of design and analysis. Nat. Rev. Genet. 4:296-307
139. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-62
140. Webster MT, Smith NG, Ellegren H. 2002. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proc. Natl. Acad. Sci. USA 99:8748-53
141. Webster MT, Smith NG, Ellegren H. 2003. Compositional evolution of non-coding DNA in the human and chimpanzee genomes. Mol. Biol. Evol. 20:278-86
142. Whiten A, Goodall J, McGrew WC, Nishida T, Reynolds V, et al. 1999. Cultures in chimpanzees. Nature 399:682-85
143. Wildman DE, Uddin M, Liu G, Grossman LI, Goodman M. 2003. Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. Proc. Natl. Acad. Sci. USA 100:7181-88
144. Wolfe KH, Li WH. 2003. Molecular evolution meets the genomics revolution. Nat. Genet. 33(Suppl.):255-65
145. Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19: 908-17
146. Yi S, Ellsworth DL, Li WH. 2002. Slow molecular clocks in Old World monkeys, apes, and humans. Mol. Biol. Evol. 19:2191-98
147. Yokoyama S, Starmer WT, Yokoyama R. 1993. Paralogous origin of the red- and green-sensitive visual pigment genes in vertebrates. Mol. Biol. Evol. 10:527-38
148. Yu N, Chen FC, Ota S, Jorde LB, Pamilo P, et al. 2002. Larger genetic differences within Africans than between Africans and Eurasians. Genetics 161:269-74
149. Yu N, Jensen-Seaman MI, Chemnick L, Kidd JR, Deinard AS, et al. 2003. Low nucleotide diversity in chimpanzees and bonobos. Genetics 164:1511-18
150. Yunis JJ, Prakash O. 1982. The origin of man: a chromosomal pictorial legacy. Science 215:1525-30
151. Zhang J, Webb DM, Podlaha O. 2002. Accelerated protein evolution and origins of human-specific features: Foxp2 as an example. Genetics 162: 1825-35
152. Zhang J, Zhang YP, Rosenberg HF. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30:411-15
153. Zhi L, Karesh WB, Janczewski DN, Frazier-Taylor H, Sajuthi D, et al. 1996. Genomic differentiation among natural populations of orang-utan (Pongo pygmaeus). Curr. Biol. 6:1326-36
154. Zietkiewicz E, Richer C, Sinnett D, Labuda D. 1998. Monophyletic origin of Alu elements in primates. J. Mol. Evol. 47:172-82