Divergence, demography and gene loss along the human lineage

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 365, Issue 1552, 2010, Pages 2451-2457

  Kim, Hie Lim ^a,c   Igawa, Takeshi ^a,d   Kawashima, Ayaka ^b   Satta, Yoko ^a,b   Takahata, Naoyuki ^a  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^b Department of Evolutionary Studies of Biosystems ^*  (Japan)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d HIROSHIMA UNIVERSITY   (Japan)

Author keywords

Ancestral polymorphism; Modern humans; Primates; Pseudogenes

Indexed keywords

ANCESTRY; DEMOGRAPHY; GENETIC STRUCTURE; OLFACTORY CUE; PLEISTOCENE; POLYMORPHISM; POPULATION BOTTLENECK; POPULATION SIZE; PRIMATE;

HOMO SAPIENS; PAN; PRIMATES;

ANIMAL; BIOLOGICAL MODEL; DNA SEQUENCE; EVOLUTION; FOUNDER EFFECT; GENETICS; HUMAN; MOLECULAR EVOLUTION; MONTE CARLO METHOD; POPULATION DYNAMICS; POPULATION GENETICS; PRIMATE; PROBABILITY; PSEUDOGENE; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; FOUNDER EFFECT; GENETICS, POPULATION; HUMANS; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; POPULATION DYNAMICS; PRIMATES; PSEUDOGENES; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 77956471324     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2010.0004     Document Type: Article

References (54)

1. Angata, T., Margulies, E., Green, E. & Varki, A. 2004 Largescale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms. Proc. Natl Acad. Sci. USA 101, 13 251-13 256. (doi:10.1073/pnas.0404833101) (Pubitemid 39209651)
2. Barreiro, L. B., Patin, E., Neyrolles, O., Cann, H. M., Gicquel, B. & Quintana-Murci, L. 2005 The heritage of pathogen pressures and ancient demography in the human innate-immunity CD209/CD209L region. Am. J. Hum. Genet. 77, 869-886. (doi:10.1086/497613) (Pubitemid 41513286)
3. Bogin, B. 2009 Childhood, adolescence, and longevity: a multilevel model of the evolution of reserve capacity in human life history. Am. J. Hum. Biol. 21, 567-577. (doi:10.1002/ajhb.20895)
4. Brenner, S. 1991 Summary and concluding remarks. In Evolution of life (eds S. Osawa & S. T. Honjo), pp. 453-456. Tokyo, Japan: Springer.
5. Burgess, R. & Yang, Z. 2008 Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequence errors. Mol. Biol. Evol. 25, 1979-1994. (doi:10.1093/molbev/msn148)
6. Cann, R. L., Stoneking, M. & Wilson, A. C. 1987 Mitochondrial DNA and human evolution. Nature 325, 31-36. (doi:10.1038/325031a0)
7. Chen, F.-C. & Li, 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, 444-456. (doi:10.1086/318206) (Pubitemid 32147813)
8. Cox, M. P., Mendez, F. L., Karafet, T. M., Pilkington, M. M., Kingan, S. B., Destro-Bisol, G., Strassmann, B. I. & Hammer, M. F. 2008 Testing for archaic hominin admixture on the X chromosome: model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent. Genetics 178, 427-437. (doi:10.1534/genetics.107.080432) (Pubitemid 351398759)
9. Darwin, C. 1859 The origin of species by means of natural selection. London, UK: John Murray.
10. Darwin, C. 1871 The descent of man, and selection in relation to sex. London, UK: John Murray.
11. Edgar, A. 2002 The human L-threonine 3-dehydrogenase gene is an expressed pseudogene. BMC Genet. 3, 18. (doi:10.1186/1471-2156-3-18) (Pubitemid 38751031)
12. Fujiyama, A. et al. 2002 Construction and analysis of a human-chimpanzee comparative clone map. Science 295, 131-134. (doi:10.1126/science.1065199) (Pubitemid 34052362)
13. Fullerton, S. M. et al. 2000 Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. Am. J. Hum. Genet 67, 881-900. (doi:10. 1086/303070)
14. Go, Y. & Niimura, Y. 2008 Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Mol. Biol. Evol. 25, 1897-1907. (doi:10. 1093/molbev/msn135)
15. Hahn, Y. & Lee, B. 2006 Human-specific nonsense mutations identified by genome sequence comparisons. Hum. Genet. 119, 169-178. (doi:10.1007/s00439- 005-0125-6)
16. Hahn, Y., Jeong, S. & Lee, B. 2007 Inactivation of MOXD2 and S100A15A by exon deletion during human evolution. Mol. Biol. Evol. 24, 2203-2212. (doi:10.1093/molbev/msm146) (Pubitemid 47574717)
17. Hayakawa, T., Aki, I., Varki, A., Satta, Y. & Takahata, N. 2006 Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution. Genetics 172, 1139-1146. (doi:10.1534/genetics.105.046995) (Pubitemid 43345445)
18. IHGSC (International Human Genome Sequencing Consortium) 2001 Initial sequencing and analysis of the human genome. Nature 409, 860-921. (doi:10.1038/35057062)
19. Kim, H. L. & Satta, Y. 2008 Population genetic analysis of the N-acylsphingosine amidohydrolase gene associated with mental activity in humans. Genetics 178, 1505-1515. (doi:10.1534/genetics.107.083691)
20. Kimura, M. 1968 Evolutionary rate at the molecular level. Nature 217, 624-626. (doi:10.1038/217624a0)
21. Kingman, J. F. C. 1982 On the genealogy in large populations. J. Appl. Prob. 19A, 27-43.
22. Klein, J. & Takahata, N. 2002 Where do we come from? The molecular evidence for human descent. Berlin, Germany: Springer.
23. Kumar, S. & Hedges, S. B. 1998 A molecular timescale for vertebrate evolution. Nature 392, 917-919. (doi:10.1038/31927) (Pubitemid 28232061)
24. Leakey, R. 1994 The origin of humankind. New York, NY: BasicBooks.
25. Li, W.-H. & Sadler, L. A. 1991 Low nucleotide diversity in man. Genetics 129, 513-523.
26. Linster, C. L. & Van Schaftingen, E. 2007 Vitamin C: biosynthesis, recycling and degradation in mammals. FEBS J. 274, 1-22.
27. Nachman, M. W., D'Agostino, S. L., Tillquist, C. R., Mobasher, Z. & Hammer, M. F. 2004 Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans. Genetics 167, 423-437. (doi:10.1534/genetics.167.1.423) (Pubitemid 38736399)
28. 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.
29. Olson, M. V. 1999 When less is more: gene loss as an engine of evolutionary change. Am. J. Hum. Genet. 64, 18-23. (doi:10.1086/302219) (Pubitemid 30428952)
30. Patin, E. et al. 2006 Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes. Am. J. Hum. Genet. 78, 423-436. (doi:10.1086/500614) (Pubitemid 43291225)
31. Patterson, N., Richter, D. J., Gnerre, S., Lander, E. S. & Reich, D. 2006 Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103-1108. (doi:10.1038/nature04789) (Pubitemid 43990725)
32. Rannala, B. & Yang, Z. 2003 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645-1656.
33. Satta, Y. & Takahata, N. 2002 Out of Africa with regional interbreeding? Modern human origins. BioEssays 24, 871-875. (doi:10.1002/bies. 10166) (Pubitemid 35180841)
34. Satta, Y. & Takahata, N. 2004 The distribution of the ancestral haplotype in finite stepping-stone models with population expansion. Mol. Ecol. 13, 877-886. (doi:10.1046/j.1365-294X.2003.02069.x) (Pubitemid 38390593)
35. Satta, Y., Hickerson, M., Watanabe, H., O'Huigin, C. & Klein, J. 2004 Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences. J. Mol. Evol. 59, 478-487. (doi:10.1007/s00239-004-2639-2) (Pubitemid 39305139)
36. Stedman, H. H. et al. 2004 Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 428, 415-418. (doi:10.1038/nature02358) (Pubitemid 38419685)
37. Takahata, N. 1993 Allelic genealogy and human evolution. Mol. Biol. Evol. 10, 2-22.
38. Takahata, N. 1999 Genetic understanding of mutually sustaining biodiversities (in Japanese). AERA Mook (Asahi Shimbun) 54, 166-175.
39. Takahata, N. 2001 Molecular phylogeny and demographic history of humans. In Humanity from African naissance to coming millennia (eds P. V. Tobias, M. A. Raath, J. Moggi-Cecchi & G. A. Doyle), pp. 299-305. Johannesburg, South Africa: Firenze University Press.
40. Takahata, N. & Nei, M. 1985 Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110, 325-344.
41. 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. USA 94, 4811-4815.
42. Takahata, N., Satta, Y. & Klein, J. 1995 Divergence time and population size in the lineage leading to modern humans. Theory Popul. Biol. 48, 198-221.
43. Takahata, N., Lee, S.-H. & Satta, Y. 2001 Testing multiregionality of modern human origins. Mol. Biol. Evol. 18, 172-183.
44. Templeton, A. 2002 Out of Africa again and again. Nature 416, 45-51. (doi:10.1038/416045a) (Pubitemid 34215394)
45. Torrents, D., Suyama, M., Zdobnov, E. & Bork, P. 2003 A genome-wide survey of human pseudogenes. Genome Res. 13, 2559-2567. (doi:10.1101/gr.1455503) (Pubitemid 37541144)
46. Wang, X., Grus, W. E. & Zhang, J. 2006 Gene losses during human origins. PLoS Biol. 4, 366-377. (doi:10.1371/journal.pbio.0040052)
47. Watterson, G. A. 1975 On the number of segregating sites genetical models without recombination. Theory Popul. Biol. 7, 256-276.
48. Winter, H., Langbein, L., Krawczak, M., Cooper, D. N., Jave-Suarez, L. F., Rogers, M. A., Praetzel, S., Heidt, P. J. & Schweizer, J. 2001 Human type I hair keratin pseudogene phihHaA has functional orthologs in the chimpanzee and gorilla: evidence for recent inactivation of the human gene after the Pan-Homo divergence. Hum. Genet. 108, 37-42. (doi:10.1007/s004390000439) (Pubitemid 32140540)
49. Wolpoff, M. H., Hawks, J. & Caspari, R. 2000 Multiregional, not multiple origins. Am. J. Phys. Anthropol. 112, 129-136.
50. Yang, Z. 1997 On the estimation of ancestral population sizes of modern humans. Genet. Res. 69, 111-116.
51. Yang, Z. 2002 Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162, 1811-1823.
52. Yu, N., Fu, Y.-X. & Li, H. 2002 DNA polymorphism in a worldwide sample of human X chromosomes. Mol. Biol. Evol. 19, 2131-2141.
53. Zhao, Z., Yu, N., Fu, Y.-X. & Li, H. 2006 Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics 174, 399-409. (doi:10.1534/genetics.106.060301) (Pubitemid 44427682)
54. Zuckerkandl, E. & Pauling, L. 1965 Evolutionary divergence and convergence in proteins. In Evolving genes and proteins (eds V. Bryson & H. Vogel), pp. 97-166. New York, NY: Academic Press.