Can a sex-biased human demography account for the reduced effective population size of chromosome X in non-Africans?

Molecular Biology and Evolution

Volumn 27, Issue 10, 2010, Pages 2312-2321

  Keinan, Alon ^a   Reich, David ^b,c  

^a Program on Infrastructure Policy   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

autosomes; chromosome X; coalescent simulations; effective population size; gender biased demography; human

Indexed keywords

AFRICA; ARTICLE; AUTOSOME; CHROMOSOME; DEMOGRAPHY; EFFECTIVE POPULATION SIZE; FEMALE; GENDER; GENE FLOW; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; MALE; MIGRATION; NEGRO; X CHROMOSOME;

CHROMOSOMES, HUMAN, X; COMPUTER SIMULATION; DEMOGRAPHY; EMIGRATION AND IMMIGRATION; EVOLUTION, MOLECULAR; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MALE; MODELS, GENETIC; POPULATION DENSITY; SEX FACTORS;

EID: 77953086802     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq117     Document Type: Article

References (31)

1. Adams AM, Hudson RR. 2004. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics 168:1699-1712.
2. Amato R, Pinelli M, Monticelli A, Marino D, Miele G, Cocozza S. 2009. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases. PLoS One. 4:e7927.
3. Bamshad M, Kivisild T, Watkins WS, et al. (18 co-authors). 2001. Genetic evidence on the origins of Indian caste populations. Genome Res. 11:994-1004.
4. Bar-Yosef O, Belfer-Cohen A. 1989. The Levantine "PPNB" interaction sphere. In: Hershkovitz I, editor. People and culture in change. Oxford: British Archaeological Reports. p. 59-72.
5. Bedoya G, Montoya P, Garcia J, et al. (11 co-authors). 2006. Admixture dynamics in Hispanics: a shift in the nuclear genetic ancestry of a South American population isolate. Proc Natl Acad Sci\USA. 103:7234-7239.
6. Bustamante CD, Ramachandran S. 2009. Evaluating signatures of sex-specific processes in the human genome. Nat Genet. 41:8-10.
7. Caballero A. 1995. On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139:1007-1011.
8. Cavalli-Sforza LL, Menozzi P, Piazza A. 1994. The history and geography of human genes. Princeton (NJ): Princeton University Press.
9. Charlesworth B. 2001. The effect of life-history and mode of inheritance on neutral genetic variability. Genet Res. 77:153-166.
10. Cox MP, Morales DA, Woerner AE, Sozanski J, Wall JD, Hammer MF. 2009. Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations. PLoS One. 4:e6366.
11. 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.
12. Helgason A, Sigureth ardottir S, Nicholson J, Sykes B, Hill EW, Bradley DG, Bosnes V, Gulcher JR, Ward R, Stefansson K. 2000. Estimating Scandinavian and Gaelic ancestry in the male settlers of Iceland. Am J Hum Genet. 67:697-717.
13. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338.
14. International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437:1299-1320.
15. International HapMap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
16. Kayser M, Brauer S, Weiss G, Schiefenhovel W, Underhill P, Shen P, Oefner P, Tommaseo-Ponzetta M, Stoneking M. 2003. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am J Hum Genet. 72:281-302.
17. Keinan A, Mullikin JC, Patterson N, Reich D. 2007. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet. 39:1251-1255.
18. Keinan A, Mullikin JC, Patterson N, Reich D. 2008. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet. 41:66-70.
19. Labuda D, Lefebvre JF, Nadeau P, Roy-Gagnon MH. 2010. Female-to-male breeding ratio in modern humans-an analysis based on historical recombinations. Am J Hum Genet. 86:353-363.
20. Laporte V, Charlesworth B. 2002. Effective population size and population subdivision in demographically structured populations. Genetics 162:501-519.
21. Marlowe FW. 2005. Hunter-gatherers and human evolution. Evol Anthropol. 14:54-67.
22. Marth GT, Czabarka E, Murvai J, Sherry ST. 2004. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166:351-372.
23. Parra EJ, Marcini A, Akey J, et al. (11 co-authors). 1998. Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet. 63:1839-1851.
24. Pluzhnikov A, Di Rienzo A, Hudson RR. 2002. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics. 161:1209-1218.
25. Pool JE, Nielsen R. 2007. Population size changes reshape geno-mic patterns of diversity. Evolution Int J Org Evolution. 61:3001-3006.
26. Pool JE, Nielsen R. 2008. The impact of founder events on chromosomal variability in multiply mating species. Mol Biol Evol. 25:1728-1736.
27. Reich DE, Cargill M, Bolk S, et al. (11 co-authors). 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
28. Seielstad MT, Minch E, Cavalli-Sforza LL. 1998. Genetic evidence for a higher female migration rate in humans. Nat Genet. 20:278-280.
29. Storz JF, Payseur BA, Nachman MW. 2004. Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol Biol Evol. 21:1800-1811.
30. Thomas MG, Stumpf MP, Harke H. 2006. Evidence for an apartheidlike social structure in early Anglo-Saxon England. Proc Biol Sci. 273:2651-2657.
31. 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\USA. 102:18508-18513.