Beyond 2/3 and 1/3: The complex signatures of sex-biased admixture on the X chromosome

Genetics

Volumn 201, Issue 1, 2015, Pages 263-279

  Goldberg, Amy ^a   Rosenberg, Noah A ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Admixture; African American genetics; Mechanistic model; Sex bias; X chromosome

Indexed keywords

AFRICAN AMERICAN; ARTICLE; AUTOSOME; DEMOGRAPHY; EUROPEAN; GENDER BIAS; HUMAN; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL; X CHROMOSOME; ALGORITHM; BIOLOGICAL MODEL; FEMALE; GENETICS; MALE; MIGRATION; POPULATION DENSITY; SEX DIFFERENCE;

AFRICAN AMERICANS; ALGORITHMS; CHROMOSOMES, HUMAN, X; FEMALE; HUMAN MIGRATION; HUMANS; MALE; MODELS, GENETIC; POPULATION DENSITY; SEX FACTORS;

EID: 84941206474     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.178509     Document Type: Article

References (63)

1. Arbiza, L, S. Gottipati, A. Siepel, and A. Keinan, 2014 Contrasting X-linked and autosomal diversity across 14 human populations. Am. J. Hum. Genet. 94: 827–844.
2. Basin, S, 1963 The Fibonacci sequence as it appears in nature. Fibonacci Q 1: 53–56.
3. Bedoya, G, P. Montoya, J. García, I. Soto, S. Bourgeois et al, 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.
4. Beleza, S, J. Campos, J. Lopes, I. I. Araújo, A. H. Almada et al, 2012 The admixture structure and genetic variation of the archipelago of Cape Verde and its implications for admixture mapping studies. PLoS ONE 7: e51103.
5. Berniell-Lee, G, S. Plaza, E. Bosch, F. Calafell, E. Jourdan et al, 2008 Admixture and sexual bias in the population settlement of La Réunion Island (Indian Ocean). Am. J. Phys. Anthropol. 136: 100–107.
6. Bryc, K, A. Auton, M. R. Nelson, J. R. Oksenberg, S. L. Hauser et al, 2010a Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc. Natl. Acad. Sci. USA 107: 786–791.
7. Bryc, K, C. Velez, T. Karafet, A. Moreno-Estrada, A. Reynolds et al, 2010b Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc. Natl. Acad. Sci. USA 107: 8954–8961.
8. Bryc, K, E. Y. Durand, J. M. Macpherson, D. Reich, and J. L. Mountain, 2015 The genetic ancestry of African Americans, Latinos, and European Americans across the United States. Am. J. Hum. Genet. 96: 37–53.
9. Bustamante, C. D, and S. Ramachandran, 2009 Evaluating signatures of sex-specific processes in the human genome. Nat. Genet. 41: 8–10.
10. Caballero, A, 1995 On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139: 1007–1011.
11. Casto, A. M, J. Z. Li, D. Absher, R. Myers, S. Ramachandran et al, 2010 Characterization of X-linked SNP genotypic variation in globally distributed human populations. Genome Biol. 11: R10.
12. Charlesworth, B, 2001 The effect of life-history and mode of inheritance on neutral genetic variability. Genet. Res. 77: 153–166.
13. Cheng, C.-Y, W. H. L. Kao, N. Patterson, A. Tandon, C. A. Haiman et al, 2009 Admixture mapping of 15,280 African Americans identifies obesity susceptibility loci on chromosomes 5 and X. PLoS Genet. 5: e1000490.
14. Cox, M. P, T. M. Karafet, J. S. Lansing, H. Sudoyo, and M. F. Hammer, 2010 Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates. Proc. R. Soc. Lond. B Biol. Sci. 277: 1589–1596.
15. Crow, J. F, and M. Kimura, 1970 An Introduction to Population Genetics Theory. Burgess, Minneapolis.
16. Davis, F. J, 2010 Who Is Black? One Nation’s Definition. Penn State Press, University Park, PA.
17. Ellegren, H, 2009 The different levels of genetic diversity in sex chromosomes and autosomes. Trends Genet. 25: 278–284.
18. Eltis, D, and D. Richardson, 2010 Atlas of the Transatlantic Slave Trade. Yale University Press, New Haven, CT.
19. Emery, L. S, J. Felsenstein, and J. M. Akey, 2010 Estimators of the human effective sex ratio detect sex biases on different timescales. Am. J. Hum. Genet. 87: 848–856.
20. Fredrickson, G. M, 1982 White Supremacy: A Comparative Study of American and South African History. Oxford University Press, Oxford.
21. Goldberg, A, P. Verdu, and N. A. Rosenberg, 2014 Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209–1229.
22. Gottipati, S, L. Arbiza, A. Siepel, A. G. Clark, and A. Keinan, 2011 Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat. Genet. 43: 741–743.
23. Gravel, S, 2012 Population genetics models of local ancestry. Genetics 191: 607–619.
24. Hammer, M. F, F. L. Mendez, M. P. Cox, A. E. Woerner, and J. D. Wall, 2008 Sex-biased evolutionary forces shape genomic patterns of human diversity. PLoS Genet. 4: e1000202.
25. Hammer, M. F, A. E. Woerner, F. L. Mendez, J. C. Watkins, M. P. Cox et al, 2010 The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nat. Genet. 42: 830–831.
26. Hartl, D. L, and A. G. Clark, 2007 Principles of Population Genetics, Ed. 4. Sinauer Associates, Sunderland, MA.
27. Hedrick, P. W, 2007 Sex: differences in mutation, recombination, selection, gene flow, and genetic drift. Evolution 61: 2750–2771.
28. Heyer, E, R. Chaix, S. Pavard, and F. Austerlitz, 2012 Sex-specific demographic behaviours that shape human genomic variation. Mol. Ecol. 21: 597–612.
29. Jennings, H. S, 1914 Formulae for the results of inbreeding. Am. Nat. 48: 693–696.
30. Jennings, H. S, 1916a The numerical results of diverse systems of breeding. Genetics 1: 53–89.
31. Jennings, H. S, 1916b The numerical results of diverse systems of breeding. Proc. Natl. Acad. Sci. USA 2: 45–50.
32. Keinan, A, J. C. Mullikin, N. Patterson, and D. Reich, 2009 Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat. Genet. 41: 66–70.
33. Koshy, T, 2001 Fibonacci and Lucas Numbers with Applications. John Wiley & Sons, Hoboken, NJ.
34. Labuda, D, J.-F. Lefebvre, P. Nadeau, and M.-H. Roy-Gagnon, 2010 Female-to-male breeding ratio in modern humans—an analysis based on historical recombinations. Am. J. Hum. Genet. 86: 353–363.
35. Lambert, C. A, C. F. Connelly, J. Madeoy, R. Qiu, M. V. Olson et al, 2010 Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history. Am. J. Hum. Genet. 86: 34–44.
36. Liang, M, and R. Nielsen, 2014 The lengths of admixture tracts. Genetics 197: 953–967.
37. Lind, J. M, H. B. Hutcheson-Dilks, S. M. Williams, J. H. Moore, M. Essex et al, 2007 Elevated male European and female African contributions to the genomes of African American individuals. Hum. Genet. 120: 713–722.
38. Long, J. C, 1991 The genetic structure of admixed populations. Genetics 127: 417–428.
39. Marcheco-Teruel, B, E. J. Parra, E. Fuentes-Smith, A. Salas, H. N. Buttenschøn et al, 2014 Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers. PLoS Genet. 10: e1004488.
40. McLean, Jr, D. C, I. Spruill, G. Argyropoulos, G. P. Page, M. D. Shriver et al, 2005 Mitochondrial DNA (mtDNA) haplotypes reveal maternal population genetic affinities of Sea Island Gullah-speaking African Americans. Am. J. Phys. Anthropol. 127: 427–438.
41. Moreno-Estrada, A, S. Gravel, F. Zakharia, J. L. McCauley, J. K. Byrnes et al, 2013 Reconstructing the population genetic history of the Caribbean. PLoS Genet. 9: e1003925.
42. Painter, N. I, 2006 Creating Black Americans: African-American History and Its Meanings, 1619 to the Present. Oxford University Press, Oxford.
43. Parra, E. J, A. Marcini, J. Akey, J. Martinson, M. A. Batzer et al, 1998 Estimating African American admixture proportions by use of population-specific alleles. Am. J. Hum. Genet. 63: 1839–1851.
44. Parra, E. J, R. A. Kittles, G. Argyropoulos, C. L. Pfaff, K. Hiester et al, 2001 Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. Am. J. Phys. Anthropol. 114: 18–29.
45. Pool, J. E, and R. Nielsen, 2007 Population size changes reshape genomic patterns of diversity. Evolution 61: 3001–3006.
46. Pool, J. E, and R. Nielsen, 2009 Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711–719.
47. Quintana-Murci, L, C. Harmant, H. Quach, O. Balanovsky, V. Zaporozhchenko et al, 2010 Strong maternal Khoisan contribution to the South African coloured population: a case of gender-biased admixture. Am. J. Hum. Genet. 86: 611–620.
48. Ramachandran, S, N. A. Rosenberg, L. A. Zhivotovsky, and M. W. Feldman, 2004 Robustness of the inference of human population structure: a comparison of X–chromosomal and autosomal microsatellites. Hum. Genomics 1: 87–97.
49. Ramachandran, S, N. A. Rosenberg, M. W. Feldman, and J. Wakeley, 2008 Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X–linked loci. Theor. Popul. Biol. 74: 291–301.
50. Salzano, F. M, and M. Sans, 2014 Interethnic admixture and the evolution of Latin American populations. Genet. Mol. Biol. 37: 151–170.
51. Ségurel, L, M. J. Wyman, and M. Przeworski, 2014 Determinants of mutation rate variation in the human germline. Annu. Rev. Genomics Hum. Genet. 15: 47–70.
52. Sloane, N. J. A, 2015 The Online Encyclopedia of Integer Sequences. Available at: https://oeis.org/.
53. Stefflova, K, M. C. Dulik, A. A. Pai, A. H. Walker, C. M. Zeigler-Johnson et al, 2009 Evaluation of group genetic ancestry of populations from Philadelphia and Dakar in the context of sexbiased admixture in the Americas. PLoS ONE 4: e7842.
54. Tian, C, D. A. Hinds, R. Shigeta, R. Kittles, D. G. Ballinger et al, 2006 A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am. J. Hum. Genet. 79: 640–649.
55. Veeramah, K. R, R. N. Gutenkunst, A. E. Woerner, J. C. Watkins, and M. F. Hammer, 2014 Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans. Mol. Biol. Evol. 31: 2267–2282.
56. Verdu, P, and N. A. Rosenberg, 2011 A general mechanistic model for admixture histories of hybrid populations. Genetics 189: 1413–1426.
57. Verdu, P, N. S. Becker, A. Froment, M. Georges, V. Grugni et al, 2013 Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies. Mol. Biol. Evol. 30: 918–937.
58. Wang, S, N. Ray, W. Rojas, M. V. Parra, G. Bedoya et al, 2008 Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet. 4: e1000037.
59. Wilkins, J. F, 2006 Unraveling male and female histories from human genetic data. Curr. Opin. Genet. Dev. 16: 611–617.
60. Wilkins, J. F, and F. W. Marlowe, 2006 Sex-biased migration in humans: What should we expect from genetic data? BioEssays 28: 290–300.
61. Wright, S, 1921 Systems of mating II. The effects of inbreeding on the genetic composition of a population. Genetics 6: 124–143.
62. Wright, S, 1933 Inbreeding and homozygosis. Proc. Natl. Acad. Sci. USA 19: 411–420.
63. Wright, S, 1969 The Theory of Gene Frequencies (Evolution and the Genetics of Populations), Vol. 2. University of Chicago Press, Chicago.