title: The effect of recent admixture on inference of ancient human population history.
abstract: Despite the widespread study of genetic variation in admixed human populations, such as African-Americans, there has not been an evaluation of the effects of recent admixture on patterns of polymorphism or inferences about population demography. These issues are particularly relevant because estimates of the timing and magnitude of population growth in Africa have differed among previous studies, some of which examined African-American individuals. Here we use simulations and single-nucleotide polymorphism (SNP) data collected through direct resequencing and genotyping to investigate these issues. We find that when estimating the current population size and magnitude of recent growth in an ancestral population using the site frequency spectrum (SFS), it is possible to obtain reasonably accurate estimates of the parameters when using samples drawn from the admixed population under certain conditions. We also show that methods for demographic inference that use haplotype patterns are more sensitive to recent admixture than are methods based on the SFS. The analysis of human genetic variation data from the Yoruba people of Ibadan, Nigeria and African-Americans supports the predictions from the simulations. Our results have important implications for the evaluation of previous population genetic studies that have considered African-American individuals as a proxy for individuals from West Africa as well as for future population genetic studies of additional admixed populations.
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA. k.lohmueller@berkeley.edu
authors.forename: Kirk E
authors.initials: KE
authors.lastname: Lohmueller
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Clark
mesh_terms: D000349:Africa; D001741:Black or African American / Q000235:genetics*; D044383:Black People / Q000235:genetics*; D003710:Demography; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D009549:Nigeria; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D044382:Population Groups / Q000235:genetics
references.citation: Genetics. 2009 May;182(1):217-31
references.pmid: 19255370
references.citation: Am J Hum Genet. 2008 Feb;82(2):290-303
references.pmid: 18252211
references.citation: PLoS Genet. 2009 Oct;5(10):e1000695
references.pmid: 19851460
references.citation: Am J Hum Genet. 1998 Dec;63(6):1839-51
references.pmid: 9837836
references.citation: Genetics. 2005 Jul;170(3):1411-21
references.pmid: 15879513
references.citation: Proc Natl Acad Sci U S A. 1988 Dec;85(23):9119-23
references.pmid: 3194414
references.citation: Mol Biol Evol. 1990 Mar;7(2):111-22
references.pmid: 2108305
references.citation: PLoS Biol. 2004 Oct;2(10):e286
references.pmid: 15361935
references.citation: PLoS Genet. 2007 Sep;3(9):1745-56
references.pmid: 17907810
references.citation: Nature. 2008 Feb 21;451(7181):994-7
references.pmid: 18288194
references.citation: Am J Hum Genet. 2000 Mar;66(3):969-78
references.pmid: 10712211
references.citation: Nat Genet. 2007 Oct;39(10):1251-5
references.pmid: 17828266
references.citation: Theor Popul Biol. 1995 Oct;48(2):172-97
references.pmid: 7482370
references.citation: Genetics. 2004 Nov;168(3):1699-712
references.pmid: 15579718
references.citation: Annu Rev Genomics Hum Genet. 2008;9:403-33
references.pmid: 18593304
references.citation: Genome Res. 2008 Aug;18(8):1354-61
references.pmid: 18493019
references.citation: Science. 2008 Feb 22;319(5866):1100-4
references.pmid: 18292342
references.citation: Am J Hum Genet. 2004 May;74(5):979-1000
references.pmid: 15088269
references.citation: Am J Hum Genet. 2006 Jul;79(1):1-12
references.pmid: 16773560
references.citation: Curr Opin Genet Dev. 2006 Dec;16(6):597-605
references.pmid: 17056248
references.citation: Am J Hum Genet. 2006 Oct;79(4):640-9
references.pmid: 16960800
references.citation: Nat Rev Genet. 2006 Sep;7(9):669-80
references.pmid: 16921345
references.citation: Trends Genet. 2002 Nov;18(11):559-63
references.pmid: 12414185
references.citation: Genetics. 2004 Jan;166(1):351-72
references.pmid: 15020430
references.citation: Science. 2005 Feb 18;307(5712):1072-9
references.pmid: 15718463
references.citation: Mol Biol Evol. 2007 Sep;24(9):2049-58
references.pmid: 17630283
references.citation: Nat Rev Genet. 2002 Aug;3(8):611-21
references.pmid: 12154384
references.citation: Proc Natl Acad Sci U S A. 2005 May 31;102(22):7882-7
references.pmid: 15905331
references.citation: Nature. 2005 Oct 20;437(7062):1153-7
references.pmid: 16237444
references.citation: PLoS Genet. 2008 May 30;4(5):e1000083
references.pmid: 18516229
references.citation: Genetics. 2004 Dec;168(4):2373-82
references.pmid: 15371362
references.citation: Annu Rev Genomics Hum Genet. 2004;5:119-50
references.pmid: 15485345
references.citation: Hum Genet. 2007 Jan;120(5):713-22
references.pmid: 17006671
references.citation: Genome Res. 2004 Oct;14(10A):1821-31
references.pmid: 15364900
references.citation: Genome Res. 2008 Apr;18(4):668-75
references.pmid: 18353809
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):786-91
references.pmid: 20080753
references.citation: PLoS Genet. 2009 Jun;5(6):e1000519
references.pmid: 19543370
references.citation: PLoS One. 2009 Jul 29;4(7):e6366
references.pmid: 19641603
references.citation: Genetics. 1989 Nov;123(3):597-601
references.pmid: 2599369
references.citation: Genetics. 2009 May;182(1):205-16
references.pmid: 19237689
references.citation: Genetics. 2000 Feb;154(2):931-42
references.pmid: 10655242
references.citation: Genome Res. 2005 Nov;15(11):1576-83
references.pmid: 16251467
references.citation: Hum Genet. 2007 Jun;121(5):565-75
references.pmid: 17356887
references.citation: Science. 2007 Apr 13;316(5822):240-3
references.pmid: 17431170
references.citation: Nature. 2008 Feb 21;451(7181):998-1003
references.pmid: 18288195
references.citation: Mol Biol Evol. 2009 Aug;26(8):1823-7
references.pmid: 19420049
references.citation: Genetics. 2002 Jul;161(3):1209-18
references.pmid: 12136023
references.citation: Genome Res. 2009 May;19(5):838-49
references.pmid: 19279335
references.citation: Am J Hum Genet. 2001 Jan;68(1):198-207
references.pmid: 11112661
references.citation: Genome Res. 2004 Jun;14(6):1076-84
references.pmid: 15140829
references.citation: Genetics. 1989 Nov;123(3):585-95
references.pmid: 2513255
references.citation: Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18508-13
references.pmid: 16352722
references.citation: Genetics. 1991 Oct;129(2):555-62
references.pmid: 1743491
references.citation: Genetics. 2003 Aug;164(4):1567-87
references.pmid: 12930761