title: A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia.
abstract: The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called "three-stage model" consisting of a very early expansion into Beringia followed by approximately 20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the "three-stage model", since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes.
authors.affiliation: Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Nelson J R
authors.initials: NJ
authors.lastname: Fagundes
authors.forename: Ricardo
authors.initials: R
authors.lastname: Kanitz
authors.forename: Sandro L
authors.initials: SL
authors.lastname: Bonatto
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D005075:Biological Evolution; D001938:Brazil; D004272:DNA, Mitochondrial / Q000235:genetics*; D004641:Emigration and Immigration; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D007198:Indians, North American / Q000235:genetics*; D015233:Models, Statistical; D013997:Time Factors
chemical_list: D004272:DNA, Mitochondrial
references.citation: Science. 2005 May 13;308(5724):1034-6
references.pmid: 15890885
references.citation: Ann Hum Genet. 2005 Jul;69(Pt 4):389-400
references.pmid: 15996168
references.citation: Ann Hum Genet. 2003 Nov;67(Pt 6):512-24
references.pmid: 14641239
references.citation: Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1866-71
references.pmid: 9050871
references.citation: PLoS One. 2008 Mar 12;3(3):e1764
references.pmid: 18335039
references.citation: Mol Phylogenet Evol. 2008 Feb;46(2):673-82
references.pmid: 17977749
references.citation: Nature. 2000 Dec 7;408(6813):708-13
references.pmid: 11130070
references.citation: Mol Biol Evol. 2005 May;22(5):1185-92
references.pmid: 15703244
references.citation: Mol Biol Evol. 2008 Feb;25(2):468-74
references.pmid: 18093996
references.citation: Am J Hum Genet. 2002 May;70(5):1152-71
references.pmid: 11938495
references.citation: Am J Hum Genet. 2008 Mar;82(3):583-92
references.pmid: 18313026
references.citation: PLoS Genet. 2007 Nov;3(11):e185
references.pmid: 18039031
references.citation: Am J Hum Genet. 1990 Mar;46(3):613-23
references.pmid: 1968708
references.citation: Am J Hum Genet. 1997 Dec;61(6):1413-23
references.pmid: 9399887
references.citation: Mol Biol Evol. 2005 Jul;22(7):1561-8
references.pmid: 15814826
references.citation: Nature. 1987 Jan 1-7;325(6099):31-6
references.pmid: 3025745
references.citation: Ann Hum Genet. 2007 Jan;71(Pt 1):64-76
references.pmid: 17227477
references.citation: Science. 2008 May 9;320(5877):784-6
references.pmid: 18467586
references.citation: Biochem Biophys Res Commun. 2007 Jan 12;352(2):283-91
references.pmid: 17123466
references.citation: Int J Legal Med. 2008 Jan;122(1):11-21
references.pmid: 17347766
references.citation: Genome Res. 2002 Feb;12(2):339-48
references.pmid: 11827954
references.citation: Trends Genet. 2006 Jun;22(6):339-45
references.pmid: 16678300
references.citation: Ann Hum Biol. 2006 Mar-Apr;33(2):142-60
references.pmid: 16684689
references.citation: Genetics. 2006 Jan;172(1):373-87
references.pmid: 16172508
references.citation: Am J Hum Genet. 1998 Dec;63(6):1852-61
references.pmid: 9837837
references.citation: Science. 2008 Mar 14;319(5869):1497-502
references.pmid: 18339930
references.citation: Syst Biol. 2007 Jun;56(3):515-22
references.pmid: 17562475
references.citation: Am J Phys Anthropol. 2008 Oct;137(2):175-87
references.pmid: 18481303
references.citation: Science. 2008 May 9;320(5877):786-9
references.pmid: 18388261
references.citation: PLoS One. 2007 Sep 05;2(9):e829
references.pmid: 17786201
references.citation: Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):171-6
references.pmid: 12509511
references.citation: Am J Hum Genet. 1996 Oct;59(4):935-45
references.pmid: 8808611
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17614-9
references.pmid: 17978179
references.citation: Am J Hum Genet. 2004 Nov;75(5):910-8
references.pmid: 15382008
references.citation: PLoS One. 2008 Feb 13;3(2):e1596
references.pmid: 18270583