title: Updated three-stage model for the peopling of the Americas.
abstract: BACKGROUND
  We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. approximately 40,000 years ago) expansion signal we had proposed for the proto-Amerind population.
  
  
  RESULTS
  Bayesian skyline plot analysis of a new dataset of Native American mitochondrial coding genomes confirms the absence of an early expansion signal for the proto-Amerind population and allows us to reduce the variation around our estimate of the New World founder population size. In addition, genetic variants that define New World founder haplogroups are used to estimate the amount of time required between divergence of proto-Amerinds from the Asian gene pool and expansion into the New World.
  
  
  CONCLUSIONS
  The period of population isolation required for the generation of New World mitochondrial founder haplogroup-defining genetic variants makes the existence of three stages of colonization a logical conclusion. Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.
authors.affiliation: Department of Anthropology, University of Florida, Gainesville, Florida, USA.
authors.forename: Connie J
authors.initials: CJ
authors.lastname: Mulligan
authors.forename: Andrew
authors.initials: A
authors.lastname: Kitchen
authors.forename: Michael M
authors.initials: MM
authors.lastname: Miyamoto
mesh_terms: D000465:Algorithms; D000569:Americas; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D004272:DNA, Mitochondrial / Q000235:genetics*; D005006:Ethnicity; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D006801:Humans; D007198:Indians, North American / Q000235:genetics; D016013:Likelihood Functions; D008954:Models, Biological; D010802:Phylogeny; D012984:Software
chemical_list: D004272:DNA, Mitochondrial
references.citation: Science. 2007 Jan 12;315(5809):194-6
references.pmid: 17218514
references.citation: Annu Rev Genomics Hum Genet. 2004;5:295-315
references.pmid: 15485351
references.citation: Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1866-71
references.pmid: 9050871
references.citation: Science. 2004 Jan 2;303(5654):52-6
references.pmid: 14704419
references.citation: Mol Phylogenet Evol. 2008 Feb;46(2):673-82
references.pmid: 17977749
references.citation: Mol Biol Evol. 2006 Mar;23(3):691-700
references.pmid: 16364968
references.citation: PLoS One. 2007 Sep 05;2(9):e829
references.pmid: 17786201
references.citation: Mol Biol Evol. 2008 Feb;25(2):468-74
references.pmid: 18093996
references.citation: PLoS One. 2008 Feb 13;3(2):e1596
references.pmid: 18270583
references.citation: Am J Hum Genet. 2008 Jul;83(1):142-6; author reply 146-7
references.pmid: 18606310
references.citation: Am J Hum Genet. 2008 Mar;82(3):583-92
references.pmid: 18313026
references.citation: PLoS Biol. 2005 Jun;3(6):e193
references.pmid: 15898833
references.citation: Ann Hum Genet. 2003 Nov;67(Pt 6):512-24
references.pmid: 14641239
references.citation: PLoS One. 2008 Mar 12;3(3):e1764
references.pmid: 18335039
references.citation: Science. 1993 Jan 1;259(5091):46-53
references.pmid: 17757472
references.citation: PLoS One. 2008 Sep 17;3(9):e3157
references.pmid: 18797501
references.citation: Nature. 2000 Dec 7;408(6813):708-13
references.pmid: 11130070
references.citation: Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):171-6
references.pmid: 12509511
references.citation: Nature. 2003 Jun 5;423(6940):603
references.pmid: 12789326
references.citation: Mol Biol Evol. 2005 May;22(5):1185-92
references.pmid: 15703244
references.citation: Am J Hum Genet. 2003 Mar;72(3):659-70
references.pmid: 12571803