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, 82 (3), 583-92

Mitochondrial Population Genomics Supports a Single pre-Clovis Origin With a Coastal Route for the Peopling of the Americas

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Mitochondrial Population Genomics Supports a Single pre-Clovis Origin With a Coastal Route for the Peopling of the Americas

Nelson J R Fagundes et al. Am J Hum Genet.

Abstract

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.

Figures

Figure 1
Figure 1
Schematic Tree from the Five Native American mtDNA Haplogroups with Sequences Obtained Here and Indicating the Coding-Region Substitutions Letters following positions indicate transversions, and the others are transitions. Transition 3552 in the X2a haplogroup was absent in the individual Na3X from, so it is not considered to be a marker for this haplogroup.
Figure 2
Figure 2
Mismatch Distributions from Native American Haplogroups The frequency of the number of differences between all pairs of mtDNA genomes compared within each haplogroup.
Figure 3
Figure 3
Bayesian Estimation of TMRCA Density from Native American Haplogroups Relative density of age estimated by BEAST in kya for each haplogroup.
Figure 4
Figure 4
Phylogenetic Tree and Bayesian Skyline Plot for Native American mtDNAs (A) Maximum-likelihood tree from 80 Native American mtDNA coding-region haplotypes. The time axis (in kya) was estimated with a parametric molecular-clock model calibrated with the assumption of human versus chimpanzee divergence at 6.5 million yr ago. Branches with bootstrap support < 0.5 were collapsed. (B) mtDNA Bayesian skyline plot showing the Native American population size trend with a log-normal relaxed clock with the standard substitution rate of 1.26 × 10−8 sites/yr and a generation time of 25 yr. The y axis is the effective number of females. The thick solid line is the median estimate and the thin lines (blue) show the 95% highest posterior density limits estimated with 60 million chains. Approximate dates for the LGM, Monte Verde, and Clovis sites are shown in the middle panel. The time axis is limited to < 30 kya.

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