Updated Three-Stage Model for the Peopling of the Americas

Citation: Mulligan CJ, Kitchen A, Miyamoto MM ( Updated Three-Stage Model for the Peopling of the Americas Connie J. Mulligan 0 Andrew Kitchen 0 Michael M. Miyamoto 0 Henry Harpending, University of Utah, United States of America 0 1 Department of Anthropology, University of Florida, Gainesville, Florida, United States of America, 2 Department of Zoology, University of Florida , Gainesville, Florida , United States of America 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. ,40,000 years ago) expansion signal we had proposed for the proto-Amerind population. Methodology/Findings: 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/Significance: 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. - Funding: This study was supported by a grant from the National Science Foundation to CJM (BSR-0518530) and by funds from the Department of Zoology, University of Florida to MMM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. We recently published a three stage model for the peopling of the Americas [1]. Specifically, we proposed that a recent, rapid expansion into the Americas was preceded by a long period of population stability in greater Beringia by the proto-Amerind population after divergence from their ancestral Asian population. We used two complementary coalescent methods, Bayesian skyline plot [2] and isolation-by-migration [3] analyses, to estimate past population growth patterns in Native American populations and to estimate a New World founder effective population size. We explicitly incorporated archaeological, geological, and paleoecological constraints into our analyses to enhance the anthropological relevance of the results and to provide a comprehensive model for the initial settlement of the Americas. Fagundes et al. [4] have published a re-analysis of the data we used in developing our three stage model for the peopling of the Americas [1]. Specifically, they identified nine mitochondrial coding region sequences that we assumed were Native American sequences, but instead are likely to derive from Asian or European individuals. Fagundes et al. are correct in this assessment, i.e. five sequences were reclassified as Asian after their publication as Native American sequences [5] and four sequences were mistakenly included in our original study. The effect of removing these sequences from the Bayesian skyline plot analysis is that the suggestion of an early expansion event in the skyline plot is no longer apparent, a finding that we have reconfirmed by re-running our original dataset without these nine genomes. It appears that the non-Native American sequences introduced additional variation that created an expansion signal that does not exist in an analysis of only Native American sequences. In light of these facts, we have now analyzed the largest dataset of Native American mitochondrial coding genomes using publicly available sequences (n = 148; [6]) in a Bayesian skyline plot analysis. We also provide an estimate for the duration of the period of population isolation required for the generation of New World founder haplogroup-defining variants. As in our previous analysis, we evaluate the significance of our results in concert with other non-genetic data. We use a Bayesian skyline plot to visually illustrate changes in Native American female effective population size (Ne) over time. Bayesian skyline plots assume a single migration event, which makes the approach ideal for questions concerning the peopling of the Americas since it is generally agreed that there was a single migration [7]. Our new skyline plot (Fig. 1) strongly supports a large population expansion (,1.8 orders of magnitude, or 80-fold) that occurred ,1612 thousand years ago (kya). This timing Figure 1. Bayesian skyline plot of 148 Native American mitochondrial coding genome sequences. The curve plots median Nef with 95% credible intervals indicated by light gray lines. The shaded gray box highlights the significant increase of Nef during the colonization of the Americas 1612 kya. The blue box depicts the calculated time required for the generation of New World defining mitochondrial variants and its shaded region represents the variation in these estimates, i.e. 715 thousand years before entry to the New World (see Table 1). The green arrow identifies the date of the Yana River site of human occupation in western Beringia [21]. doi:10.1371/journal.pone.0003199.g001 suggests an entry to the New World that was coincident with the retreat of the North American ice sheets, i.e. the opening of an icefree corridor ,1714 kya [8,9]. Immediately before this expansion, there is a small drop in effective population size ,1716 kya (this is an insignificant change, as judged by the overlap in 95% confidence intervals at the beginning and end of the population decrease), possibly corresponding to a population bottleneck prior to entry to the Americas. Before 17 kya, the skyline plot is flat with no evidence of the early (,40 kya) population expansion we reported previously [1]. The absence of an early expansion signal in the skyline plot may simply indicate that divergence of proto-Amerinds from the Asian gene pool was not accompanied by significant population growth. These results are highly consistent with our earlier analysis of only 20 Native American mitochondrial coding genomes [10], in support of theoretical expectations by Felsenstein [11] that increasing sample size is an inefficient way to improve the accuracy of maximum likelihood estimations from coalescent analyses of population genetic data. Our new analysis (with non-Native American sequences eliminated and more Native American sequences added) shows a larger population increase (80-fold vs 16-fold) over a smaller period of time (...truncated)