Wednesday, August 5, 2015

Genomic evidence for the Pleistocene and recent population history of Native Americans

Raghavan et al.
July 21, 2015

"We explored the genetic structure of Native American populations in the context of worldwide populations using ADMIXTURE (36), employing a reference panel consisting of 3,053 individuals from 169 populations (table S3) (28). The panel included SNP chip genotype data from present-day individuals generated in this study and previously published studies, as well as the 4,000 year-old Saqqaq individual from Greenland (29) and the 12,600 year-old Anzick-1 (Clovis culture) individual from Montana (5) (table S3). When assuming four ancestral populations (K=4), we found a Native American-specific genetic component, indicating a shared genetic ancestry for all Native Americans including Amerindians and Athabascans (fig. S4). Assuming K=15, there is structure within the Native Americans. Athabascans and northern Amerindians (primarily from Canada) differ from the rest of the Native Americans in sharing their own genetic component (fig. S4). As reported previously, Anzick-1 falls within the genetic variation of southern Native Americans (5), while the Saqqaq individual shares genetic components with Siberian populations (fig. S4) (29)."

Part of Fig. S4 C. shows Admixture run at K=14 for North and Central American Native Groups.  Looking closely, the figure shows that Southern Athabascans, CanAmerican 1, and Ojibwa are similar.

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Fig. S1. Geographical locations of populations from the Americas that were analyzed in this study. See Section S1 and Tables S1, S3and S4 for further information.

 D-stats in Figure S9 also show that Southern Athabascans, CanAmerican 1, and Ojibwa group closely. 

"We applied diCal2.0 (28) (Method 1), a new version of diCal (41) extended to handle complex demographic models involving multiple populations with migration (42), and an identity-by-state (IBS) tract method (43) (Method 2) to the modern genome dataset (28). With these, we first estimated divergence times between Native Americans and the Koryak of Siberia, one of the genetically closest sampled East Asian populations to Native Americans (fig. S5), using demograph-ic models that reflect a clean split between the populations (28). With both diCal2.0 and IBS tract method, the split of Native Americans (including Amerindians and Athabascans) from the Koryak dates to ca. 20 KYA (28) (tables S11A and S12 and fig. S15)."

"We further applied diCal2.0 to models with gene flow post-dating the split between Native Americans and Koryak (Fig. 2A) and found that they provided a better fit to the data than the models without gene flow (28). Overall, simulated databased on the models inferred using diCal2.0 and real data show very similar IBS tract length distributions (Fig. 2B) and relative cross coalescence rates (CCR) between pairs of individuals estimated using the Multiple Sequentially Markovian Coalescent (MSMC) method (Method 3) (28, 44) (Figs. 2, C and D). This serves as a confirmation for the model estimates from diCal2.0. We evaluated all the three methods using simulations under complex demographic models, and additionally investigated the effects of switch-errors in haplotype phasing on the estimates (28)."

"We then applied the diCal2.0 model that allows for gene flow between populations after their split to estimate divergence times for Native Americans from more geographically and genetically distant East Asian groups, including the Siberian Nivkh and Han Chinese. As before, the divergence estimates for Amerindians and Athabascans were very simi-lar to one another, ca. 23 KYA (table S11B and figs. S18 and S21)."

"Hence, our results suggest that Amerindians and Athabascans were, by three different methods, consistently equidistant in time to populations that were sampled from different regions of East Asia, including some proximate to Beringia, and with varied population histories. This suggests that these two major Native American sub-groups are descendants of the same source population that split off from ancestral East Asians during the LGM. It is conceivable that harsh climatic conditions during the LGM may have contributed to the isolation of ancestral Native Americans, ultimately leading to their genetic divergence from their East Asian ancestors."

"We also modeled the peopling of the Americas using a climate-informed spatial genetic model (CISGeM), in which the genetic history and local demography is informed by paleoclimatic and paleovegetation reconstructions (28, 45), and found the results to be in accordance with the conclusion of a single migration source for all Native Americans. Using present-day and ancient high coverage genomes, we found that Athabascans and Anzick-1, but not Greenlandic Inuit and Saqqaq (29, 39), belong to the same initial migration wave that also gave rise to present-day Amerindians from southern North America and Central and South America (Fig. 3), and that this migration likely followed a coastal route, given our current understanding of the glacial geological and paleoenvironmental parameters of the Late Pleistocene (fig. S31)."

"Overall, our results support a common Siberian origin for all Native Americans, contradicting claims for an early migration to the Americas from Europe (49), with their initial isolation and entrance into the Americas occurring no earlier than 23 KYA, but with subsequent admixture with East Asian populations. This additionally suggests that the Mal’ta-related admixture into the early Americans (4), representing ancestors of both Amerindians and Athabascans (Fig. 1 and fig. S5), occurred sometime after 23 KYA, following the Native American split from East Asians."

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