Native American Y Chromosomes

MBE Advance Access published online ahead of print on October 31, 2003
Molecular Biology and Evolution, 10.1093/molbev/msh009

High Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas

Stephen L. Zegura

Abstract

A total of 63 binary polymorphisms and 10 STRs were genotyped on a sample of 2,344 Y chromosomes from 18 Native American, 28 Asian, and 5 European populations to investigate the origin(s) of Native American paternal lineages. All three of Greenberg's major linguistic divisions (including 342 Amerind speakers, 186 Na-Dene speakers, and 60 Aleut-Eskimo speakers) were represented in our sample of 588 Native Americans. SNP analysis indicated that three major haplogroups, denoted as C, Q, and R, accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y-chromosome lineages; however, most haplogroup R lineages present in Native Americans most likely came from recent admixture with Europeans. Although different phylogeographic and STR diversity patterns for the two major founding haplogroups previously led to the inference that they were carried from Asia to the Americas separately, the hypothesis of a single migration of a polymorphic founding population better fits our expanded database. Phylogenetic analyses of STR variation within haplogroups C and Q traced both lineages to a probable ancestral homeland in the vicinity of the Altai Mountains in Southwest Siberia. Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas.

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The ancestral nodes leading to both Q-M3 (figure 3) and CP39 (figure 4), the two Native American-specific haplogroups, were present in the southern Altai individuals. Although the Kets and Sekups currently inhabit the eastern part of Western Siberia and the Yenisey River Valley, according to Russian ethnographers, their ancient homelands are thought to lie farther south on the slopes of the Sayan and Altai Mountains (Popov and Dolgikh 1964; Prokof'yeva 1964; Karafet et al.1999). Thus, our present data support the hypothesis that the Altai Mountain region is the principal candidate for the geographic source of the founding Native American Y chromosomes.

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In contrast, all of our divergence time estimates range from 10,100 to 17,200 years ago irrespective of statistical method, population comparison, or haplogroup employed, while standard errors range from 3,200 to 6,000 years (table 3). Especially noteworthy is the general lack of temporal separation between the divergence dates based on the Q and C lineages with only the Upper Bound TD date hinting at an earlier separation for the Q-lineage. Our divergence dates are most compatible with the late entry (<20,000 BP) school championed by most American archaeologists (Meltzer 1993, 1997; West 1996; Fiedel 2000).

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Our new data and analyses are most consistent with the single-migration alternative... Therefore, we have no compelling data that would refute Laughlin's (1986:490) contention that a "single small migration some 16,000 years ago appears most parsimonious."

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In sum, our evidence supports the admixture hypothesis for the presence of R-P25 individuals in Native American populations and concurs with the recent findings of Bosch et al. (2003) who concluded that all 18 of their haplogroup R Greenlandic Inuit (n= 69) are the result of European admixture.

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