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, 73 (3), 524-39

Y-chromosome Evidence for Differing Ancient Demographic Histories in the Americas

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Y-chromosome Evidence for Differing Ancient Demographic Histories in the Americas

Maria-Catira Bortolini et al. Am J Hum Genet.

Abstract

To scrutinize the male ancestry of extant Native American populations, we examined eight biallelic and six microsatellite polymorphisms from the nonrecombining portion of the Y chromosome, in 438 individuals from 24 Native American populations (1 Na Dené and 23 South Amerinds) and in 404 Mongolians. One of the biallelic markers typed is a recently identified mutation (M242) characterizing a novel founder Native American haplogroup. The distribution, relatedness, and diversity of Y lineages in Native Americans indicate a differentiated male ancestry for populations from North and South America, strongly supporting a diverse demographic history for populations from these areas. These data are consistent with the occurrence of two major male migrations from southern/central Siberia to the Americas (with the second migration being restricted to North America) and a shared ancestry in central Asia for some of the initial migrants to Europe and the Americas. The microsatellite diversity and distribution of a Y lineage specific to South America (Q-M19) indicates that certain Amerind populations have been isolated since the initial colonization of the region, suggesting an early onset for tribalization of Native Americans. Age estimates based on Y-chromosome microsatellite diversity place the initial settlement of the American continent at approximately 14,000 years ago, in relative agreement with the age of well-established archaeological evidence.

Figures

Figure  1
Figure 1
Maps showing the approximate geographic location of the Native American populations examined (left) and the distribution of the ethnic groups sampled in Mongolia (inset).
Figure  2
Figure 2
Phylogenetic relationship of nine Y-chromosome lineages and their frequency in Native Americans, Mongolians, Europeans, and sub-Saharan Africans. The tree at the top displays the relationship of these lineages and the markers that were examined to identify them. The lineage frequency (%) in the populations examined here (with sample size in parentheses) is indicated in the middle. The mean lineage frequencies for major population groups are given at the bottom and were calculated from the data of Karafet et al. (1999) and Lell et al. (2002) and from the data collected here (the Na Dené being represented by the Chipewayan sample). The nomenclature of lineages follows the guidelines of the Y Chromosome Consortium (2002). Asterisks indicate lineages characterized by the derived state at that marker but the ancestral state at the other loci examined within that clade. For example, “P-M45*” refers to chromosomes carrying the derived M45 allele but the ancestral allele at marker M242—that is, P-M45*(x M242)—and Y* chromosomes carry the ancestral allele at all markers examined—that is, Y*(x M9, RPS4Y711, YAP).
Figure  3
Figure 3
Principal-component analysis based on the frequency of six Y-chromosome lineages (Q-M3, P-M45*, C-RPS4Y711, K-M9, DE-YAP, and Y*) in 64 Asian and Native American populations (with sample sizes >10). For the populations typed here, the frequency of haplogroups Q-M19 and Q-M242* shown in figure 2 was added to that of lineages Q-M3* and P-M45*, respectively. The Mongolian data collected here were analyzed separately for the Khalkh, Buryad, and Durvud samples. Data for the other populations are from Karafet et al. (1999) and Lell et al. (2002). Eastern Asians are shown as crosses, central Asians as squares, northern Asians as blackened circles, and Native Americans as unblackened circles. “S. Amerind” refers to nine South American populations in which the only lineage observed is Q-M3.
Figure  4
Figure 4
Median-joining networks relating haplotypes within lineages Q-M3* (A), Q-M19 (B), Amerind Q-M242* (C), and P-M45* (D). Haplotype numbers are as indicated in tables 1, 3, and 4. In D, Native American haplotypes are shown as blackened circles, and Mongolian haplotypes are shown as unblackened circles. The star highlights a haplotype seen both in Native Americans and Mongolians.
Figure  5
Figure 5
Neighbor-joining tree relating P-M45 Y lineages on the basis of Nei’s standard genetic distance (Nei 1987), calculated from the allele frequencies observed at the six microsatellite loci examined (table 2). Numbers indicate bootstrap values (%) for 1,000 replicates.

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