Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations

Abstract

For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich’in, and Tłįchǫ populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįchǫ being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized.

Reconciling migration models to the Americas with the variation of North American native mitogenomes

“…Our phylogeographic data indicate that the present-day A2a mitogenomes coalesce to ∼4-7 ka and the variants detected among the Eskimo-Aleut speakers of both Northeast Asia and northern North America experienced the steepest population expansion ∼4 ka, thus confirming that this lineage is a good candidate marker for a separate and more recent migratory wave associated with the first Paleo-Eskimo settlement of the northernmost part of Canada and Greenland (Fig. 4), as also supported by the Y-chromosome prevalence (and diversity) of the Q1a6-NWT01 sublineage in the Western Canadian Inuit (Inuvialuit) (20). The ancestral A2a Paleo-Eskimo carriers undertook both a back-migration to Asia and an eastward path along the circumpolar region of Canada and Greenland.…”

“…More than one migration wave was originally hypothesized to explain the introduction of distinct linguistic families, such as Eskimo-Aleut and Na-Dene, into the Americas. Recent Y-chromosome data supported the scenario that the Eskimoan-and Athapaskan-speaking groups were the result of two population expansions that occurred after the initial wave of American settlement (20). The old tripartite linguistic subdivision into Eskimo-Aleuts, Na-Dene, and Amerinds of Greenberg et al (19) has been somehow recently revived to explain the pattern of nuclear diversity (over 364,000 SNPs) identified in 52 Native populations: 3 Eskimo-Aleutians, 1 Na-Dene (the North Athapaskan-speaking Chipewyan of the Northwest Territories of Canada), and 48 other Native American groups from North, Central, and South America (26).…”

The ancestry and affiliations of Kennewick Man

“…The mitochondrial genome was sequenced to ~71× coverage and is placed at the root of haplogroup X2a (Extended Data Fig. 1, Supplementary Information 2), and the Y-chromosome haplogroup is Q-M3 (Extended Data Fi.g 2, Supplementary Information 5); both uniparental lineages are found almost exclusively among contemporary Native Americans 15,16 . We used the X chromosome to conservatively estimate contamination to be 2.5%, which is within the normal range obtained observed in genomic data from ancient human remains 17 , and we further show this contamination to be of European origin (Supplementary Information 4).…”

Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

“…Genetic clues for the peopling of the Northwest Coast, however, may be obscured by later demographic events in the region. Studies based on mtDNA and Y-chromosomal markers suggest that populations in the region likely experienced admixture from other groups that entered the region after the initial peopling (4)(5)(6). Studies using genome-wide data (7-9) inferred ancient gene flow into North America likely stemming from subsequent movements after the initial settlement.…”