Y-STR loci diversity in native Alaskan populations

Abstract

Y chromosome short tandem repeat (Y-STR) loci are important genetic markers for forensic biological evidence analyses. However, paternal inheritance, reduced effective population size, and lack of independence between loci can reduce Y-STR diversity and may yield greater population substructure effects on a locus-by-locus basis compared with the autosomal STR loci. Population studies are necessary to assess the genetic variation of forensically relevant markers so that proper inferences can be made about the rarity of DNA profiles. This study examined 16 Y-STRs in three sampled populations of Native Americans from Alaska: Inupiat, Yupik, and Athabaskan. Population genetic and statistical issues addressed were: (1) the degree of diversity at locus and haplotype levels, (2) determination of the loci that contribute more so to haplotype diversity, and (3) the effects of population substructure on forensic statistical calculations of the rarity of a Y-STR profile. All three population samples were highly polymorphic at the haplotype level for the 16 Y-STR markers; however, the Native Americans demonstrated reduced genetic diversity compared with major US populations. The degree of substructure indicated that the three populations were related and admixed in terms of paternal lineage. The examination of more polymorphic loci may be needed to increase the power of discrimination of Y-STR systems in these populations.

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

“…Another Q1a3a1* lineage belonged to a Mi'kmaq from Nova Scotia, but it is not clear that this person's Y chromosome also shares a recent origin with these other haplotypes. Finally, one Tłįchǫ and one Slave belonged to Q1a5, whereas a similar Ychromosome short tandem repeat (Y-STR) haplotype was found in one Alaskan Athapaskan (22). This SNP was previously described in the work by Karafet et al (19), although its geographic distribution was not discussed.…”

“…Four samples (three Gwich'in and one First Nation member from British Columbia) belonged to paragroup Q1a3a1*. We also identified 10 samples (9 Athapaskans and 1 Inupiat samples) (22) that clustered with these haplotypes, suggesting a common origin for them. Another Q1a3a1* lineage belonged to a Mi'kmaq from Nova Scotia, but it is not clear that this person's Y chromosome also shares a recent origin with these other haplotypes.…”

“…Q1a6 is especially important, because it is largely confined to the Inuvialuit, Inuit, and Inupiat populations. Although no SNP data were presented in the work by Davis et al (22), a number of their STR haplotypes were similar to the Q1a6 lineages and in several cases, shared with the Inuvialuit (Fig. S2).…”

“…S3). We reduced our NRY data to 8-STR loci haplotypes to compare them with published data (17,22,28) and determine the directionality of movement by bearers of C3b Y chromosomes. Vp estimates for the 8-STR haplotypes showed the greatest diversity in the Tanana Athapaskans and Alaskan Athapaskans of the work by Davis et al (22), moderate values among the Tłįchǫ and Gwich'in, and the lowest values in the Apache, thus forming a north to south gradient of C3b diversity.…”

“…This SNP, named NWT01, is a C to G transversion at np 65 in the amplicon (Y position 2,888,083 in Build 37.2). Comparative data came from published literature (Table S2) (22,27,(48)(49)(50). Statistical analysis included estimates of haplotype diversity, mean pairwise differences and analysis of molecular variance using Arlequin v3.11 (51), and Vp estimates assessed as in the work by Kayser et al (52).…”