Y chromosome polymorphisms in Native American and Siberian populations: identification of Native American Y chromosome haplotypes

Abstract

We have initiated a study of ancient male migrations from Siberia to the Americas using Y chromosome polymorphisms. The first polymorphism examined, a C→T transition at nucleotide position 181 of the DYS199 locus, was previously reported only in Native American populations. To investigate the origin of this DYS199 polymorphism, we screened Y chromosomes from a number of Siberian, Asian, and Native American populations for this and other markers. This survey detected the T allele in all five Native American populations studied at an average frequency of 61%, and in two of nine native Siberian populations, the Siberian Eskimo (21%) and the Chukchi (17%). This finding suggested that the DYS199 T allele may have originated in Beringia and was then spread throughout the New World by the founding populations of the major subgroups of modern Native Americans. We further characterized Native American Y chromosome variation by analyzing two additional Y chromo-some polymorphisms, the DYS287 Y Alu polymorphic (YAP) element insertion and a YAP-associated A→G transition at DYS271, both commonly found in Africans. We found neither African allele associated with the DYS199 T allele in any of the Native American or native Siberian populations. However, we did find DYS287 YAP+ individuals who harbored the DYS199 C allele in one Native American population, the Mixe, and in one Asian group, the Tibetans. A correlation of these Y chromosome alleles in Native Americans with those of the DYS1 locus, as detected by the p49a/p49f (p49a,f) probes on TaqI-digested genomic DNA, revealed a complete association of DYS1 alleles (p49a,f haplotypes) 13, 18, 66, 67 and 69 with the DYS199 T allele, while DYS1 alleles 8 and 63 were associated with both the DYS199 C and T allele.

Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a

“…Earlier, haplogroup Q1a3a has been discovered at a low frequency in Siberian Eskimos, Chukchi and Evens. 43,44 Karafet et al 43 have hypothesized that this haplogroup may have originated in the New World/eastern Beringia and that its infrequent presence in Northeast Siberian populations can be explained by back-migration from Alaska to Siberia. A search of Q1a3a-M3 STRhaplotypes revealed in Evens in the YHRD 3.0 database (http:// www.yhrd.org; release 36 built on 15 April 2011; 91 493 haplotypes within 686 world populations) has shown that matching haplotypes (for loci DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) are rarely present in modern Native American populations.…”

Ancestry informative markers and admixture proportions in northeastern Mexico

“…The remaining two markers, the YAP marker, common in populations of African ancestry, and the M3 SNP, characteristic of Native Americans, were genotyped by PCR and PCR-restriction fragment length polymorphisms, respectively, as described earlier. 13,14 The definition of the different haplogroups was made according to the YChromosome Consortium recommendations. 15 Native American, European and African paternal contributions were determined directly from haplogroup frequencies, considering worldwide phylogeographic information.…”

Microsatellites provide evidence for Y chromosome diversity among the founders of the New World

“…Although genetic approaches to the population history of Native Americans have mostly used either autosomal or mtDNA markers, a number of recent analyses have begun to exploit Y chromosome-specific variation (6)(7)(8)(9)(10)(11)(12). These studies have shown a consistent pattern of scarce haplotypic diversity in Native American populations.…”

“…Of particular interest, because it is most likely a single event polymorphism, the DYS199 T allele has been detected only in Chuckchan populations of extreme northeastern Siberia (11,12). The presence of the T allele in these populations could imply that they inherited it from an ancestral population shared with Native Americans.…”