A private allele ubiquitous in the Americas

Abstract

migrations from the same source population may produce patterns of variation similar to that produced from a single migration. Although the number of migrations might not be inferable from genetic data, whether all Native American populations descend from the same founding population can be addressed if a unique autosomal variant absent from Asian populations is identified throughout the Americas. In their analysis of the HGDP–CEPH human genome diversity panel (henceforth HGDP) genotypes for 377 microsatellites, Zhivotovsky et al. (2003) noted that only in a single instance could a regional group could be distinguished by a private marker. A 275 bp allele at D9S1120 (also known as GATA81C04 or GATA11E11) was observed at high frequencies in all American populations (all of which are Amerind: Pima; Maya; Colombian; Karitiana; and Surui) and was absent from 47 other worldwide populations. This allele had a frequency of 36.5% in the pooled American sample, while no other allele among the 4688 studied was private to a major geographical region (defined as sub-Saharan Africa, Europe and the part of Asia south and west of the Himalayas (including North Africa), East Asia, Oceania and the Americas) with a frequency above 13%. Expansion of the dataset to 783 loci and 9346 alleles (Rosenberg et al. 2005) did not reveal any additional regionally private allele with a frequency above 13% (figure 1, inset). The 275 bp allele was the smallest one observed at D9S1120 in the HGDP. We have determined through sequencing that this allele contains nine tetranucleotide repeats and is the result of slippage in the repetitive section, as opposed to a deletion elsewhere in the amplicon. Henceforth, we shall refer to alleles at this locus by the corresponding number of repeats and to the 9-repeat allele as ‘9RA’. The next largest allele in the HGDP outside the Americas is 11 repeats and was observed only in three chromosomes. The lack of regionally specific private alleles at a high frequency (figure 1, inset), the striking distribution of 9RA and the rarity of intermediate-sized alleles (table 1) strongly suggests that all or nearly all copies of 9RA descend from a single mutational event. We hypothesized that if the Aleut-Eskimo, Na-Dene and other indigenous populations throughout the Americas share common ancestry with the American populations in the HGDP, then we would observe 9RA across the Americas. Additionally, if further sampling did not reveal 9RA in putative Asian source populations, then we could conclude that modern Native American populations share more recent common ancestry with each other than with any Asian population.