Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians

Abstract

Analyses of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in the same populations are sometimes concordant but sometimes discordant. Perhaps the most dramatic example known of the latter concerns Polynesians, in which about 94% of Polynesian mtDNAs are of East Asian origin, while about 66% of Polynesian Y chromosomes are of Melanesian origin. Here we analyze on a genome-wide scale, to our knowledge for the first time, the origins of the autosomal gene pool of Polynesians by screening 377 autosomal short tandem repeat (STR) loci in 47 Pacific Islanders and compare the results with those obtained from 44 Chinese and 24 individuals from Papua New Guinea. Our data indicate that on average about 79% of the Polynesian autosomal gene pool is of East Asian origin and 21% is of Melanesian origin. The genetic data thus suggest a dual origin of Polynesians with a high East Asian but also considerable Melanesian component, reflecting sex-biased admixture in Polynesian history in agreement with the Slow Boat model. More generally, these results also demonstrate that conclusions based solely on uniparental markers, which are frequently used in population history studies, may not accurately reflect the history of the autosomal gene pool of a population.

Figure 1

Model of Admixture Assumed in This Study, as Proposed Elsewhere In this model, the Polynesian population is considered to be the result of a single admixture event between the Asian and Melanesian parental populations, and after this event no further migration is observed between the three populations. Ne, effective population size; λ, the amount of parental ancestry of the Chinese population. The “c” index indicates the Chinese population, the “p” index the Polynesian population, the “m” index the Melanesian population, and the “a” index the ancestral population.

Figure 2

Prior and Posterior Distribution of the Amount of Asian Admixture (Expressed as λ) in Polynesians.

Figure 3

Estimated Proportion of Asian and Melanesian Ancestry in 47 Polynesians Based on the 377 autosomal STR loci (aSTR-1, based on LEADMIX; aSTR-2, based on the ABC approach). The estimated contribution of Asian and Melanesian mtDNA and NRY haplogroups for this sample of 47 Polynesians does not differ significantly from a larger sample of 321 Polynesians (data not shown). For the mtDNA and NRY data, standard errors were calculated from frequency estimates of haplogroups of Asian and Melanasian origin among those Polynesian individuals also analyzed for the aSTRs. For the aSTR data, standard errors were estimated from the 95% CI values of the amount of Asian admixture (expressed as λ) in the Polynesian individuals analyzed by the two simulation approaches. Only the positive errors are shown because they are symmetrical.