A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania

Abstract

Modern humans reached Southeast Asia and Oceania in one of the first dispersals out of Africa. The resulting temporal overlap of modern and archaic humans-and the apparent morphological continuity between them-has led to claims of gene flow between Homo sapiens and H. erectus. Much more recently, an agricultural technology from mainland Asia spread into the region, possibly in association with Austronesian languages. Using detailed genealogical study of Y chromosome variation, we show that the majority of current Austronesian speakers trace their paternal heritage to Pleistocene settlers in the region, as opposed to more-recent agricultural immigrants. A fraction of the paternal heritage, however, appears to be associated with more-recent immigrants from northern populations. We also show that the northern Neolithic component is very unevenly dispersed through the region, with a higher contribution in Southeast Asia and a nearly complete absence in Melanesia. Contrary to claims of gene flow (under regional continuity) between H. erectus and H. sapiens, we found no ancestral Y chromosome lineages in a set of 1,209 samples. The finding excludes the possibility that early hominids contributed significantly to the paternal heritage of the region.

Figure 1

Geographic locations of the analyzed populations. Charts represent haplogroup frequencies. No haplogroup A chromosomes were found.

Figure 2

Genealogy showing haplogroup designations and the defining mutations. The coalescence time, in generations, of chromosomes within indicated haplogroups was estimated by inferring the founder haplotype, where possible, as the modal allele at each locus and by using methods described by Thomas et al. (1998), corrected for length dependence (Goldstein et al., in press). The applied mutation rate was 2.8×10^-3 (Kayser et al. 2000), which resulted in the following estimates for indicated haplogroups: E, 304 generations; G, 344 generations; H, 179 generations; L, 524 generations; and C, 871 generations.

Figure 3

Genealogical tree of Y chromosome haplotypes in haplogroups C (a) and L (b). Neighbor-joining trees were reconstructed using the program NEIGHBOR (PHYLIP), on the basis of the average squared distance calculated by MICROSAT. Colored bars indicate haplotype geographic association as follows: red indicates Polynesia; green indicates Melanesia; blue indicates Southeast Asia; orange indicates southern China, India, and Mongolia; black indicates Taiwan; and purple indicates Philippines. Shared haplotypes across geographic regions are indicated by multicolored bars.

Figure 4

Graphic representation of the principal-component analysis of haplogroup frequencies