Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis

Abstract

Eastern Indonesia possesses more linguistic diversity than any other region in Southeast Asia, with both Austronesian (AN) languages that are of East Asian origin, as well as non-Austronesian (NAN) languages of likely Melanesian origin. Here, we investigated the genetic history of human populations from seven eastern Indonesian islands, including AN and NAN speakers, as well as the relationship between languages and genes, by means of nonrecombining Y-chromosomal (NRY) and mitochondrial DNA (mtDNA) analysis. We found that the eastern Indonesian gene pool consists of East Asian as well as Melanesian components, as might be expected based on linguistic evidence, but also harbors putative indigenous eastern Indonesian signatures that perhaps reflect the initial occupation of the Wallacea by aboriginal huntergatherers already in Palaeolithic times. Furthermore, both NRY and mtDNA data showed a complete lack of correlation between linguistic and genetic relationships, most likely reflecting genetic admixture and/or language shift. In addition, we noted a small fraction of the NRY and mtDNA data shared between eastern Indonesians and Australian Aborigines likely reflecting an ancient link between Asia and Australia. Our data thus provide insights into the complex genetic ancestry history of eastern Indonesian islanders characterized by several admixture episodes and demonstrate a clear example of the lack of the often-assumed correlation between the genes and languages of human populations.

Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

“…For comparison, the gross frequencies of these haplogroups as observed in other regions of Asia/Oceania, pooled from different population samples, are included as well using previously published data. 7,10,16,18,42 For practical reasons, the PNG Highlands group includes Kapuna, a Papuan-speaking group from the Gulf Province of PNG with an assumed origin in the highlands, while the PNG Coast group includes Bereina, an Austronesian-speaking group from the southern coastal area of PNG. Figure S1) indeed showed that its haplotypes are quite diverse.…”

“…For comparisons in a wider geographic context, we included previously described population data from East Asia, Island Southeast Asia, and Near and Remote Oceania, using a minimal sample size of 20 individuals per population for both NRY and mtDNA 7,10,16,18,42,43 (for an overview, see Supplementary Table S1). …”

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

“…For population comparisons, a reference data set was assembled from previously published works, [20][21][22][23][24] composed of 1756 males from 60 groups representing five Asia-Pacific regions ( Figure 1). Reference data set population codes and measures to ensure compatibility with the Filipino data set are discussed in Supplementary Text.…”

“…[20][21][22][23][24] Figure 1 shows the distribution of shared Y-SNP haplogroups among FE groups and the reference data set. AMOVA results (Table 3) show that the heterogeneity of FE groups were comparable to or exceeded the heterogeneity of the other regions in the reference data set.…”

“…The DYS390.1 deletion has been associated with DYS390 allele lengths ranging from 18 to 22 repeats and so far is specific to Australians. 20,24,29 Several FE groups (Ivatan, Agta, Ati, Surigaonon, Mamanwa, and Manobo) have C-RPS4Y/DYS390 allele lengths within this range (Supplementary Table 2). Although sequence analysis would be required to definitely Figure 3).…”