Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia

Abstract

BackgroundThe islands of North Maluku, Indonesia occupy a central position in the major prehistoric dispersal streams that shaped the peoples of Island Southeast Asia and the Pacific. Within this region a linguistic contact zone exists where speakers of Papuan and Austronesian languages reside in close proximity. Here we use population genetic data to assess the extent to which North Maluku populations experienced admixture of Asian genetic material, and whether linguistic boundaries reflect genetic differentiation today.ResultsAutosomal and X-linked markers reveal overall Asian admixture of 67% in North Maluku, demonstrating a substantial contribution of genetic material into the region from Asia. We observe no evidence of population structure associated with ethnicity or language affiliation.ConclusionsOur data support a model of widespread Asian admixture in North Maluku, likely mediated by the expansion of Austronesian-speaking peoples into the region during the mid Holocene. In North Maluku there is no genetic differentiation in terms of Austronesian- versus Papuan-speakers, suggesting extensive gene flow across linguistic boundaries. In a regional context, our results illuminate a major genetic divide at the Molucca Sea, between the islands of Sulawesi and North Maluku. West of this divide, populations exhibit predominantly Asian ancestry, with very little contribution of Papuan genetic material. East of the Molucca Sea, populations show diminished rates of Asian admixture and substantial persistence of Papuan genetic diversity.

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia

“…Reference data comprise estimates of Asian/Papuan admixture from 2299 individuals in 84 populations across Island Southeast Asia (Cox et al 2010), including additional data points for North Maluku (Wilder et al 2011) and West Timor (Tumonggor et al 2014). Asian admixture proportions were calculated for both the autosomes and the X chromosome using 39 ancestry informative markers (AIMs), which were chosen for their high F ST between proxy parental populations, southern Han Chinese, and Papua New Guinea highlanders.…”

“…For modeling purposes, admixture values were averaged across multiple populations on small islands, and simulations were based on autosome and X chromosome admixture proportions for 16 regional groups (Supplemental Material, File S1, Table S1). Information on the design of the AIM markers, as well as access to the publicly available genetic data sets, is described in full elsewhere (Cox et al 2010; Wilder, et al 2011; Tumonggor et al 2014). …”

“…The mean proportions of Asian ancestry on the autosomes and X chromosome for simulated populations can be related directly to the admixture proportions observed for real human groups: here, AIM data for human populations distributed across Island Southeast Asia (Cox et al 2010; Wilder et al 2011; Tumonggor et al 2014). Model parameters were then inferred by minimizing the fit between the simulated and real ancestry values.…”

“…Our choice of model framework reflects the complexity of regional history, including a challenging geography (a complex arrangement of islands and sea), migration at variable scales (both short and long distance mobility), and the action of social behaviors (such as sex-biased Asian–Papuan marriage preferences), all while requiring patterns of genetic diversity to be tracked simultaneously across a full gamut of marker types [autosomes, X chromosome, mitochondrial DNA (mtDNA), and Y chromosome]. Importantly, this model is not intended as an end in itself, but is instead integrated with Bayesian statistical inference to explicitly estimate demographic and social parameters that may have led to the Asian ancestry proportions observed in nuclear genetic markers across Island Southeast Asia today (Cox et al 2010; Wilder, et al 2011; Tumonggor, et al 2014). Key questions include (i) whether incoming individuals with Asian ancestry had greater fecundity and/or propensity to migrate than local individuals with Papuan ancestry (perhaps due to improved farming and maritime technologies); (ii) whether a widely proposed bias favoring marriages between Asian women and Papuan men is required to explain increased rates of Asian variants on the X chromosome relative to the autosomes (Hage and Marck 2003; Cox et al 2010); and (iii) how far individuals with Asian ancestry had encroached into western Island Southeast Asia prior to the Neolithic expansion (Spriggs 2012; Lipson et al 2014).…”

Climate Change Influenced Female Population Sizes Through Time Across the Indonesian Archipelago

“…The region's prehistory is dominated by population movements, beginning with its first settlement by modern humans approximately 50 kya and continuing to the Islamization of Indonesia during the historic period. Reflecting the rich cultural and linguistic diversity of Indonesia's inhabitants, these eras have also left their mark on the genetic diversity of the individuals who inhabit Indonesia today (Cox et al 2012;Jinam et al 2012;Karafet et al 2010;Kayser 2010;Kayser et al 2003;Lansing et al 2008Lansing et al , 2009Mona et al 2009;Wilder et al 2011;Xu et al 2012).…”