Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date-2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region's complex history of immigration, transitory migrants and populations that have endured in situ since the region's first settlement.

The settlement of Madagascar is one of the most unusual, and least understood, episodes in human prehistory. Madagascar was one of the last landmasses to be reached by people, and despite the island's location just off the east coast of Africa, evidence from genetics, language and culture all attests that it was settled jointly by Africans, and more surprisingly, Indonesians. Nevertheless, extremely little is known about the settlement process itself. Here, we report broad geographical screening of Malagasy and Indonesian genetic variation, from which we infer a statistically robust coalescent model of the island's initial settlement. Maximum-likelihood estimates favour a scenario in which Madagascar was settled approximately 1200 years ago by a very small group of women (approx. 30), most of Indonesian descent (approx. 93%). This highly restricted founding population raises the possibility that Madagascar was settled not as a large-scale planned colonization event from Indonesia, but rather through a small, perhaps even unintended, transoceanic crossing.

Timor, an eastern Indonesian island linking mainland Asia with Australia and the Pacific world, had a complex history, including its role as a contact zone between two language families (Austronesian and Trans-New Guinean), as well as preserving elements of a rich Austronesian cultural heritage, such as matrilocal marriage practices. Using an array of biparental (autosomal and X-chromosome single-nucleotide polymorphisms) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstruct a broad genetic profile of Timorese in the Belu regency of West Timor, including the traditional princedom of Wehali, focusing on the effects of cultural practices, such as language and social change, on patterns of genetic diversity. Sex-linked data highlight the different histories and social pressures experienced by women and men. Measures of diversity and population structure show that Timorese men had greater local mobility than women, as expected in matrilocal communities, where women remain in their natal village, whereas men move to the home village of their wife. Reaching further back in time, maternal loci (mitochondrial DNA and the X chromosome) are dominated by lineages with immigrant Asian origins, whereas paternal loci (Y chromosome) tend to exhibit lineages of the earliest settlers in the eastern Indonesian region. The dominance of Asian female lineages is especially apparent in the X chromosome compared with the autosomes, suggesting that women played a paramount role during and after the period of Asian immigration into Timor, perhaps driven by the matrilocal marriage practices of expanding Austronesian communities.