Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul (original) (raw)
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The gateway into Remote Oceania: new insights from genome-wide data
ABSTRACTA widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration ca 50,000 ya, and one of the most geographically-widespread dispersals of people, known as the Austronesian expansion, which reached the Bismarck Archipelago by about 3,450 ya. While earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide dataset of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal SNPs. We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a “leapfrog” fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a b...
Papuan mitochondrial genomes and the settlement of Sahul
Journal of Human Genetics, 2020
New Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuan mitochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50–65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania.
Genomic insights into population history and biological adaptation in Oceania
Nature, 2021
Archaeological data indicate that Near Oceania, which includes New Guinea, the Bismarck archipelago and the Solomon Islands, was peopled around 45 thousand years ago (ka) 5 .The rest of the Pacific-known as Remote Oceania, and including Micronesia, Santa Cruz, Vanuatu, New Caledonia, Fiji and Polynesia-was not settled until around 35 thousand years later. This dispersal, associated with the spread of Austronesian languages and the Lapita cultural complex, is thought to have started in Taiwan around 5 ka, reaching Remote Oceania by about 0.8-3.2 ka 6. Although genetic studies of Oceanian populations have revealed admixture with populations of East Asian origin 7-13 , attributed to the Austronesian expansion, questions regarding the peopling history of Oceania remain. It is also unknown how the settlement of the Pacific was accompanied by genetic adaptation to island environments, and whether archaic introgression facilitated this process in Oceanian individuals, who present the highest levels of combined Neanderthal and Denisovan ancestry worldwide 14-17. We report here a whole-genome-based survey that addresses a wide range of questions relating to the demographic and adaptive history of Pacific populations. Genomic dataset and population structure We sequenced the genomes of 317 individuals from 20 populations spanning a geographical transect that is thought to underlie the peopling history of Near and Remote Oceania (Fig. 1a and Supplementary Note 1). These high-coverage genomes (around 36×) were
The genomic landscape of contemporary western Remote Oceanians
2022
SUMMARYThe Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands, ~3,000 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet, there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world’s highest linguistic and cultural diversity. Here, we report new genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous, sex-biased admixture events that occurred ~1,700-2,300 years ago, indicating a peopling history common to all the archipelago. However, East Asian-relat...
Origins and genetic legacy of the first people in Remote Oceania
The appearance of people associated with the Lapita culture in the South Pacific ~3,000 53 years ago 1 marked the beginning of the last major human dispersal to unpopulated 54 lands, culminating in the settlement of eastern Polynesia ~1,000-700 years ago. 55 However, the genetic relationship of these pioneers to the long established Papuans of 56 the New Guinea region is debated. We report the first genome-wide ancient DNA data 57 from the South Pacific, from four ~2,900 to ~2,500 year old Lapita culture individuals 58 from Vanuatu and Tonga, and co-analyze them with new data from 356 present-day 59 Oceanians. Today, all indigenous people of the South Pacific harbor a mixture of 60 ancestry from Papuans and a population of East Asian origin that is a statistical match 61 to the ancient Lapita individuals. Most analyses have interpreted the ubiquitous Papuan 62 ancestry in the region today-at least 25%-as evidence that the first humans to reach 63 Remote Oceania were derived from mixtures near New Guinea prior to the Lapita 64 expansion into Remote Oceania. Our results refute this scenario, as none of the 65 geographically and temporally diverse Lapita individuals had detectable Papuan 66 ancestry. These results imply later major human population movements, which spread 67 Papuan ancestry through the South Pacific after the islands' first peopling. 68 69
Genes
The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history ...
A genomic history of Aboriginal Australia
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
Ancient genomes from the last three millennia support multiple human dispersals into Wallacea
2021
Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region’s demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estim...
Genomic insights into the peopling of the Southwest Pacific
Nature, 2016
The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.