Population structure and migration in the Eastern Highlands of Papua New Guinea, a region impacted by the kuru epidemic.

Populations of the Eastern Highlands of Papua New Guinea (EHPNG, area 11,157 km2) lived in relative isolation from the rest of the world until the mid-20th century, and the region contains a wealth of linguistic and cultural diversity. Notably, several populations of EHPNG were devastated by an epidemic prion disease, kuru, which at its peak in the mid-twentieth century led to some villages being almost depleted of adult women. Until now, population genetic analyses to learn about genetic diversity, migration, admixture, and the impact of the kuru epidemic have been restricted to a small number of variants or samples. Here, we present a population genetic analysis of the region based on genome-wide genotype data of 943 individuals from 21 linguistic groups and 68 villages in EHPNG, including 34 villages in the South Fore linguistic group, the group most affected by kuru. We find a striking degree of genetic population structure in the relatively small region (average FST between linguistic groups 0.024). The genetic population structure correlates well with linguistic grouping, with some noticeable exceptions that reflect the clan system of community organization that has historically existed in EHPNG. We also detect the presence of migrant individuals within the EHPNG region and observe a significant excess of females among migrants compared to among non-migrants in areas of high kuru exposure (p = 0.0145, chi-squared test). This likely reflects the continued practice of patrilocality despite documented fears and strains placed on communities as a result of kuru and its associated skew in female incidence.

A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies.

Genomic insights into the peopling of the Southwest Pacific.

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.

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.

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.

Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion.

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.

Distribution of an allele associated with blond hair color across Northern Island Melanesia.

Pigmentation of the skin, hair, and eyes is a complex trait controlled by multiple genetic loci. Recently a non-synonymous mutation in the pigmentation candidate gene TYRP1 was shown to be significantly associated with a blond-hair phenotype in populations from the Solomon Islands. The distribution of this mutation in the islands of Northern Island Melanesia, where the blondism phenotype is also prevalent, was unknown. Here, we present data describing the distribution of this allele in 550 individuals sampled from across this region, and test for associations between genotype at this locus and quantitatively measured skin and hair pigmentation phenotype. We report that the frequency of the 93C allele is notably lower than observed in the Solomons (0.12 vs. 0.26). The allele exhibits significant geographic heterogeneity across the islands sampled (χ(2) = 108.4, P < 0.0001). It is observed at its highest frequencies on the islands of New Ireland and New Hanover, while being almost completely absent from the large island of New Britain. Using linear regression with age, sex, and island as covariates we report that, as in the Solomons, the 93C allele is significantly associated with a decrease in hair pigmentation but not skin pigmentation. We discuss the distribution of the 93C allele across the Southwest Pacific in light of its possible place of origin and dispersal.

Characterization of population structure from the mitochondrial DNA vis-à-vis language and geography in Papua New Guinea.

Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea. We analyzed these samples with a large data set of Oceania populations to examine the role of geography and language in shaping population structure within New Guinea and between the region and Island Melanesia. Our results from median-joining networks, star-cluster age estimates, and population genetic analyses show that while highland New Guinea populations seem to be the oldest settlers, there has been significant gene flow within New Guinea with little influence from geography or language. The highest genetic division is between Papuan speakers of New Guinea versus East Papuan speakers located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring among populations in close contact and highlights the complexity of understanding the genetic histories of Papua New Guinea in association with language and geography.

Genetic and linguistic coevolution in Northern Island Melanesia.

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions.

The genetic structure of Pacific Islanders.

Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small "Austronesian" genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there.

Melanesian mtDNA complexity.

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.

Unexpected NRY chromosome variation in Northern Island Melanesia.

To investigate the paternal population history of populations in Northern Island Melanesia, 685 paternally unrelated males from 36 populations in this region and New Guinea were analyzed at 14 regionally informative binary markers and 7 short tandem repeat (STR) loci from the nonrecombining portion of the Y chromosome. Three newly defined binary markers (K6-P79, K7-P117, and M2-P87) aided in identifying considerable heterozygosity that would have otherwise gone undetected. Judging from their geographic distributions and network analyses of their associated STR profiles, 4 lineages appear to have developed in this region and to be of considerable age: K6-P79, K7-P117, M2-P87, and M2a-P22. The origins of K5-M230 and M-M4 are also confirmed as being located further west, probably in New Guinea. In the 25 adequately sampled populations, the number of different haplogroups ranged from 2 in the single most isolated group (the Aita of Bougainville), to 9, and measures of molecular diversity were generally not particularly low. The resulting pattern contradicts earlier findings that suggested far lower male-mediated diversity and gene exchange rates in the region. However, these earlier studies had not included the newly defined haplogroups. We could only identify a very weak signal of recent male Southeast Asian genetic influence (<10%), which was almost entirely restricted to Austronesian (Oceanic)-speaking groups. This contradicts earlier assumptions on the ancestral composition of these groups and requires a revision of hypotheses concerning the settlement of the islands of the central Pacific, which commenced from this region.

Skin and hair pigmentation variation in Island Melanesia.

Skin and hair pigmentation are two of the most easily visible examples of human phenotypic variation. Selection-based explanations for pigmentation variation in humans have focused on the relationship between melanin and ultraviolet radiation, which is largely dependent on latitude. In this study, skin and hair pigmentation were measured as the melanin (M) index, using narrow-band reflectance spectroscopy for 1,135 individuals from Island Melanesia. Overall, the results show remarkable pigmentation variation, given the small geographic region surveyed. This variation is discussed in terms of differences between males and females, among islands, and among neighborhoods within those islands. The relationship of pigmentation to age, latitude, and longitude is also examined. We found that male skin pigmentation was significantly darker than females in 5 of 6 islands examined. Hair pigmentation showed a negative, but weak, correlation with age, while skin pigmentation showed a positive, but also weak, correlation with age. Skin and hair pigmentation varied significantly between islands as well as between neighborhoods within those islands. Bougainvilleans showed significantly darker skin than individuals from any other island considered, and are darker than a previously described African-American population. These findings are discussed in relation to prevailing hypotheses about the role of natural selection in shaping pigmentation variation in the human species, as well as the role of demographic processes such as admixture and drift in Island Melanesia.

Ancient mitochondrial M haplogroups identified in the Southwest Pacific.

Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.

Expanding Southwest Pacific mitochondrial haplogroups P and Q.

Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole-mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other (approximately 50,000 years old) and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples as well as complete mtDNA-coding region sequencing. Our estimates are roughly in accord with the current suggested dates for the first settlement of New Guinea-Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea-Island Melanesia from Australia that may have existed from the time of the first settlement. While Q subsequently diversified extensively in New Guinea-Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.