Abstract Highlanders and lowlanders of Papua New Guinea (PNG) have faced distinct environmental conditions. These environmental differences lead to specific stress on PNG highlanders and lowlanders, such as hypoxia and environment-specific pathogen exposure, respectively. We hypothesise that these constraints induced specific selective pressures that shaped the genomes of both populations. In this study, we explored signatures of selection in newly sequenced whole genomes of 54 PNG highlanders and 74 PNG lowlanders. Based on multiple methods to detect selection, we investigated the 21 and 23 genomic top candidate regions for positive selection in PNG highlanders and PNG lowlanders, respectively. To identify the most likely candidate SNP driving selection in each of these regions, we computationally reconstructed allele frequency trajectories of variants in each of these regions and chose the SNP with the highest likelihood of being under selection with CLUES. We show that regions with signatures of positive selection in PNG highlanders genomes encompass genes associated with the hypoxia-inducible factors pathway, brain development, blood composition, and immunity, while selected genomic regions in PNG lowlanders contain genes related to immunity and blood composition. We found that several candidate driver SNPs are associated with haematological phenotypes in the UK biobank. Moreover, using phenotypes measured from the sequenced Papuans, we found that two candidate SNPs are significantly associated with altered heart rates in PNG highlanders and lowlanders. Furthermore, we found that 16 of the 44 selection candidate regions harboured archaic introgression. In four of these regions, the selection signal might be driven by the introgressed archaic haplotypes, suggesting a significant role of archaic admixture in local adaptation in PNG populations.
when Martin Gunther, the Officer-in-Charge over the previous 10 years, told him of the impending closure of some of the research stations of the Department of Agriculture and Livestock, as the Department of Primary Industry was now called.The reason for this was the suspension of operations the previous year at the Panguna mine on Bougainville, which had become a target of the secessionist Bougainville Revolutionary Army.By the time of its closure and after 15 years of operation, Bougainville Copper managing director reckoned that the mine had provided 40-50 per cent of PNG's foreign earnings and 15-20 per cent of revenue (cited by Denoon 2000: 192-193).Of the two highlands research stations, Aiyura, near Kainantu, and Kuk, it was anticipated that Kuk would continue because of recent investment in housing and facilities there.In the event it was Aiyura that survived, on the grounds of perceived security problems for staff at Kuk.However, the Western Highlands Provincial Government was interested in the housing and the land.Consequently, before his departure, OIC Gunther (pers.comm., 2006) negotiated the transfer of the Station to the provincial administration for 'mothballing' for three years from
Abstract Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count – both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.
Recent studies have enlightened the complexity of the genetic landscape present in New Guinean populations. From the New Guinean genome, inherited from the Out-of-Africa dispersal 60 000 years ago, to the gene flows from Austronesian groups during the Holocene, and even to the high percentage of genetic introgression from an extinct Homo species named Denisova, the biological diversity of New Guineans is unique. It is a result of the various human migrations to the island but also within its territory, composed by a variety of different ecosystems. These processes created high genetic differentiations between New Guinean groups, a pattern that superficially mirrors the one drawn from the linguistic diversity, one of the highest in the world, with more than 900 languages. Despite these results, major issues remain unresolved regarding New Guinean genetic history.
Since 2016, thanks to the French Ministry of Foreign Affairs and the University of Papua New Guinea, we have developed an international and interdisciplinary research project aiming to reconstruct the demographic and adaptive history of New Guinean populations. A particular focus is put on the interaction between the New Guinean and Non-New Guinean genetic diversities, and how this mirror the highland and lowland division and the main New Guinean language families distribution, in structuring the current human biological landscape of the island.
In this paper we will present results based on the analysis of whole-genome sequencing data from New Guinean samples originated from the 22 provinces of Papua New Guinea, and from West Papua (Indonesia). Analyses used an exhaustive comparative dataset, SNP frequency-based (e.g., f3 and f4-statistics) and haplotype-based approaches (FineSTRUCTURE, GLOBETROTTER), and a large interpretative framework (archaeology, anthropology, linguistic). This allows to propose a better description of the different phases of human settlement in New Guinea Island, and better understand the current anthropological landscape.
Archaeological investigations have documented an ideological and occupied frontier in the Lower Tagali Valley along the southern margins of the Highlands of Papua New Guinea. Open-area excavations document two types of house structure associated with Huli occupation of the Lower Tagali Valley landscape, a women's house ( wandia ) and a lodge and ceremonial complex associated with a bachelor cult ( ibagiyaanda) . Excavation revealed the complete floor plan of the women's house site and multiple structural elements of the ceremonial complex. Radiocarbon dating provides a chronology for both sites that accords with genealogical histories for the colonization of this landscape by Huli during the early nineteenth century, or approximately eight generations ago. These archaeological findings are consistent with the strategies still employed today by Huli in the initial ideological incorporation of new territory and anchoring of expansionary claims through subsequent settlement and cultivation.
The archaeology of the island of New Guinea is ancient and surprising, yet it is highly fragmentary in space and time. Consequently, archaeology provides only local and fleeting glimpses of social life in the distant past. In this review, we consider several key themes, such as initial colonization at least 55,000 years ago, the emergence of agriculture by at least 7,000–6,400 years ago, and social diversification in the last few thousand years. We build our discussions around robust archaeological records that convey a coherent impression of what people were doing in the past. We also highlight the ways in which archaeology can be repurposed to address contemporary issues, including social and environmental problems, and flag how a distinctive New Guinean archaeology could be rooted in a vegecultural conception of social life and time.
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