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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\u201365 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.<\/jats:p>","DOI":"10.1038\/s10038-020-0781-3","type":"journal-article","created":{"date-parts":[[2020,6,1]],"date-time":"2020-06-01T06:02:32Z","timestamp":1590991352000},"page":"875-887","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["Papuan mitochondrial genomes and the settlement of Sahul"],"prefix":"10.1038","volume":"65","author":[{"given":"Nicole","family":"Pedro","sequence":"first","affiliation":[]},{"given":"Nicolas","family":"Brucato","sequence":"additional","affiliation":[]},{"given":"Veronica","family":"Fernandes","sequence":"additional","affiliation":[]},{"given":"Mathilde","family":"Andr\u00e9","sequence":"additional","affiliation":[]},{"given":"Lauri","family":"Saag","sequence":"additional","affiliation":[]},{"given":"William","family":"Pomat","sequence":"additional","affiliation":[]},{"given":"C\u00e9line","family":"Besse","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8789-5676","authenticated-orcid":false,"given":"Anne","family":"Boland","sequence":"additional","affiliation":[]},{"given":"Jean-Fran\u00e7ois","family":"Deleuze","sequence":"additional","affiliation":[]},{"given":"Chris","family":"Clarkson","sequence":"additional","affiliation":[]},{"given":"Herawati","family":"Sudoyo","sequence":"additional","affiliation":[]},{"given":"Mait","family":"Metspalu","sequence":"additional","affiliation":[]},{"given":"Mark","family":"Stoneking","sequence":"additional","affiliation":[]},{"given":"Murray P.","family":"Cox","sequence":"additional","affiliation":[]},{"given":"Matthew","family":"Leavesley","sequence":"additional","affiliation":[]},{"given":"Luisa","family":"Pereira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7609-7898","authenticated-orcid":false,"given":"Fran\u00e7ois-Xavier","family":"Ricaut","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,1]]},"reference":[{"key":"781_CR1","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.ecolind.2005.02.005","volume":"5","author":"J Loh","year":"2005","unstructured":"Loh J, Harmon D. 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Diliman, Quezon City: University of Philippines Press, Philippines; 2006."}],"container-title":["Journal of Human Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/s10038-020-0781-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s10038-020-0781-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s10038-020-0781-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T21:09:08Z","timestamp":1684616948000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s10038-020-0781-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,1]]},"references-count":62,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2020,10]]}},"alternative-id":["781"],"URL":"https:\/\/doi.org\/10.1038\/s10038-020-0781-3","relation":{},"ISSN":["1434-5161","1435-232X"],"issn-type":[{"value":"1434-5161","type":"print"},{"value":"1435-232X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,1]]},"assertion":[{"value":"5 February 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 April 2020","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2020","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 June 2020","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"The authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"This study was approved by the Medical Research Advisory Committee of Papua New Guinea (National Department of Health) under research ethics clearance MRAC 16.21 and by the French Ethics Committees (Committees of Protection of Persons IE-2015\u2013837 (1)). Permission to conduct research in Papua New Guinea was granted by the National Research Institute of Papua New Guinea (permit 99902292358), with full support from the School of Humanities and Social Sciences, University of Papua New Guinea. Biological sampling was conducted by FXR, NB, and ML with the assistance of a team from the University of Papua New Guinea. All samples were collected with written informed consent.Archive samples used in this study were collected between 1986 and 1988 under supervision and with regulatory approval from the Institute of Medical Research of Papua New Guinea and approval by the Medical Research Advisory Committee of Papua New Guinea (National Department of Health). Following a brief description of the project, a discussion with each individual willing to participate ensured that the project was fully understood. The description stated clearly that the aims were to use the blood of individuals to investigate settlement history and migration patterns in Papua New Guinea. Once participants had given oral consent, information was collected on their age, sex, date and place of birth, and their spoken language(s). All samples were anonymised and coded at the time of sampling. The DNA samples have been stored with approval from the IMR for future research. Contemporary approvals for the present work have been obtained from the French Ethics Committees (Committees of Protection of Persons IE-2015\u2013837 (1)), and the Medical Research Advisory Committee of Papua New Guinea (National Department of Health) under research ethics clearance MRAC 16.21. (Revised paper: page 6, lines 136\u2013149).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}