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Shipton C, Morley MW, Kealy S, Norman K, Boulanger C, Hawkins S, Litster M, Withnell C, O'Connor S. Abrupt onset of intensive human occupation 44,000 years ago on the threshold of Sahul. Nat Commun 2024; 15:4193. [PMID: 38778054 PMCID: PMC11111772 DOI: 10.1038/s41467-024-48395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Archaeological evidence attests multiple early dispersals of Homo sapiens out of Africa, but genetic evidence points to the primacy of a single dispersal 70-40 ka. Laili in Timor-Leste is on the southern dispersal route between Eurasia and Australasia and has the earliest record of human occupation in the eastern Wallacean archipelago. New evidence from the site shows that, unusually in the region, sediment accumulated in the shelter without human occupation, in the window 59-54 ka. This was followed by an abrupt onset of intensive human habitation beginning ~44 ka. The initial occupation is distinctive from overlying layers in the aquatic focus of faunal exploitation, while it has similarities in material culture to other early Homo sapiens sites in Wallacea. We suggest that the intensive early occupation at Laili represents a colonisation phase, which may have overwhelmed previous human dispersals in this part of the world.
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Affiliation(s)
- Ceri Shipton
- Institute of Archaeology, University College London, London, UK.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia.
- Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, ACT, Australia.
| | - Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, Australia.
| | - Shimona Kealy
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia.
- Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, ACT, Australia.
| | - Kasih Norman
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia
- Australian Research Centre for Human Evolution, Griffith University, Griffith, QLD, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Clara Boulanger
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia
- Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, ACT, Australia
- Japan Society for the Promotion of Science, Department of Modern Society and Civilization, National Museum of Ethnology, Osaka, 565-8511, Japan
- UMR 7194 Histoire Naturelle de l'Homme Préhistorique, Muséum National d'Histoire Naturelle, Paris, France
| | - Stuart Hawkins
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia
- Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, ACT, Australia
| | - Mirani Litster
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia
- Archaeology, College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, Australia
| | | | - Sue O'Connor
- ARC Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, ACT, Australia
- Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, ACT, Australia
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Salles T, Joannes-Boyau R, Moffat I, Husson L, Lorcery M. Physiography, foraging mobility, and the first peopling of Sahul. Nat Commun 2024; 15:3430. [PMID: 38653772 DOI: 10.1038/s41467-024-47662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
The route and speed of migration into Sahul by Homo sapiens remain a major research question in archaeology. Here, we introduce an approach which models the impact of the physical environment on human mobility by combining time-evolving landscapes with Lévy walk foraging patterns, this latter accounting for a combination of short-distance steps and occasional longer moves that hunter-gatherers likely utilised for efficient exploration of new environments. Our results suggest a wave of dispersal radiating across Sahul following riverine corridors and coastlines. Estimated migration speeds, based on archaeological sites and predicted travelled distances, fall within previously reported range from Sahul and other regions. From our mechanistic movement simulations, we then analyse the likelihood of archaeological sites and highlight areas in Australia that hold archaeological potential. Our approach complements existing methods and provides interesting perspectives on the Pleistocene archaeology of Sahul that could be applied to other regions around the world.
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Affiliation(s)
- Tristan Salles
- School of Geosciences, The University of Sydney, Sydney, NSW, Australia.
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group, Southern Cross University, Lismore, NSW, Australia
| | - Ian Moffat
- Geoarchaeology and Archaeometry Research Group, Southern Cross University, Lismore, NSW, Australia
- Archaeology, College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, Australia
| | - Laurent Husson
- ISTerre, CNRS, Université Grenoble-Alpes, Grenoble, France
| | - Manon Lorcery
- School of Geosciences, The University of Sydney, Sydney, NSW, Australia
- ISTerre, CNRS, Université Grenoble-Alpes, Grenoble, France
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3
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Hanson J, Radlof S, Littlejohn M, Hempenstall A, Edwards R, Nakata Y, Gregson S, Hayes R, Smith S, McKinnon M, Binks P, Tong SYC, Davies J, Davis JS. Hepatitis B genotypes in Aboriginal and Torres Strait Islander Australians: correlation with clinical course and implications for management. Intern Med J 2024; 54:647-656. [PMID: 37548345 DOI: 10.1111/imj.16181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND The prevalence of chronic hepatitis B (CHB) in Aboriginal and Torres Strait Islander Australians in Far North Queensland (FNQ) is greater than twice that of the general Australian population. CHB is common in Torres Strait Islanders diagnosed with hepatocellular carcinoma (HCC) - and in Aboriginals with HCC living in the Northern Territory - however, Aboriginals diagnosed with HCC in FNQ very rarely have CHB. The explanation for this apparent disparity is uncertain. AIMS To determine the HBV genotypes in the FNQ Aboriginal and Torres Strait Islander population and their correlation with clinical phenotype. METHODS We determined the HBV genotype of Aboriginal and Torres Strait Islander Australians living with CHB in FNQ and correlated this with demographic and clinical findings. RESULTS 134/197 (68%) enrolled individuals had a sufficient viral load for genotyping. All 40 people with HBV/D genotype had Aboriginal heritage, whereas 85/93 (91%) with HBV/C had Torres Strait Islander heritage (P < 0.0001). Individuals with HBV/D were younger than those with HBV/C (median (interquartile range) age: 43 (39-48) vs 53 (42-66) years, P = 0.0002). However, they were less likely to be HBeAg positive (1/40 (3%) vs 23/93 (25%), P = 0.001). All three HCCs developed in Torres Strait Islanders; two-thirds were infected with HBV/C14; genotyping was not possible in the other individual. All 10 diagnoses of cirrhosis occurred in Torres Strait Islanders, 6/10 were infected with HBV/C14, genotyping was not possible in the other four individuals. CONCLUSIONS HBV genotypes in Aboriginal and Torres Strait Islander Australians in FNQ differ markedly, which could explain the significant differences in the clinical phenotype in the two populations and might be used to inform cost-effective CHB care in the region.
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Affiliation(s)
- Josh Hanson
- Cairns and Hinterland Hospital and Health Service, Cairns, Queensland, Australia
- The Kirby Institute, UNSW, Sydney, New South Wales, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sharna Radlof
- Cairns and Hinterland Hospital and Health Service, Cairns, Queensland, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Ros Edwards
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia
| | - Yoko Nakata
- Torres and Cape Health and Hospital Service, Cairns, Queensland, Australia
| | - Sandra Gregson
- Torres and Cape Health and Hospital Service, Cairns, Queensland, Australia
| | - Richard Hayes
- Torres and Cape Health and Hospital Service, Cairns, Queensland, Australia
| | - Simon Smith
- Cairns and Hinterland Hospital and Health Service, Cairns, Queensland, Australia
| | - Melita McKinnon
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Paula Binks
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Steven Y C Tong
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jane Davies
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Joshua S Davis
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
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Silcocks M, Farlow A, Hermes A, Tsambos G, Patel HR, Huebner S, Baynam G, Jenkins MR, Vukcevic D, Easteal S, Leslie S. Indigenous Australian genomes show deep structure and rich novel variation. Nature 2023; 624:593-601. [PMID: 38093005 PMCID: PMC10733150 DOI: 10.1038/s41586-023-06831-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama-Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000-35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.
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Affiliation(s)
- Matthew Silcocks
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Melbourne, School of Biosciences, Parkville, Victoria, Australia
| | - Ashley Farlow
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georgia Tsambos
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sharon Huebner
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gareth Baynam
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital and Rare Care Centre, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Misty R Jenkins
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
| | - Damjan Vukcevic
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stephen Leslie
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
- University of Melbourne, School of Biosciences, Parkville, Victoria, Australia.
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia.
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Woravatin W, Stoneking M, Srikummool M, Kampuansai J, Arias L, Kutanan W. South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture. PLoS One 2023; 18:e0291547. [PMID: 37708147 PMCID: PMC10501589 DOI: 10.1371/journal.pone.0291547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35-45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.
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Affiliation(s)
- Wipada Woravatin
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Biométrie et Biologie Évolutive, UMR 5558, CNRS & Université de Lyon, Lyon, France
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Centre for Linguistics, Faculty of Humanities, Leiden University, Leiden, The Netherlands
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
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Tran HL, Mai HP, Le Thi D, Thi ND, Le Tung L, Thanh TP, Manh HT, Mau HN, Chu HH, Hoang H. The first maternal genetic study of hunter-gatherers from Vietnam. Mol Genet Genomics 2023:10.1007/s00438-023-02050-0. [PMID: 37438447 DOI: 10.1007/s00438-023-02050-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.
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Affiliation(s)
- Huyen Linh Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Pham Mai
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Dung Le Thi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nhung Doan Thi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Lam Le Tung
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Tung Pham Thanh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Ha Tran Manh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Hung Nguyen Mau
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam.
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Martin G, Cottin A, Baurens FC, Labadie K, Hervouet C, Salmon F, Paulo-de-la-Reberdiere N, Van den Houwe I, Sardos J, Aury JM, D'Hont A, Yahiaoui N. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:802-818. [PMID: 36575919 DOI: 10.1111/tpj.16086] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
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Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélien Cottin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Salmon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
| | - Nilda Paulo-de-la-Reberdiere
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, CRB-PT, F-97170 Roujol Petit-Bourg, Guadeloupe, France
| | - Ines Van den Houwe
- Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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8
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Taufik L, Teixeira JC, Llamas B, Sudoyo H, Tobler R, Purnomo GA. Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. Genes (Basel) 2022; 13:genes13122373. [PMID: 36553640 PMCID: PMC9778601 DOI: 10.3390/genes13122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
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Affiliation(s)
- Leonard Taufik
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
- Correspondence: (L.T.); (G.A.P.)
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
- Centre for Interdisciplinary Studies, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia
| | - Herawati Sudoyo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
| | - Gludhug A. Purnomo
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (L.T.); (G.A.P.)
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9
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Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, Ricaut FX. Chronology of natural selection in Oceanian genomes. iScience 2022; 25:104583. [PMID: 35880026 PMCID: PMC9308150 DOI: 10.1016/j.isci.2022.104583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul. 239 human genomes from both sides of the Wallacean ecogeographical barriers Signals of selection are dated between -54,000 to -52,000 in modern Oceanian genomes Genes related to immunity and diet were under strong selection Denisovan introgressions participated to the genetic adaptations present in Oceanians
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
| | - Mathilde André
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France.,Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Georgi Hudjashov
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, National Capital District 134, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, QLD 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
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10
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Karmin M, Flores RJ, Saag L, Hudjashov G, Brucato N, Crenna-Darusallam C, Larena M, Endicott PL, Jakobsson M, Lansing JS, Sudoyo H, Leavesley M, Metspalu M, Ricaut FX, Cox MP. Episodes of diversification and isolation in Island Southeast Asian and Near Oceanian male lineages. Mol Biol Evol 2022; 39:6539761. [PMID: 35294555 PMCID: PMC8926390 DOI: 10.1093/molbev/msac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40–25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.
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Affiliation(s)
- Monika Karmin
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Rodrigo J Flores
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
- Institute of Computer Science,University of Tartu, Tartu, 51009, Estonia
| | - Lauri Saag
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Georgi Hudjashov
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Nicolas Brucato
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées,CNRS, IRD, UPS, Toulouse
| | - Chelzie Crenna-Darusallam
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
| | - Maximilian Larena
- Department of Organismal Biology, University of Uppsala, Uppsala, 75236, Sweden
| | - Phillip L Endicott
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
- Department Hommes Natures Societies, Musée de l’Homme, Paris, Ile de France, 75016, France
| | - Mattias Jakobsson
- Department of Organismal Biology, University of Uppsala, Uppsala, 75236, Sweden
| | | | - Herawati Sudoyo
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Mait Metspalu
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - François-Xavier Ricaut
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées,CNRS, IRD, UPS, Toulouse
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
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11
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Bouckaert RR. An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference. Syst Biol 2022; 71:1549-1560. [PMID: 35212733 PMCID: PMC9773037 DOI: 10.1093/sysbio/syac015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/24/2022] [Accepted: 02/22/2022] [Indexed: 12/25/2022] Open
Abstract
We present a two-headed approach called Bayesian Integrated Coalescent Epoch PlotS (BICEPS) for efficient inference of coalescent epoch models. Firstly, we integrate out population size parameters, and secondly, we introduce a set of more powerful Markov chain Monte Carlo (MCMC) proposals for flexing and stretching trees. Even though population sizes are integrated out and not explicitly sampled through MCMC, we are still able to generate samples from the population size posteriors. This allows demographic reconstruction through time and estimating the timing and magnitude of population bottlenecks and full population histories. Altogether, BICEPS can be considered a more muscular version of the popular Bayesian skyline model. We demonstrate its power and correctness by a well-calibrated simulation study. Furthermore, we demonstrate with an application to SARS-CoV-2 genomic data that some analyses that have trouble converging with the traditional Bayesian skyline prior and standard MCMC proposals can do well with the BICEPS approach. BICEPS is available as open-source package for BEAST 2 under GPL license and has a user-friendly graphical user interface.[Bayesian phylogenetics; BEAST 2; BICEPS; coalescent model.].
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Affiliation(s)
- Remco R Bouckaert
- Correspondence to be sent to: University of Auckland, Thomas
Building, Room 407 3 Symonds St Auckland 1010 New Zealand E-mail:
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12
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Kun Á. Is there still evolution in the human population? Biol Futur 2022; 73:359-374. [PMID: 36592324 PMCID: PMC9806833 DOI: 10.1007/s42977-022-00146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/08/2022] [Indexed: 01/03/2023]
Abstract
It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics knowledge, that we expect humanity to evolve. The results from genome sequencing projects have repeatedly affirmed that there are still recent signs of selection in our genomes. I give some examples of such adaptation. Then I briefly discuss what our evolutionary future has in store for us.
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Affiliation(s)
- Ádám Kun
- grid.5591.80000 0001 2294 6276Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary ,Parmenides Center for the Conceptual Foundations of Science, Pöcking, Germany ,grid.481817.3Institute of Evolution, Centre for Ecological Research, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
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13
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Late Pleistocene/Early Holocene sites in the montane forests of New Guinea yield early record of cassowary hunting and egg harvesting. Proc Natl Acad Sci U S A 2021; 118:2100117118. [PMID: 34580213 DOI: 10.1073/pnas.2100117118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 11/18/2022] Open
Abstract
How early human foragers impacted insular forests is a topic with implications across multiple disciplines, including resource management. Paradoxically, terminal Pleistocene and Early Holocene impacts of foraging communities have been characterized as both extreme-as in debates over human-driven faunal extinctions-and minimal compared to later landscape transformations by farmers and herders. We investigated how rainforest hunter-gatherers managed resources in montane New Guinea and present some of the earliest documentation of Late Pleistocene through mid-Holocene exploitation of cassowaries (Aves: Casuariidae). Worldwide, most insular ratites were extirpated by the Late Holocene, following human arrivals, including elephant birds of Madagascar (Aepyornithidae) and moa of Aotearoa/New Zealand (Dinornithiformes)-icons of anthropogenic island devastation. Cassowaries are exceptional, however, with populations persisting in New Guinea and Australia. Little is known of past human exploitation and what factors contributed to their survival. We present a method for inferring past human interaction with mega-avifauna via analysis of microstructural features of archaeological eggshell. We then contextualize cassowary hunting and egg harvesting by montane foragers and discuss the implications of human exploitation. Our data suggest cassowary egg harvesting may have been more common than the harvesting of adults. Furthermore, our analysis of cassowary eggshell microstructural variation reveals a distinct pattern of harvesting eggs in late ontogenetic stages. Harvesting eggs in later stages of embryonic growth may reflect human dietary preferences and foraging seasonality, but the observed pattern also supports the possibility that-as early as the Late Pleistocene-people were collecting eggs in order to hatch and rear cassowary chicks.
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14
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Crabtree SA, White DA, Bradshaw CJA, Saltré F, Williams AN, Beaman RJ, Bird MI, Ulm S. Landscape rules predict optimal superhighways for the first peopling of Sahul. Nat Hum Behav 2021; 5:1303-1313. [PMID: 33927367 DOI: 10.1038/s41562-021-01106-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
Archaeological data and demographic modelling suggest that the peopling of Sahul required substantial populations, occurred rapidly within a few thousand years and encompassed environments ranging from hyper-arid deserts to temperate uplands and tropical rainforests. How this migration occurred and how humans responded to the physical environments they encountered have, however, remained largely speculative. By constructing a high-resolution digital elevation model for Sahul and coupling it with fine-scale viewshed analysis of landscape prominence, least-cost pedestrian travel modelling and high-performance computing, we create over 125 billion potential migratory pathways, whereby the most parsimonious routes traversed emerge. Our analysis revealed several major pathways-superhighways-transecting the continent, that we evaluated using archaeological data. These results suggest that the earliest Australian ancestors adopted a set of fundamental rules shaped by physiological capacity, attraction to visually prominent landscape features and freshwater distribution to maximize survival, even without previous experience of the landscapes they encountered.
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Affiliation(s)
- Stefani A Crabtree
- Department of Environment and Society, Utah State University, Logan, UT, USA. .,The Santa Fe Institute, Santa Fe, NM, USA. .,ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook University, Cairns, Queensland, Australia. .,Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France.
| | - Devin A White
- Autonomous Sensing and Perception, Sandia National Laboratories, Albuquerque, NM, USA.,Department of Anthropology, University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Corey J A Bradshaw
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Flinders University, Adelaide, South Australia, Australia.,Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Frédérik Saltré
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Flinders University, Adelaide, South Australia, Australia.,Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Alan N Williams
- Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, Australia.,EMM Consulting Pty Ltd, St Leonards, New South Wales, Australia
| | - Robin J Beaman
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Michael I Bird
- ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook University, Cairns, Queensland, Australia.,College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Sean Ulm
- ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook University, Cairns, Queensland, Australia.,College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
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15
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Brucato N, André M, Tsang R, Saag L, Kariwiga J, Sesuki K, Beni T, Pomat W, Muke J, Meyer V, Boland A, Deleuze JF, Sudoyo H, Mondal M, Pagani L, Romero IG, Metspalu M, Cox MP, Leavesley M, Ricaut FX. Papua New Guinean genomes reveal the complex settlement of north Sahul. Mol Biol Evol 2021; 38:5107-5121. [PMID: 34383935 PMCID: PMC8557464 DOI: 10.1093/molbev/msab238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our dataset, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Mathilde André
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France.,Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Roxanne Tsang
- School of Humanities, Languages and Social Science and Place, Evolution and Rock Art Heritage Unit, Griffith University Centre for Social and Cultural Research, Griffith University, Australia.,Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,School of Social Science, University of Queensland, Australia, St Lucia, QLD 4072, Australia
| | - Kylie Sesuki
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Teppsy Beni
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - John Muke
- Social Research Institute, Papua New Guinea
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia.,Department of Biology, University of Padua, Italy
| | | | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, Queensland, 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New south Wales, 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
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16
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André M, Brucato N, Plutniak S, Kariwiga J, Muke J, Morez A, Leavesley M, Mondal M, Ricaut FX. Phenotypic differences between highlanders and lowlanders in Papua New Guinea. PLoS One 2021; 16:e0253921. [PMID: 34288918 PMCID: PMC8294550 DOI: 10.1371/journal.pone.0253921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Altitude is one of the most demanding environmental pressures for human populations. Highlanders from Asia, America and Africa have been shown to exhibit different biological adaptations, but Oceanian populations remain understudied [Woolcock et al., 1972; Cotes et al., 1974; Senn et al., 2010]. We tested the hypothesis that highlanders phenotypically differ from lowlanders in Papua New Guinea, as a result of inhabiting the highest mountains in Oceania for at least 20,000 years. MATERIALS AND METHODS We collected data for 13 different phenotypes related to altitude for 162 Papua New Guineans living at high altitude (Mont Wilhelm, 2,300-2,700 m above sea level (a.s.l.) and low altitude (Daru, <100m a.s.l.). Multilinear regressions were performed to detect differences between highlanders and lowlanders for phenotypic measurements related to body proportions, pulmonary function, and the circulatory system. RESULTS Six phenotypes were significantly different between Papua New Guinean highlanders and lowlanders. Highlanders show shorter height (p-value = 0.001), smaller waist circumference (p-value = 0.002), larger Forced Vital Capacity (FVC) (p-value = 0.008), larger maximal (p-value = 3.20e -4) and minimal chest depth (p-value = 2.37e -5) and higher haemoglobin concentration (p-value = 3.36e -4). DISCUSSION Our study reports specific phenotypes in Papua New Guinean highlanders potentially related to altitude adaptation. Similar to other human groups adapted to high altitude, the evolutionary history of Papua New Guineans appears to have also followed an adaptive biological strategy for altitude.
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Affiliation(s)
- Mathilde André
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Tartumaa, Estonia
| | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Sébastien Plutniak
- Laboratoire Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés (TRACES, UMR 5608), Université Toulouse Jean Jaurès, Maison de la Recherche, Toulouse, France
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities & Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- School of Social Science, University of Queensland, Australia, St Lucia, Australia
| | - John Muke
- Social Research Institute Ltd, Port Moresby, Papua New Guinea
| | - Adeline Morez
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities & Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, Australia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Tartumaa, Estonia
| | - François-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
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17
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Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact. Genes (Basel) 2021; 12:genes12070965. [PMID: 34202821 PMCID: PMC8306604 DOI: 10.3390/genes12070965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/17/2022] Open
Abstract
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 in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.
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18
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Bradshaw CJA, Norman K, Ulm S, Williams AN, Clarkson C, Chadœuf J, Lin SC, Jacobs Z, Roberts RG, Bird MI, Weyrich LS, Haberle SG, O'Connor S, Llamas B, Cohen TJ, Friedrich T, Veth P, Leavesley M, Saltré F. Stochastic models support rapid peopling of Late Pleistocene Sahul. Nat Commun 2021; 12:2440. [PMID: 33927195 PMCID: PMC8085232 DOI: 10.1038/s41467-021-21551-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 02/02/2021] [Indexed: 02/02/2023] Open
Abstract
The peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model's emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156-208 human generations (4368-5599 years) and at a plausible rate of 0.71-0.92 km year-1. More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000-90,000 years ago, and the peopling of Eurasia in as little as 12,000-15,000 years via inland routes.
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Affiliation(s)
- Corey J A Bradshaw
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia.
| | - Kasih Norman
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Sean Ulm
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- College of Arts, Society and Education, James Cook University, Cairns, QLD, Australia
| | - Alan N Williams
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- EMM Consulting, St Leonards, NSW, Australia
| | - Chris Clarkson
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Max Planck Institute for the Science of Human History, Jena, Germany
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Joël Chadœuf
- UR 1052, French National Institute for Agricultural Research (INRA), Montfavet, France
| | - Sam C Lin
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Zenobia Jacobs
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Richard G Roberts
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Michael I Bird
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Laura S Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Simon G Haberle
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Department of Archaeology and Natural History, School of Culture, History and Language, Australian National University, Canberra, ACT, Australia
| | - Sue O'Connor
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Department of Archaeology and Natural History, School of Culture, History and Language, Australian National University, Canberra, ACT, Australia
| | - Bastien Llamas
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
| | - Tim J Cohen
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Tobias Friedrich
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, Hawai'i, USA
| | - Peter Veth
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Archaeology and the Centre for Rock Art Research and Management M257, School of Social Sciences, University of Western Australia, Crawley, WA, Australia
| | - Matthew Leavesley
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- College of Arts, Society and Education, James Cook University, Cairns, QLD, Australia
- Department of Anthropology and Sociology, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Frédérik Saltré
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
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