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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, Kinipi C, Ricaut FX, Cox MP, Gallego Romero I. Denisovan introgression has shaped the immune system of present-day Papuans. PLoS Genet 2022; 18:e1010470. [PMID: 36480515 PMCID: PMC9731433 DOI: 10.1371/journal.pgen.1010470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/10/2022] [Indexed: 12/13/2022] Open
Abstract
Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.
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Affiliation(s)
- Davide M. Vespasiani
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Guy S. Jacobs
- Department of Archaeology, University of Cambridge, Cambridge, Uniteed Kingdom
| | - Laura E. Cook
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Nicolas Brucato
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
- College of Arts, Society and Education, James Cook University, Cairns, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, Australia
| | - Christopher Kinipi
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - François-Xavier Ricaut
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Murray P. Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
- Center for Stem Cell Systems, University of Melbourne, Parkville, Australia
- Center for Genomics, Evolution and Medicine, University of Tartu, Tartu, Estonia
- * E-mail:
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Alva O, Leroy A, Heiske M, Pereda-Loth V, Tisseyre L, Boland A, Deleuze JF, Rocha J, Schlebusch C, Fortes-Lima C, Stoneking M, Radimilahy C, Rakotoarisoa JA, Letellier T, Pierron D. The loss of biodiversity in Madagascar is contemporaneous with major demographic events. Curr Biol 2022; 32:4997-5007.e5. [PMID: 36334586 DOI: 10.1016/j.cub.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large-bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.
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Affiliation(s)
- Omar Alva
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anaïs Leroy
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Margit Heiske
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Lenka Tisseyre
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jorge Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Villeurbanne, France
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | | | - Thierry Letellier
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Denis Pierron
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France.
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Samper-carro SC, O’connor S, Mahirta, Kealy S, Shipton C. Talking Dead. New burials from Tron Bon Lei (Alor Island, Indonesia) inform on the evolution of mortuary practices from the terminal Pleistocene to the Holocene in Southeast Asia. PLoS One 2022; 17:e0267635. [PMID: 36001542 PMCID: PMC9401180 DOI: 10.1371/journal.pone.0267635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/12/2022] [Indexed: 11/19/2022] Open
Abstract
Burial elaborations are a human behaviour that, in recent contexts can inform on social diversification, belief systems, and the introduction of new practices resulting from migration or cultural transmission. The study of mortuary practices in Mainland and Island Southeast Asia has revealed complex and diverse treatments of the deceased. This paper contributes to this topic with the description of three new burials excavated in Tron Bon Lei (Alor Island, Indonesia) dated to 7.5, 10, and 12 kya cal BP. In addition to the bioskeletal profiles and palaeohealth observations, we propose the adoption of archaeothanatological methods to characterise burial types in the region. Through the analysis of skeletal element representation, body position, articulation, and grave associations, we provide an example of a holistic approach to mortuary treatments in the Lesser Sunda Islands. Our results provide significant new data for understanding the evolution and diversification of burial practices in Southeast Asia, contributing to a growing body of literature describing prehistoric socio-cultural behaviour in this region.
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Aghakhanian F, Hoh BP, Yew CW, Kumar Subbiah V, Xue Y, Tyler-Smith C, Ayub Q, Phipps ME. Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers. Sci Rep 2022; 12:13743. [PMID: 35962005 PMCID: PMC9374673 DOI: 10.1038/s41598-022-17884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.
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Affiliation(s)
- Farhang Aghakhanian
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.,Department of Medicine, Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia.,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Chee-Wei Yew
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Qasim Ayub
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Maude E Phipps
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Oliveira S, Nägele K, Carlhoff S, Pugach I, Koesbardiati T, Hübner A, Meyer M, Oktaviana AA, Takenaka M, Katagiri C, Murti DB, Putri RS, Mahirta, Petchey F, Higham T, Higham CFW, O'Connor S, Hawkins S, Kinaston R, Bellwood P, Ono R, Powell A, Krause J, Posth C, Stoneking M. Ancient genomes from the last three millennia support multiple human dispersals into Wallacea. Nat Ecol Evol 2022. [PMID: 35681000 DOI: 10.1038/s41559-022-01775-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022]
Abstract
Previous research indicates that human genetic diversity in Wallacea-islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves-has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Hoh BP, Deng L, Xu S. The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years. Front Genet 2022; 13:767018. [PMID: 35154269 PMCID: PMC8829068 DOI: 10.3389/fgene.2022.767018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/07/2022] [Indexed: 12/05/2022] Open
Abstract
Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Markers; 3) Protein Markers; 4) Mitochondrial and Autosomal DNA Markers; and 5) Whole Genome Analysis. Subsequently some missing gaps of the study are identified. In the later part of this review, challenges of studying the population genetics of natives will be elaborated. Finally, we conclude our review by reiterating the importance of unveiling migration history and genetic diversity of the indigenous populations as a steppingstone towards comprehending disease evolution and etiology.
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Affiliation(s)
- Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, UCSI Hospital, Port Dickson, Malaysia
- *Correspondence: Boon-Peng Hoh,
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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10
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Natri HM, Hudjashov G, Jacobs G, Kusuma P, Saag L, Darusallam CC, Metspalu M, Sudoyo H, Cox MP, Gallego Romero I, Banovich NE. Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries. Am J Hum Genet 2022; 109:50-65. [PMID: 34919805 PMCID: PMC8764200 DOI: 10.1016/j.ajhg.2021.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023] Open
Abstract
Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations.
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Affiliation(s)
- Heini M Natri
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Georgi Hudjashov
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand; Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Guy Jacobs
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge CB2 1QH, UK; Complexity Institute, Nanyang Technological University, Singapore, 637460
| | - Pradiptajati Kusuma
- Complexity Institute, Nanyang Technological University, Singapore, 637460; Laboratory of Genome Diversity and Disease, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Chelzie Crenna Darusallam
- Laboratory of Genome Diversity and Disease, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Herawati Sudoyo
- Laboratory of Genome Diversity and Disease, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Irene Gallego Romero
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC 3010, Australia; School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; Centre for Stem Cell Systems, University of Melbourne, Parkville, VIC 3010, Australia
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Purnomo GA, Mitchell KJ, O'Connor S, Kealy S, Taufik L, Schiller S, Rohrlach A, Cooper A, Llamas B, Sudoyo H, Teixeira JC, Tobler R. Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact. Genes (Basel) 2021; 12:965. [PMID: 34202821 DOI: 10.3390/genes12070965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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13
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Babigumira BM, Sölkner J, Mészáros G, Pfeiffer C, Lewis CRG, Ouma E, Wurzinger M, Marshall K. A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda. Front Genet 2021; 12:676047. [PMID: 34249095 PMCID: PMC8261304 DOI: 10.3389/fgene.2021.676047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2-50% while "local" blood contributed 69.2% (36.9-95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.
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Affiliation(s)
- Brian Martin Babigumira
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
- International Livestock Research Institute, Kampala, Uganda
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Pfeiffer
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
- PIG Austria GmbH, Steinhaus, Wels, Austria
| | | | - Emily Ouma
- International Livestock Research Institute, Kampala, Uganda
| | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Karen Marshall
- International Livestock Research Institute, Nairobi, Kenya
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14
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Abstract
Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, PA.,Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
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15
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Larena M, Sanchez-Quinto F, Sjödin P, McKenna J, Ebeo C, Reyes R, Casel O, Huang JY, Hagada KP, Guilay D, Reyes J, Allian FP, Mori V, Azarcon LS, Manera A, Terando C, Jamero L Jr, Sireg G, Manginsay-Tremedal R, Labos MS, Vilar RD, Latiph A, Saway RL, Marte E, Magbanua P, Morales A, Java I, Reveche R, Barrios B, Burton E, Salon JC, Kels MJT, Albano A, Cruz-Angeles RB, Molanida E, Granehäll L, Vicente M, Edlund H, Loo JH, Trejaut J, Ho SYW, Reid L, Malmström H, Schlebusch C, Lambeck K, Endicott P, Jakobsson M. Multiple migrations to the Philippines during the last 50,000 years. Proc Natl Acad Sci U S A 2021; 118:e2026132118. [PMID: 33753512 DOI: 10.1073/pnas.2026132118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We analyzed the most comprehensive set of population-genomic data for the Philippines: 1,028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by at least five waves of human migration. The Cordillerans migrated into the Philippines prior to the arrival of rice agriculture, where some remain as the least admixed East Asians carrying an ancestry shared by all Austronesian-speaking populations, thereby challenging an exclusive out-of-Taiwan model of joint farming–language–people dispersal. Altogether, our findings portray the Philippines as a crucial gateway, with a multilayered history, that ultimately changed the genetic landscape of the Asia-Pacific region. Island Southeast Asia has recently produced several surprises regarding human history, but the region’s complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive “out-of-Taiwan” model of farming–language–people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.
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16
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Abstract
Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.
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Affiliation(s)
- Katharine L. Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
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17
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Abstract
Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.
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18
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Evans BJ, Gansauge M, Tocheri MW, Schillaci MA, Sutikna T, Jatmiko, Saptomo EW, Klegarth A, Tosi AJ, Melnick DJ, Meyer M. Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals. J Hum Evol 2020; 146:102852. [DOI: 10.1016/j.jhevol.2020.102852] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 11/17/2022]
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19
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Pankratov V, Montinaro F, Kushniarevich A, Hudjashov G, Jay F, Saag L, Flores R, Marnetto D, Seppel M, Kals M, Võsa U, Taccioli C, Möls M, Milani L, Aasa A, Lawson DJ, Esko T, Mägi R, Pagani L, Metspalu A, Metspalu M. Differences in local population history at the finest level: the case of the Estonian population. Eur J Hum Genet 2020; 28:1580-91. [PMID: 32712624 DOI: 10.1038/s41431-020-0699-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/24/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022] Open
Abstract
Several recent studies detected fine-scale genetic structure in human populations. Hence, groups conventionally treated as single populations harbour significant variation in terms of allele frequencies and patterns of haplotype sharing. It has been shown that these findings should be considered when performing studies of genetic associations and natural selection, especially when dealing with polygenic phenotypes. However, there is little understanding of the practical effects of such genetic structure on demography reconstructions and selection scans when focusing on recent population history. Here we tested the impact of population structure on such inferences using high-coverage (~30×) genome sequences of 2305 Estonians. We show that different regions of Estonia differ in both effective population size dynamics and signatures of natural selection. By analyzing identity-by-descent segments we also reveal that some Estonian regions exhibit evidence of a bottleneck 10-15 generations ago reflecting sequential episodes of wars, plague and famine, although this signal is virtually undetected when treating Estonia as a single population. Besides that, we provide a framework for relating effective population size estimated from genetic data to actual census size and validate it on the Estonian population. This approach may be widely used both to cross-check estimates based on historical sources as well as to get insight into times and/or regions with no other information available. Our results suggest that the history of human populations within the last few millennia can be highly region specific and cannot be properly studied without taking local genetic structure into account.
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20
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Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS. Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa. Cell 2020; 179:984-1002.e36. [PMID: 31675503 DOI: 10.1016/j.cell.2019.10.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/03/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.
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Affiliation(s)
- Deepti Gurdasani
- William Harvey Research Institute, Queen Mary's University of London, London, UK
| | | | - Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI)/National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | | | | | | | - Marc Haber
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ioanna Tachmazidou
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY, UK
| | - Iain Mathieson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth Ekoru
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Chris Finan
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Li Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Yuan Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Alex J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Georg Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Charles L Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Dermot Maher
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Stephen B Montgomery
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet Seeley
- London School of Hygiene and Tropical Medicine, London, UK; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Elizabeth H Young
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew P Morris
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Biostatistics, University of Liverpool, Liverpool, UK
| | | | | | - Ayesha A Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa.
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA.
| | - Pontiano Kaleebu
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda.
| | - Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Manj S Sandhu
- Department of Medicine, University of Cambridge, Cambridge, UK.
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21
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Natri HM, Bobowik KS, Kusuma P, Crenna Darusallam C, Jacobs GS, Hudjashov G, Lansing JS, Sudoyo H, Banovich NE, Cox MP, Gallego Romero I. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLoS Genet 2020; 16:e1008749. [PMID: 32453742 PMCID: PMC7274483 DOI: 10.1371/journal.pgen.1008749] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 06/05/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.
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Affiliation(s)
- Heini M. Natri
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Katalina S. Bobowik
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of BioSciences, University of Melbourne, Parkville, Australia
- Centre for Stem Cell Systems, University of Melbourne, Parkville, Australia
| | - Pradiptajati Kusuma
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Complexity Institute, Nanyang Technological University, Singapore, Singapore
| | - Chelzie Crenna Darusallam
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Guy S. Jacobs
- Complexity Institute, Nanyang Technological University, Singapore, Singapore
| | - Georgi Hudjashov
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - J. Stephen Lansing
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Vienna Complexity Science Hub, Vienna, Austria
- Stockholm Resilience Center, Kräftriket, Stockholm, Sweden
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Nicholas E. Banovich
- The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of BioSciences, University of Melbourne, Parkville, Australia
- Centre for Stem Cell Systems, University of Melbourne, Parkville, Australia
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22
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Sufriyana H, Wu YW, Su ECY. Artificial intelligence-assisted prediction of preeclampsia: Development and external validation of a nationwide health insurance dataset of the BPJS Kesehatan in Indonesia. EBioMedicine 2020; 54:102710. [PMID: 32283530 PMCID: PMC7152721 DOI: 10.1016/j.ebiom.2020.102710] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/24/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background We developed and validated an artificial intelligence (AI)-assisted prediction of preeclampsia applied to a nationwide health insurance dataset in Indonesia. Methods The BPJS Kesehatan dataset have been preprocessed using a nested case-control design into preeclampsia/eclampsia (n = 3318) and normotensive pregnant women (n = 19,883) from all women with one pregnancy. The dataset provided 95 features consisting of demographic variables and medical histories started from 24 months to event and ended by delivery as the event. Six algorithms were compared by area under the receiver operating characteristics curve (AUROC) with a subgroup analysis by time to the event. We compared our model to similar prediction models from systematically reviewed studies. In addition, we conducted a text mining analysis based on natural language processing techniques to interpret our modeling results. Findings The best model consisted of 17 predictors extracted by a random forest algorithm. Nine∼12 months to the event was the period that had the best AUROC in external validation by either geographical (0.88, 95% confidence interval (CI) 0.88–0.89) or temporal split (0.86, 95% CI 0.85–0.86). We compared this model to prediction models in seven studies from 869 records in PUBMED, EMBASE, and SCOPUS. This model outperformed the previous models in terms of the precision, sensitivity, and specificity in all validation sets. Interpretation Our low-cost model improved preliminary prediction to decide pregnant women that will be predicted by the models with high specificity and advanced predictors. Funding This work was supported by grant no. MOST108-2221-E-038-018 from the Ministry of Science and Technology of Taiwan.
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Affiliation(s)
- Herdiantri Sufriyana
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Department of Medical Physiology, College of Medicine, University of Nahdlatul Ulama Surabaya, Surabaya 60237, Indonesia.
| | - Yu-Wei Wu
- Department of Medical Physiology, College of Medicine, University of Nahdlatul Ulama Surabaya, Surabaya 60237, Indonesia; Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan.
| | - Emily Chia-Yu Su
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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23
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Khrunin AV, Khvorykh GV, Fedorov AN, Limborska SA. Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia. PLoS One 2020; 15:e0228778. [PMID: 32023328 PMCID: PMC7001972 DOI: 10.1371/journal.pone.0228778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populations have hardly been analyzed. We searched for the genomic signatures of positive selection in (1) the genome-wide microarray data of 432 people from eight different northern Russian populations and (2) the whole-genome sequences of 250 people from Northern Eurasia from a public repository through testing the extended haplotype homozigosity (EHH) and direct comparison of allele frequency, respectively. The 20 loci with the strongest selection signals were characterized in detail. Among the top EHH hits were the NRG3 and NBEA genes, which are involved in the development and functioning of the neural system, the PTPRM gene, which mediates cell-cell interactions and adhesion, and a region on chromosome 4 (chr4:28.7-28.9 Mb) that contained several loci affiliated with different classes of non-coding RNAs (RN7SL101P, MIR4275, MESTP3, and LINC02364). NBEA and the region on chromosome 4 were novel selection targets that were identified for the first time in Western Siberian populations. Cross-population comparisons of EHH profiles suggested a particular role for the chr4:28.7-28.9 Mb region in the local adaptation of Western Siberians. The strongest selection signal identified in Siberian sequenced genomes was formed by six SNPs on chromosome 11 (chr11:124.9-125.2 Mb). This region included well-known genes SLC37A2 and PKNOX2. SLC37A2 is most-highly expressed in the gut. Its expression is regulated by vitamin D, which is often deficient in northern regions. The PKNOX2 gene is a transcription factor of the homeobox family that is expressed in the brain and many other tissues. This gene is associated with alcohol addiction, which is widespread in many Northern Eurasian populations.
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Affiliation(s)
- Andrey V. Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Gennady V. Khvorykh
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Alexei N. Fedorov
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
- Department of Medicine, University of Toledo, Toledo, Ohio, United States of America
| | - Svetlana A. Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
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24
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Macholdt E, Arias L, Duong NT, Ton ND, Van Phong N, Schröder R, Pakendorf B, Van Hai N, Stoneking M. The paternal and maternal genetic history of Vietnamese populations. Eur J Hum Genet 2020; 28:636-45. [PMID: 31827276 DOI: 10.1038/s41431-019-0557-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/14/2019] [Accepted: 11/17/2019] [Indexed: 11/08/2022] Open
Abstract
Vietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.
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25
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Abstract
In Human, Major Histocompatibility Complex known as Human Leukocyte Antigen (HLA). The HLA grouped into three subclasses regions: the class I region, the class II region, and the class III region. There are thousands of polymorphic HLAs, many of them are proven to have correlations with diseases. Indonesia consists of diverse ethnicity people and populations. It carries a unique genetic diversity between one and another geographical positions. This paper aims to extract Indonesians HLA allele data, mapping the data, and correlating them with global diseases. From the study, it is found that global diseases, like Crohn's disease, rheumatoid arthritis, Graves' disease, gelatin allergy, T1D, HIV, systemic lupus erythematosus, juvenile chronic arthritis, and Mycobacterial disease (tuberculosis and leprosy) suspected associated with the Indonesian HLA profiles.
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Affiliation(s)
- Krisnawan Andy Pradana
- Faculty of Biotechnology, University of Surabaya, Surabaya City, Indonesia.,Department of Anatomy and Histology Faculty of Medicine, Airlangga University, Tambaksari, Surabaya City, Indonesia
| | | | - Mariana Wahjudi
- Faculty of Biotechnology, University of Surabaya, Surabaya City, Indonesia
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26
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Zammit NW, Siggs OM, Gray PE, Horikawa K, Langley DB, Walters SN, Daley SR, Loetsch C, Warren J, Yap JY, Cultrone D, Russell A, Malle EK, Villanueva JE, Cowley MJ, Gayevskiy V, Dinger ME, Brink R, Zahra D, Chaudhri G, Karupiah G, Whittle B, Roots C, Bertram E, Yamada M, Jeelall Y, Enders A, Clifton BE, Mabbitt PD, Jackson CJ, Watson SR, Jenne CN, Lanier LL, Wiltshire T, Spitzer MH, Nolan GP, Schmitz F, Aderem A, Porebski BT, Buckle AM, Abbott DW, Ziegler JB, Craig ME, Benitez-Aguirre P, Teo J, Tangye SG, King C, Wong M, Cox MP, Phung W, Tang J, Sandoval W, Wertz IE, Christ D, Goodnow CC, Grey ST. Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity. Nat Immunol 2019; 20:1299-310. [PMID: 31534238 DOI: 10.1038/s41590-019-0492-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/12/2019] [Indexed: 12/13/2022]
Abstract
Resisting and tolerating microbes are alternative strategies to survive infection, but little is known about the evolutionary mechanisms controlling this balance. Here genomic analyses of anatomically modern humans, extinct Denisovan hominins and mice revealed a TNFAIP3 allelic series with alterations in the encoded immune response inhibitor A20. Each TNFAIP3 allele encoded substitutions at non-catalytic residues of the ubiquitin protease OTU domain that diminished IκB kinase-dependent phosphorylation and activation of A20. Two TNFAIP3 alleles encoding A20 proteins with partial phosphorylation deficits seemed to be beneficial by increasing immunity without causing spontaneous inflammatory disease: A20 T108A;I207L, originating in Denisovans and introgressed in modern humans throughout Oceania, and A20 I325N, from an N-ethyl-N-nitrosourea (ENU)-mutagenized mouse strain. By contrast, a rare human TNFAIP3 allele encoding an A20 protein with 95% loss of phosphorylation, C243Y, caused spontaneous inflammatory disease in humans and mice. Analysis of the partial-phosphorylation A20 I325N allele in mice revealed diminished tolerance of bacterial lipopolysaccharide and poxvirus inoculation as tradeoffs for enhanced immunity.
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27
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Samper Carro SC, Gilbert F, Bulbeck D, O'Connor S, Louys J, Spooner N, Questiaux D, Arnold L, Price GJ, Wood R, Mahirta. Somewhere beyond the sea: Human cranial remains from the Lesser Sunda Islands (Alor Island, Indonesia) provide insights on Late Pleistocene peopling of Island Southeast Asia. J Hum Evol 2019; 134:102638. [PMID: 31446971 DOI: 10.1016/j.jhevol.2019.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 01/29/2023]
Abstract
The migration of anatomically modern humans (AMH) from Africa to every inhabitable continent included their dispersal through Island Southeast Asia (ISEA) to Australia. Significantly, this involved overwater dispersal through the Lesser Sunda Islands between Sunda (continental Southeast Asia) and Sahul (Australia and New Guinea). However, the timing and direction of this movement is still debated. Here, we report on human skeletal material recovered from excavations at two rockshelters, known locally as Tron Bon Lei, on Alor Island, Indonesia. The remains, dated to the Late Pleistocene, are the first anatomically modern human remains recovered in Wallacea dated to this period and are associated with cultural material demonstrating intentional burial. The human remains from Tron Bon Lei represent a population osteometrically distinct from Late Pleistocene Sunda and Sahul AMH. Instead, morphometrically, they appear more similar to Holocene populations in the Lesser Sundas. Thus, they may represent the remains of a population originally from Sunda whose Lesser Sunda Island descendants survived into the Holocene.
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Affiliation(s)
- Sofía C Samper Carro
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia; School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 2601, Australia; Centre d'Estudis del Patrimoni Arqueològic de la Prehistòria, Facultat de Lletres-Edifici B, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Felicity Gilbert
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 2601, Australia
| | - David Bulbeck
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia
| | - Sue O'Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage, Australian National University, Canberra, 2601, Australia
| | - Julien Louys
- Australian Research Centre of Human Evolution (ARCHE), Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - Nigel Spooner
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia; Defence Science and Technology Group, PO Box 1500, Edinburgh, SA, 5111, UK
| | - Danielle Questiaux
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia
| | - Lee Arnold
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia
| | - Gilbert J Price
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Rachel Wood
- Earth Chemistry, Research School of Earth Sciences, Australian National University, Canberra, 2601, Australia
| | - Mahirta
- Jurusan Arkeologi, Fakultas Ilmu Budaya, Universitas Gadja Madja, Bulaksumur, Yogjakarta, 55281, Indonesia
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28
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Chung NN, Jacobs GS, Sudoyo H, Malik SG, Chew LY, Lansing JS, Cox MP. Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales. R Soc Open Sci 2019; 6:190733. [PMID: 31598251 PMCID: PMC6731738 DOI: 10.1098/rsos.190733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
Population genetics has been successful at identifying the relationships between human groups and their interconnected histories. However, the link between genetic demography inferred at large scales and the individual human behaviours that ultimately generate that demography is not always clear. While anthropological and historical context are routinely presented as adjuncts in population genetic studies to help describe the past, determining how underlying patterns of human sociocultural behaviour impact genetics still remains challenging. Here, we analyse patterns of genetic variation in village-scale samples from two islands in eastern Indonesia, patrilocal Sumba and a matrilocal region of Timor. Adopting a 'process modelling' approach, we iteratively explore combinations of structurally different models as a thinking tool. We find interconnected socio-genetic interactions involving sex-biased migration, lineage-focused founder effects, and on Sumba, heritable social dominance. Strikingly, founder ideology, a cultural model derived from anthropological and archaeological studies at larger regional scales, has both its origins and impact at the scale of villages. Process modelling lets us explore these complex interactions, first by circumventing the complexity of formal inference when studying large datasets with many interacting parts, and then by explicitly testing complex anthropological hypotheses about sociocultural behaviour from a more familiar population genetic standpoint.
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Affiliation(s)
- Ning Ning Chung
- Complexity Institute, Nanyang Technological University, Singapore
- Centre for University Core, Singapore University of Social Sciences, Singapore
| | - Guy S. Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Safarina G. Malik
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Lock Yue Chew
- Complexity Institute, Nanyang Technological University, Singapore
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - J. Stephen Lansing
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Stockholm Resilience Center, Kräftriket, 10405 Stockholm, Sweden
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
- Te Pūnaha Matatini, Centre of Research Excellence for Complex Systems, Aukland, New Zealand
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29
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Abstract
The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.
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30
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He G, Ren Z, Guo J, Zhang F, Zou X, Zhang H, Wang Q, Ji J, Yang M, Zhang Z, Zhang J, Nabijiang Y, Huang J, Wang C. Population genetics, diversity and forensic characteristics of Tai–Kadai-speaking Bouyei revealed by insertion/deletions markers. Mol Genet Genomics 2019; 294:1343-57. [DOI: 10.1007/s00438-019-01584-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 05/30/2019] [Indexed: 12/13/2022]
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31
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Post H, Németh E, Klima L, Flores R, Fehér T, Türk A, Székely G, Sahakyan H, Mondal M, Montinaro F, Karmin M, Saag L, Yunusbayev B, Khusnutdinova EK, Metspalu E, Villems R, Tambets K, Rootsi S. Y-chromosomal connection between Hungarians and geographically distant populations of the Ural Mountain region and West Siberia. Sci Rep 2019; 9:7786. [PMID: 31127140 DOI: 10.1038/s41598-019-44272-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
Hungarians who live in Central Europe today are one of the westernmost Uralic speakers. Despite of the proposed Volga-Ural/West Siberian roots of the Hungarian language, the present-day Hungarian gene pool is highly similar to that of the surrounding Indo-European speaking populations. However, a limited portion of specific Y-chromosomal lineages from haplogroup N, sometimes associated with the spread of Uralic languages, link modern Hungarians with populations living close to the Ural Mountain range on the border of Europe and Asia. Here we investigate the paternal genetic connection between these spatially separated populations. We reconstruct the phylogeny of N3a4-Z1936 clade by using 33 high-coverage Y-chromosomal sequences and estimate the coalescent times of its sub-clades. We genotype close to 5000 samples from 46 Eurasian populations to show the presence of N3a4-B539 lineages among Hungarians and in the populations from Ural Mountain region, including Ob-Ugric-speakers from West Siberia who are geographically distant but linguistically closest to Hungarians. This sub-clade splits from its sister-branch N3a4-B535, frequent today among Northeast European Uralic speakers, 4000-5000 ya, which is in the time-frame of the proposed divergence of Ugric languages.
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Jacobs GS, Hudjashov G, Saag L, Kusuma P, Darusallam CC, Lawson DJ, Mondal M, Pagani L, Ricaut FX, Stoneking M, Metspalu M, Sudoyo H, Lansing JS, Cox MP. Multiple Deeply Divergent Denisovan Ancestries in Papuans. Cell 2019; 177:1010-1021.e32. [DOI: 10.1016/j.cell.2019.02.035] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
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Tan-Koi WC, Limenta M, Mohamed EHM, Lee EJD. The Importance of Ethnicity Definitions and Pharmacogenomics in Ethnobridging and Pharmacovigilance. Pharmacogenomics 2019. [DOI: 10.1016/b978-0-12-812626-4.00011-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 2018; 19:139. [PMID: 30241495 PMCID: PMC6151024 DOI: 10.1186/s13059-018-1522-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively. RESULTS Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours. CONCLUSIONS We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.
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Affiliation(s)
- Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Anne-Mai Ilumäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Terhi Honkola
- Department of Biology, University of Turku, 20014, Turku, Finland
- Institute of Estonian and General Linguistics, University of Tartu, 51014, Tartu, Estonia
| | - Outi Vesakoski
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Quentin Atkinson
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Sergey Litvinov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Timo Rantanen
- Department of Geography and Geology, University of Turku, 20014, Turku, Finland
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Sergey I Zhadanov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Radiology, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Marina Gubina
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Larisa D Damba
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Institute of Medical and Social Problems and Control of the Healthcare Department of Tuva Republic, Kyzyl, 667003, Russia
| | - Marina Bermisheva
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Khadizhat Dibirova
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia
- Anthony Nolan, London, NW3 2NU, UK
| | - Mari Nelis
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Andres Metspalu
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Tõnu Esko
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, 119991, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450054, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, 630090, Russia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Department of Archaeology, University of Cambridge, Cambridge, CB2 1QH, UK
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science 2018; 361:88-92. [DOI: 10.1126/science.aat3628] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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Affiliation(s)
- Hugh McColl
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fabrice Demeter
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France
| | - Takashi Gakuhari
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
- University of New England, Armidale, NSW, Australia
| | - Uffe Gram Wilken
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Sally Wasef
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Thongsa Sayavongkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Mohd Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Morten E. Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Farhang A. Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | | | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thi Mai Huong Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Hsiao-chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | - Thi Minh Tran
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Huu Nghia Truong
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Giang Hai Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Shaiful Shahidan
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hiromi Matsumae
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Anne-Marie Bacon
- Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France
| | - Philippe Duringer
- École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France
- Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
| | - Jean-Luc Ponche
- Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | - Anh Tuan Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Bérénice Bellina-Pryce
- CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France
| | - Jean-Christophe Galipaud
- Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France
| | - Rebecca Kinaston
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Charles Higham
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- St. Catharine’s College, University of Cambridge, Cambridge, UK
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
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Pugach I, Duggan AT, Merriwether DA, Friedlaender FR, Friedlaender JS, Stoneking M. The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data. Mol Biol Evol 2018; 35:871-886. [PMID: 29301001 PMCID: PMC5889034 DOI: 10.1093/molbev/msx333] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration circa 50,000 years ago (ya), and the more recent Austronesian expansion, which reached the Bismarck Archipelago by 3,450 ya. Whereas earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic, and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide data set of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal single nucleotide polymorphisms (SNPs). We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a "leapfrog" fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bidirectional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ana T Duggan
- Department of Anthropology, McMaster University, Hamilton, Canada
| | | | | | | | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Yew CW, Hoque MZ, Pugh-Kitingan J, Minsong A, Voo CLY, Ransangan J, Lau STY, Wang X, Saw WY, Ong RTH, Teo YY, Xu S, Hoh BP, Phipps ME, Kumar SV. Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data. Ann Hum Genet 2018. [PMID: 29521412 DOI: 10.1111/ahg.12246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).
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Affiliation(s)
- Chee Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Mohd Zahirul Hoque
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Alexander Minsong
- Faculty of Humanities, Arts & Heritage, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Julian Ransangan
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Sophia Tiek Ying Lau
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Xu Wang
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Woei Yuh Saw
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Rick Twee-Hee Ong
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik-Ying Teo
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology (PICB), Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTec University, Shanghai, China.,Collaborative Innovation Centre of Genetics and Development, Shanghai, China
| | - Boon-Peng Hoh
- Institute for Molecular Medical Biotechnology, Universiti Teknologi MARA, Selangor, Malaysia.,Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - S Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
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Hudjashov G, Endicott P, Post H, Nagle N, Ho SYW, Lawson DJ, Reidla M, Karmin M, Rootsi S, Metspalu E, Saag L, Villems R, Cox MP, Mitchell RJ, Garcia-Bertrand RL, Metspalu M, Herrera RJ. Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Sci Rep 2018; 8:1823. [PMID: 29379068 DOI: 10.1038/s41598-018-20026-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/11/2018] [Indexed: 12/14/2022] Open
Abstract
The debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that the inhabitants' genomes also demonstrate evidence of this episode of admixture, dating to 1,700-1,200 BP. This supports a late settlement chronology for eastern Polynesia, commencing ~1,000 BP, after the internal differentiation of Polynesian society. More than 70% of the autosomal ancestry of Leeward Society Islanders derives from Island Southeast Asia with the lowland populations of the Philippines as the single largest potential source. These long-distance migrants into Polynesia experienced additional admixture with northern Melanesians prior to the secondary migrations of the 2nd millennium BP. Moreover, the genetic diversity of mtDNA and Y chromosome lineages in the Leeward Society Islands is consistent with linguistic evidence for settlement of eastern Polynesia proceeding from the central northern Polynesian outliers in the Solomon Islands. These results stress the complex demographic history of the Leeward Society Islands and challenge phylogenetic models of cultural evolution predicated on eastern Polynesia being settled from Samoa.
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Lansing JS, Abundo C, Jacobs GS, Guillot EG, Thurner S, Downey SS, Chew LY, Bhattacharya T, Chung NN, Sudoyo H, Cox MP. Kinship structures create persistent channels for language transmission. Proc Natl Acad Sci U S A 2017; 114:12910-5. [PMID: 29158378 DOI: 10.1073/pnas.1706416114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Associations between genes and languages occur even with sustained migration among communities. By comparing phylogenies of genes and languages, we identify one source of this association. In traditional tribal societies, marriage customs channel language transmission. When women remain in their natal community and men disperse (matrilocality), children learn their mothers’ language, and language correlates with maternally inherited mitochondrial DNA. For the converse kinship practice (patrilocality), language instead correlates with paternally inherited Y chromosome. Kinship rules dictating postmarital residence can persist for many generations and determine population genetic structure at the community scale. The long-term association of languages with genetic clades created by kinship systems provides information about language transmission, and about the structure and persistence of social groups. Languages are transmitted through channels created by kinship systems. Given sufficient time, these kinship channels can change the genetic and linguistic structure of populations. In traditional societies of eastern Indonesia, finely resolved cophylogenies of languages and genes reveal persistent movements between stable speech communities facilitated by kinship rules. When multiple languages are present in a region and postmarital residence rules encourage sustained directional movement between speech communities, then languages should be channeled along uniparental lines. We find strong evidence for this pattern in 982 individuals from 25 villages on two adjacent islands, where different kinship rules have been followed. Core groups of close relatives have stayed together for generations, while remaining in contact with, and marrying into, surrounding groups. Over time, these kinship systems shaped their gene and language phylogenies: Consistently following a postmarital residence rule turned social communities into speech communities.
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