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Souilmi Y, Wasef S, Williams MP, Conroy G, Bar I, Bover P, Dann J, Heiniger H, Llamas B, Ogbourne S, Archer M, Ballard JWO, Reed E, Tobler R, Koungoulos L, Walshe K, Wright JL, Balme J, O’Connor S, Cooper A, Mitchell KJ. Ancient genomes reveal over two thousand years of dingo population structure. Proc Natl Acad Sci U S A 2024; 121:e2407584121. [PMID: 38976766 PMCID: PMC11287250 DOI: 10.1073/pnas.2407584121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Sally Wasef
- Ancient DNA Facility, Defence Genomics, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, QLD4059, Australia
- Innovation Division, Forensic Science Queensland, Queensland Health, Coopers Plains, QLD4108, Australia
| | - Matthew P. Williams
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Department of Biology, The Pennsylvania State University, State College, PA16802
| | - Gabriel Conroy
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD4111, Australia
| | - Pere Bover
- Fundación Agencia Aragonesa para la Investigacióny el Desarrollo (ARAID), Zaragoza50018, Spain
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA)-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza50009, Spain
| | - Jackson Dann
- Grützner Laboratory of Comparative Genomics, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Holly Heiniger
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, ActonACT2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA5000, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Michael Archer
- Earth and Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales Sydney, SydneyNSW2052, Australia
| | - J. William O. Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC3052, Australia
| | - Elizabeth Reed
- Ecology and Evolutionary Biology, School of Biological Sciences, The University of Adelaide, AdelaideSA5005, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Acton, ACT2601, Australia
| | - Loukas Koungoulos
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW2010, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Keryn Walshe
- School of Anthropology and Archaeology, University of Auckland, Auckland1010, New Zealand
| | - Joanne L. Wright
- Queensland Department of Education, Kelvin Grove State College, Kelvin Grove, QLD4059, Australia
| | - Jane Balme
- School of Social Sciences, University of Western Australia, Crawley, WA6009, Australia
| | - Sue O’Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Alan Cooper
- Gulbali Institute, Charles Sturt University, Albury, NSW2640, Australia
| | - Kieren J. Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- Manaaki Whenua—Landcare Research, Lincoln, Canterbury7608, New Zealand
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Ávila-Arcos MC, Raghavan M, Schlebusch C. Going local with ancient DNA: A review of human histories from regional perspectives. Science 2023; 382:53-58. [PMID: 37797024 DOI: 10.1126/science.adh8140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
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