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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 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, SA 5005, Australia
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Sally Wasef
- Ancient DNA Facility, Defence Genomics, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
- Innovation Division, Forensic Science Queensland, Queensland Health, Coopers Plains, QLD 4108, Australia
| | - Matthew P Williams
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Department of Biology, The Pennsylvania State University, State College, PA 16802
| | - Gabriel Conroy
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Pere Bover
- Fundación Agencia Aragonesa para la Investigacióny el Desarrollo (ARAID), Zaragoza 50018, Spain
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA)-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Jackson Dann
- Grützner Laboratory of Comparative Genomics, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Holly Heiniger
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), Adelaide SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), Adelaide SA 5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Acton ACT 2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA 5000, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Michael Archer
- Earth and Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales Sydney, Sydney NSW 2052, Australia
| | - J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC 3052, Australia
| | - Elizabeth Reed
- Ecology and Evolutionary Biology, School of Biological Sciences, The University of Adelaide, Adelaide SA 5005, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Acton, ACT 2601, Australia
| | - Loukas Koungoulos
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT 2601, Australia
| | - Keryn Walshe
- School of Anthropology and Archaeology, University of Auckland, Auckland 1010, New Zealand
| | - Joanne L Wright
- Queensland Department of Education, Kelvin Grove State College, Kelvin Grove, QLD 4059, Australia
| | - Jane Balme
- School of Social Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Sue O'Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT 2601, Australia
| | - Alan Cooper
- Gulbali Institute, Charles Sturt University, Albury, NSW 2640, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), Adelaide SA 5005, Australia
- Manaaki Whenua-Landcare Research, Lincoln, Canterbury 7608, New Zealand
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2
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Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population. Genome Biol Evol 2024; 16:evae130. [PMID: 38913571 PMCID: PMC11221432 DOI: 10.1093/gbe/evae130] [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: 10/12/2023] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
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Affiliation(s)
- Ana V Leon-Apodaca
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | - Andres del Castillo
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabriel C Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
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3
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Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic consequences of isolation and inbreeding in an island dingo population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557950. [PMID: 37745583 PMCID: PMC10516007 DOI: 10.1101/2023.09.15.557950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
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Affiliation(s)
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | | | - Gabriel C. Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, PA, USA
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4
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Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 2023; 12:giad018. [PMID: 36994871 PMCID: PMC10353722 DOI: 10.1093/gigascience/giad018] [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: 09/26/2022] [Revised: 01/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. FINDINGS We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog. CONCLUSIONS These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg 06484, Germany
| | - Ksenia Skvortsova
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ozren Bogdanovic
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital,Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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5
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Donfrancesco V, Allen BL, Appleby R, Behrendorff L, Conroy G, Crowther MS, Dickman CR, Doherty T, Fancourt BA, Gordon CE, Jackson SM, Johnson CN, Kennedy MS, Koungoulos L, Letnic M, Leung LK, Mitchell KJ, Nesbitt B, Newsome T, Pacioni C, Phillip J, Purcell BV, Ritchie EG, Smith BP, Stephens D, Tatler J, van Eeden LM, Cairns KM. Understanding conflict among experts working on controversial species: A case study on the Australian dingo. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Benjamin L. Allen
- University of Southern Queensland Institute for Life Sciences and the Environment Toowoomba Queensland Australia
- Centre for African Conservation Ecology Nelson Mandela University Port Elizabeth South Africa
| | - Rob Appleby
- Centre for Planetary Health and Food Security Griffith University Nathan Queensland Australia
| | - Linda Behrendorff
- School of Agriculture and Food Sciences University of Queensland Gatton Queensland Australia
| | - Gabriel Conroy
- Genecology Research Centre, School of Science, Technology and Engineering University of the Sunshine Coast Maroochydore DC Queensland Australia
| | - Mathew S. Crowther
- School of Life and Environmental Sciences University of Sydney New South Wales Australia
| | - Christopher R. Dickman
- Desert Ecology Research Group, School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Tim Doherty
- Desert Ecology Research Group, School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Bronwyn A. Fancourt
- Ecosystem Management, School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Christopher E. Gordon
- Center for Biodiversity Dynamics in a Changing World Aarhus University Aarhus C Denmark
| | - Stephen M. Jackson
- Collection Care and Conservation Australian Museum Research Institute Sydney New South Wales Australia
| | - Chris N. Johnson
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage University of Tasmania Hobart Tasmania Australia
| | - Malcolm S. Kennedy
- Threatened Species Operations Department of Environment and Science Brisbane Queensland Australia
| | - Loukas Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry The University of Sydney Sydney New South Wales Australia
| | - Mike Letnic
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | - Luke K.‐P. Leung
- School of Agriculture and Food Sciences University of Queensland Gatton Queensland Australia
| | - Kieren J. Mitchell
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Bradley Nesbitt
- School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Thomas Newsome
- Global Ecology Lab, School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Carlo Pacioni
- Department of Environment, Land, Water and Planning Arthur Rylah Institute Heidelberg Victoria Australia
- Environmental and Conservation Sciences Murdoch University Murdoch Western Australia Australia
| | | | - Brad V. Purcell
- Kangaroo Management Program Office of Environment and Heritage Dubbo New South Wales Australia
| | - Euan G. Ritchie
- School of Life and Environmental Sciences and Centre for Integrative Ecology Deakin University Burwood Victoria Australia
| | - Bradley P. Smith
- College of Psychology, School of Health, Medical and Applied Sciences CQUniversity Australia Wayville South Australia Australia
| | | | - Jack Tatler
- Narla Environmental Pty Ltd Warriewood New South Wales Australia
| | - Lily M. van Eeden
- Department of Environment, Land, Water and Planning Arthur Rylah Institute Heidelberg Victoria Australia
| | - Kylie M. Cairns
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
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6
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Genetic distance from wolves affects family dogs' reactions towards howls. Commun Biol 2023; 6:129. [PMID: 36747107 PMCID: PMC9902479 DOI: 10.1038/s42003-023-04450-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023] Open
Abstract
Domestication dramatically changes behaviour, including communication, as seen in the case of dogs (Canis familiaris) and wolves (Canis lupus). We tested the hypothesis that domestication may affect an ancient, shared communication form of canids, the howling which seems to have higher individual variation in dogs: the perception and usage of howls may be affected by the genetic relatedness of the breeds to their last common ancestor with wolves ('root distance') and by other individual features like age, sex, and reproductive status. We exposed 68 purebred dogs to wolf howl playbacks and recorded their responses. We identified an interaction between root distance and age on the dogs' vocal and behavioural responses: older dogs from more ancient breeds responded longer with howls and showed more stress behaviours. Our results suggest that domestication impacts vocal behaviour significantly: disintegrating howling, a central, species-specific communication form of canids and gradually eradicating it from dogs' repertoire.
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7
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Ballard JWO, Field MA, Edwards RJ, Wilson LA, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525801. [PMID: 36747621 PMCID: PMC9900879 DOI: 10.1101/2023.01.26.525801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Background One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog. Conclusions These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J. William O. Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia,Department of Environment and Genetics, SABE, La Trobe University, Melbourne Victoria 3086, Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia,Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Laura A.B. Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G. Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, Australia 2006
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA,Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27 06484 Quedlinburg, Germany
| | | | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia,Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia,Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA,Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA,UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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8
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Thompson ER, Driscoll DA, Venn SE, Geary WL, Ritchie EG. Interspecific variation in the diet of a native apex predator and invasive mesopredator in an alpine ecosystem. AUSTRAL ECOL 2022. [DOI: 10.1111/aec.13214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eilysh R. Thompson
- School of Life and Environmental Sciences, Centre for Integrative Ecology Deakin University Burwood Victoria 3125 Australia
| | - Don A. Driscoll
- School of Life and Environmental Sciences, Centre for Integrative Ecology Deakin University Burwood Victoria 3125 Australia
| | - Susanna E. Venn
- School of Life and Environmental Sciences, Centre for Integrative Ecology Deakin University Burwood Victoria 3125 Australia
| | - William L. Geary
- School of Life and Environmental Sciences, Centre for Integrative Ecology Deakin University Burwood Victoria 3125 Australia
| | - Euan G. Ritchie
- School of Life and Environmental Sciences, Centre for Integrative Ecology Deakin University Burwood Victoria 3125 Australia
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9
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Cairns KM, Crowther MS, Nesbitt B, Letnic M. The myth of wild dogs in Australia: are there any out there? AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hybridisation between wild and domestic canids is a global conservation and management issue. In Australia, dingoes are a distinct lineage of wild-living canid with a controversial domestication status. They are mainland Australia’s apex terrestrial predator. There is ongoing concern that the identity of dingoes has been threatened from breeding with domestic dogs, and that feral dogs have established populations in rural Australia. We collate the results of microsatellite DNA testing from 5039 wild canids to explore patterns of domestic dog ancestry in dingoes and observations of feral domestic dogs across the continent. Only 31 feral dogs were detected, challenging the perception that feral dogs are widespread in Australia. First generation dingo × dog hybrids were similarly rare, with only 27 individuals identified. Spatial patterns of genetic ancestry across Australia identified that dingo populations in northern, western and central Australia were largely free from domestic dog introgression. Our findings challenge the perception that dingoes are virtually extinct in the wild and that feral dogs are common. A shift in terminology from wild dog to dingo would better reflect the identity of these wild canids and allow more nuanced debate about the balance between conservation and management of dingoes in Australia.
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10
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The Dingo Barrier Fence: Presenting the case to decommission the world's longest environmental barrier in the United Nations Decade on Ecosystem Restoration 2021-2030. Biol Futur 2021; 73:9-27. [PMID: 34807433 DOI: 10.1007/s42977-021-00106-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
The longest environmental barrier in the world is Australia's 5614 km Dingo Barrier Fence. The structure was completed in the 1950s, designed to facilitate the eradication of the country's apex predator and cultural keystone species the dingo (Canis dingo) from sheep (Ovis aries) grazing areas to the south-east of the continent. The fence and its support systems now present an immense obstacle to ecological restoration in Australia's arid zone, preventing traditional management practices, and are hazardous to all terrestrial wildlife in the immediate vicinity. The barrier presents a worst-case scenario for animal-generated seed dispersal patterns over the wider region and limits genetic transfer. Plummeting biodiversity inside the fence line and increasing pressures of climate change have left this region highly vulnerable to ecological collapse. Concurrently, sheep numbers have contracted over 75% in the arid zone since 1991, due to market forces and climate change, while demand for ethically produced goods such as predator-friendly meat production and organic produce is increasing. Decommissioning the Dingo Barrier Fence, moving the stock protection zone south and diversifying land use would not impact significantly on the current livestock production. It offers a sound economic alternative for the region, with the potential for regeneration of 82 million hectares of land, a scale encouraged for inclusion in the global initiative the United Nations Decade for Ecosystem Restoration (2021-2030). This would restore connectivity across the region, including vital access to the waters of the Murray Darling Basin. This would provide mitigation for the effects of climate change, new markets in organic and sustainable industries, and support ecological and cultural renewal.
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11
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Cairns KM, Newman KD, Crowther MS, Letnic M. Pelage variation in dingoes across southeastern Australia: implications for conservation and management. J Zool (1987) 2021. [DOI: 10.1111/jzo.12875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- K. M. Cairns
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
| | - K. D. Newman
- School of Biosciences University of Melbourne Parkville VIC Australia
| | - M. S. Crowther
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - M. Letnic
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
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12
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Tatler J, Prowse TA, Roshier DA, Cairns KM, Cassey P. Phenotypic variation and promiscuity in a wild population of pure dingoes (
Canis dingo
). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jack Tatler
- Centre for Applied Conservation Science and School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Thomas A.A. Prowse
- School of Mathematical Sciences University of Adelaide Adelaide South Australia Australia
| | - David A. Roshier
- Australian Wildlife Conservancy Subiaco East Western Australia Australia
- Centre for Ecosystem Science University of New South Wales Sydney New South Wales Australia
| | - Kylie M. Cairns
- Centre for Ecosystem Science University of New South Wales Sydney New South Wales Australia
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | - Phillip Cassey
- Centre for Applied Conservation Science and School of Biological Sciences University of Adelaide Adelaide South Australia Australia
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13
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Moore HA, Dunlop JA, Jolly CJ, Kelly E, Woinarski JCZ, Ritchie EG, Burnett S, van Leeuwen S, Valentine LE, Cowan MA, Nimmo DG. A brief history of the northern quoll (Dasyurus hallucatus): a systematic review. AUSTRALIAN MAMMALOGY 2021. [DOI: 10.1071/am21002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Shipman P. What the dingo says about dog domestication. Anat Rec (Hoboken) 2020; 304:19-30. [PMID: 33103861 PMCID: PMC7756258 DOI: 10.1002/ar.24517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 01/27/2023]
Abstract
Worldwide, dogs (Canis familiaris) are certainly the most common domesticate (900 million according to the World Atlas) and are sometimes used as a proxy for human presence. Dogs were the first and therefore arguably most important species ever to be domesticated. It is widely accepted that the domestic dog is a descendent of Pleistocene gray wolves (Canis lupus), possibly of a population now extinct. How can an extant canid, the dingo (Canis dingo or Canis familiaris), whose status as a species and as a domesticate is controversial, improve our understanding of the ancient process of domesticating the dog? Here I review anatomical, behavioral, biogeographic, and molecular evidence on the appropriate status of dingoes in a historical context. Dingoes are now the major apex predator in Australia aside from humans. Different sources of evidence have suggested different times of arrival in Greater Australia for humans and canids and different degrees of intimacy or domestication between humans and canids. Just as domestic dogs are often accorded near‐human status, dingoes have special relationships with human families, but reproductively and behaviorally they remain independent. In sum, traits of the dingo reflect its lupine ancestry, a certain degree of accommodation to human company, and unique adaptations to the demands of its habitat. Emphasizing that domestication is a long‐term process, not an event, helps clarify the ambiguous status of dingoes.
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Affiliation(s)
- Pat Shipman
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, USA
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15
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA.,University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA.,Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA.,University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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16
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Jolly CJ, Webb JK, Gillespie GR, Phillips BL. Training fails to elicit behavioral change in a marsupial suffering evolutionary loss of antipredator behaviors. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Attempts to reintroduce threatened species from ex situ populations (zoos or predator-free sanctuaries) regularly fail because of predation. When removed from their natural predators, animals may lose their ability to recognize predators and thus fail to adopt appropriate antipredator behaviors. Recently, northern quolls (Dasyurus hallucatus; Dasyuromorpha: Dasyuridae) conserved on a predator-free “island ark” for 13 generations were found to have no recognition of dingoes, a natural predator with which they had coevolved on mainland Australia for about 8,000 years. A subsequent reintroduction attempt using quolls acquired from this island ark failed due to predation by dingoes. In this study, we tested whether instrumental conditioning could be used to improve predator recognition in captive quolls sourced from a predator-free “island ark.” We used a previously successful scent-recognition assay (a giving-up density experiment) to compare predator-scent recognition of captive-born island animals before and after antipredator training. Our training was delivered by pairing live predators (dingo and domestic dog) with an electrified cage floor in repeat trials such that, when the predators were present, foraging animals would receive a shock. Our training methodology did not result in any discernible change in the ability of quolls to recognize and avoid dingo scent after training. We conclude either that our particular training method was ineffective (though ethically permissible); or that because these quolls appear unable to recognize natural predators, predator recognition may be extremely difficult to impart in a captive setting given ethical constraints. Our results point to the difficulty of reinstating lost behaviors, and to the value of maintaining antipredator behaviors in conservation populations before they are lost.
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Affiliation(s)
- Chris J Jolly
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Jonathan K Webb
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Graeme R Gillespie
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Flora and Fauna Division, Department of Environment and Natural Resources, Northern Territory Government, Berrimah, NT, Australia
| | - Ben L Phillips
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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17
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Zhang SJ, Wang GD, Ma P, Zhang LL, Yin TT, Liu YH, Otecko NO, Wang M, Ma YP, Wang L, Mao B, Savolainen P, Zhang YP. Genomic regions under selection in the feralization of the dingoes. Nat Commun 2020; 11:671. [PMID: 32015346 PMCID: PMC6997406 DOI: 10.1038/s41467-020-14515-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 12/16/2019] [Indexed: 12/30/2022] Open
Abstract
Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.
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Affiliation(s)
- Shao-Jie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Liang-Liang Zhang
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Meng Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Ya-Ping Ma
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Peter Savolainen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China.
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18
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Old dogs, new tricks: 3D geometric analysis of cranial morphology supports ancient population substructure in the Australian dingo. ZOOMORPHOLOGY 2020. [DOI: 10.1007/s00435-019-00475-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Cairns KM, Nesbitt BJ, Laffan SW, Letnic M, Crowther MS. Geographic hot spots of dingo genetic ancestry in southeastern Australia despite hybridisation with domestic dogs. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01230-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Genomic Characterization of External Morphology Traits in Kelpies Does Not Support Common Ancestry with the Australian Dingo. Genes (Basel) 2019; 10:genes10050337. [PMID: 31058880 PMCID: PMC6563003 DOI: 10.3390/genes10050337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 01/06/2023] Open
Abstract
The Kelpie is a breed developed in Australia for use as a livestock herding dog. It has been proposed that the development of the breed included gene flow from the Australian Dingo (Canis dingo), a canid species present on the Australian continent for around 4000 years. The Kelpie breed is split between working and conformation types that have readily recognizable differences in external morphology. We characterize known gene variants relating to external morphology in sequenced representatives of both Kelpie types (Australian Kelpie—conformation; Australian Working Kelpie—herding) and compare the variants present with those in sequenced Australian Dingoes, including 25 canids with locus-constrained data and one with a whole genome sequence. Variants assessed include identified coat color and ear morphology variants. We describe a new variant site in the transcribed region of methionine sulfoxide reductase 3 that may relate to ear phenotype. None of the morphology variants analyzed offer support for co-ancestry of the Kelpie breed with the Australian Dingo.
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21
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Abstract
BACKGROUND The Australian dingo continues to cause debate amongst Aboriginal people, pastoralists, scientists and the government in Australia. A lingering controversy is whether the dingo has been tamed and has now reverted to its ancestral wild state or whether its ancestors were domesticated and it now resides on the continent as a feral dog. The goal of this article is to place the discussion onto a theoretical framework, highlight what is currently known about dingo origins and taxonomy and then make a series of experimentally testable organismal, cellular and biochemical predictions that we propose can focus future research. DISCUSSION We consider a canid that has been unconsciously selected as a tamed animal and the endpoint of methodical or what we now call artificial selection as a domesticated animal. We consider wild animals that were formerly tamed as untamed and those wild animals that were formerly domesticated as feralized. Untamed canids are predicted to be marked by a signature of unconscious selection whereas feral animals are hypothesized to be marked by signatures of both unconscious and artificial selection. First, we review the movement of dingo ancestors into Australia. We then discuss how differences between taming and domestication may influence the organismal traits of skull morphometrics, brain and size, seasonal breeding, and sociability. Finally, we consider cellular and molecular level traits including hypotheses concerning the phylogenetic position of dingoes, metabolic genes that appear to be under positive selection and the potential for micronutrient compensation by the gut microbiome. CONCLUSIONS Western Australian Government policy is currently being revised to allow the widespread killing of the Australian dingo. These policies are based on an incomplete understanding of the evolutionary history of the canid and assume the dingo is feralized. However, accumulated evidence does not definitively show that the dingo was ever domesticated and additional focused research is required. We suggest that incorporating ancient DNA data into the debate concerning dingo origins will be pivotal to understanding the evolutionary history of the canid. Further, we advocate that future morphological, behavioural and genetic studies should focus on including genetically pure Alpine and Desert dingoes and not dingo-dog hybrids. Finally, we propose that future studies critically examine genes under selection in the dingo and employ the genome from a wild canid for comparison.
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Affiliation(s)
- J. William O. Ballard
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052 Australia
| | - Laura A. B. Wilson
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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22
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Diurnal pattern of pre-weaning den visits and nursing in breeding pairs of captive dingoes (Canis dingo). Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Affiliation(s)
- Euan G Ritchie
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC 3125, Australia.
| | - Bradley P Smith
- School of Health, Medical, and Applied Sciences, Appleton Institute, Central Queensland University, Wayville, SA 5034, Australia
| | - Lily M van Eeden
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dale G Nimmo
- School of Environmental Science, Institute for Land, Water, and Society, Charles Sturt University, Albury, NSW 2640, Australia
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24
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Greig K, Gosling A, Collins CJ, Boocock J, McDonald K, Addison DJ, Allen MS, David B, Gibbs M, Higham CFW, Liu F, McNiven IJ, O'Connor S, Tsang CH, Walter R, Matisoo-Smith E. Complex history of dog (Canis familiaris) origins and translocations in the Pacific revealed by ancient mitogenomes. Sci Rep 2018; 8:9130. [PMID: 29904060 PMCID: PMC6002536 DOI: 10.1038/s41598-018-27363-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/31/2018] [Indexed: 11/22/2022] Open
Abstract
Archaeological evidence suggests that dogs were introduced to the islands of Oceania via Island Southeast Asia around 3,300 years ago, and reached the eastern islands of Polynesia by the fourteenth century AD. This dispersal is intimately tied to human expansion, but the involvement of dogs in Pacific migrations is not well understood. Our analyses of seven new complete ancient mitogenomes and five partial mtDNA sequences from archaeological dog specimens from Mainland and Island Southeast Asia and the Pacific suggests at least three dog dispersal events into the region, in addition to the introduction of dingoes to Australia. We see an early introduction of dogs to Island Southeast Asia, which does not appear to extend into the islands of Oceania. A shared haplogroup identified between Iron Age Taiwanese dogs, terminal-Lapita and post-Lapita dogs suggests that at least one dog lineage was introduced to Near Oceania by or as the result of interactions with Austronesian language speakers associated with the Lapita Cultural Complex. We did not find any evidence that these dogs were successfully transported beyond New Guinea. Finally, we identify a widespread dog clade found across the Pacific, including the islands of Polynesia, which likely suggests a post-Lapita dog introduction from southern Island Southeast Asia.
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Affiliation(s)
- K Greig
- Department of Anthropology and Archaeology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
| | - A Gosling
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - C J Collins
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - J Boocock
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, 90024, United States of America
| | - K McDonald
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - D J Addison
- Archaeology Department, American Samoa Power Authority, PO Box 2545, Pago Pago, AS 96799, American Samoa, USA
| | - M S Allen
- Anthropology, School of Social Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - B David
- Monash Indigenous Studies Centre, Monash University, 20 Chancellors Walk, Clayton, VIC, 3800, Australia.,ARC Centre of Excellence for Australian Biodiversity & Heritage, Acton, ACT, 2601, Australia
| | - M Gibbs
- School of Humanities, University of New England, Armidale, NSW, 2351, Australia
| | - C F W Higham
- Department of Anthropology and Archaeology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - F Liu
- Institute of History and Philology, Academia Sinica, 128 Academia Rd, Taipei City 115, Taiwan
| | - I J McNiven
- Monash Indigenous Studies Centre, Monash University, 20 Chancellors Walk, Clayton, VIC, 3800, Australia.,ARC Centre of Excellence for Australian Biodiversity & Heritage, Acton, ACT, 2601, Australia
| | - S O'Connor
- Archaeology & Natural History, School of Culture History & Language, College of Asia & the Pacific, Australian National University, Acton, ACT, 2601, Australia.,ARC Centre of Excellence for Australian Biodiversity & Heritage, Acton, ACT, 2601, Australia
| | - C H Tsang
- Institute of History and Philology, Academia Sinica, 128 Academia Rd, Taipei City 115, Taiwan
| | - R Walter
- Department of Anthropology and Archaeology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - E Matisoo-Smith
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
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25
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Cairns KM, Shannon LM, Koler-Matznick J, Ballard JWO, Boyko AR. Elucidating biogeographical patterns in Australian native canids using genome wide SNPs. PLoS One 2018; 13:e0198754. [PMID: 29889854 PMCID: PMC5995383 DOI: 10.1371/journal.pone.0198754] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/24/2018] [Indexed: 11/19/2022] Open
Abstract
Dingoes play a strong role in Australia's ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.
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Affiliation(s)
- Kylie M. Cairns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: ,
| | - Laura M. Shannon
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Janice Koler-Matznick
- The New Guinea Singing Dog Conservation Society, Central Point, Oregon, United States of America
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
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Byosiere SE, Espinosa J, Smith BP. The function of play bows in Canis lupus and its variants: a comparison of dingo (Canis lupus dingo), dog (Canis lupus familiaris) and wolf puppies (Canis lupus). BEHAVIOUR 2018. [DOI: 10.1163/1568539x-00003495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Play bows represent a common, highly stereotyped behaviour across the genus Canis. However, much of what we know is limited to the wolf and its domestic derivative, the domestic dog. Here we continue to look at the function of play bows among subspecies/variants of Canis lupus by including the dingo. Comparing dingoes to wolves and dogs may provide further insight into the impact of domestication on play behaviour. We analysed play bows in three-to-six month old dingo puppies and compared the results to previous studies of wolves and dogs. The function of play bows in dingoes appears consistent with those observed in dogs and wolf puppies. However, subtle intraspecific differences (such as the frequency and duration of play bows, and vocalizations during play) were apparent, and warrant further investigation in the genus Canis, as well as the Family Canidae more broadly.
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Affiliation(s)
- Sarah-Elizabeth Byosiere
- aSchool of Psychology and Public Health, La Trobe University, P.O. Box 199, Bendigo VIC 3552, Australia
| | - Julia Espinosa
- bDepartment of Psychology, University of Toronto, 100 St George Street, Toronto, ON, Canada M5S 3G3
| | - Bradley P. Smith
- cAppleton Institute, Central Queensland University, 44 Greenhill Road, Wayville, SA 5034, Australia
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27
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Uncovering the origins of dog–human eye contact: dingoes establish eye contact more than wolves, but less than dogs. Anim Behav 2017. [DOI: 10.1016/j.anbehav.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Cairns KM, Brown SK, Sacks BN, Ballard JWO. Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography. Ecol Evol 2017; 7:9787-9807. [PMID: 29188009 PMCID: PMC5696388 DOI: 10.1002/ece3.3487] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/03/2017] [Accepted: 09/04/2017] [Indexed: 01/07/2023] Open
Abstract
It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.
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Affiliation(s)
- Kylie M Cairns
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Sarah K Brown
- Mammalian Ecology and Conservation Unit Veterinary Genetics Laboratory School of Veterinary Medicine University of California Davis CA USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit Veterinary Genetics Laboratory School of Veterinary Medicine University of California Davis CA USA.,Department of Population, Health and Reproduction School of Veterinary Medicine University of California Davis CA USA
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
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Smith BP, Lucas TA, Norris RM, Henneberg M. Brain size/body weight in the dingo (Canis dingo): comparisons with domestic and wild canids. AUST J ZOOL 2017. [DOI: 10.1071/zo17040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Endocranial volume was measured in a large sample (n = 128) of free-ranging dingoes (Canis dingo) where body size was known. The brain/body size relationship in the dingoes was compared with populations of wild (Family Canidae) and domestic canids (Canis familiaris). Despite a great deal of variation among wild and domestic canids, the brain/body size of dingoes forms a tight cluster within the variation of domestic dogs. Like dogs, free-ranging dingoes have paedomorphic crania; however, dingoes have a larger brain and are more encephalised than most domestic breeds of dog. The dingo’s brain/body size relationship was similar to those of other mesopredators (medium-sized predators that typically prey on smaller animals), including the dhole (Cuon alpinus) and the coyote (Canis latrans). These findings have implications for the antiquity and classification of the dingo, as well as the impact of feralisation on brain size. At the same time, it highlights the difficulty in using brain/body size to distinguish wild and domestic canids.
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