1
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Koungoulos LG, Hulme-Beaman A, Fillios M. Phenotypic diversity in early Australian dingoes revealed by traditional and 3D geometric morphometric analysis. Sci Rep 2024; 14:21228. [PMID: 39294146 PMCID: PMC11411105 DOI: 10.1038/s41598-024-65729-3] [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: 12/22/2023] [Accepted: 06/24/2024] [Indexed: 09/20/2024] Open
Abstract
The dingo is a wild dog endemic to Australia with enigmatic origins. Dingoes are one of two remaining unadmixed populations of an early East Asian dog lineage, the other being wild dogs from the New Guinea highlands, but morphological connections between these canid groups have long proved elusive. Here, we investigate this issue through a morphometric study of ancient dingo remains found at Lake Mungo and Lake Milkengay, in western New South Wales. Direct accelerated mass spectrometry (AMS) radiocarbon dates from an ancient Lake Mungo dingo demonstrate that dingoes with a considerably smaller build than the predominant modern morphotype were present in semi-arid southeastern Australia c.3000-3300 calBP. 3D geometric morphometric analysis of a near-complete Mungo cranium finds closest links to East Asian and New Guinean dogs, providing the first morphological evidence of links between early dingoes and their northern relatives. This ancient type is no longer extant within the range of modern dingo variability, but populations from nearby southeastern Australia show a closer resemblance than those to the north and west. Our results reaffirm prior characterisations of regional variability in dingo phenotype as not exclusively derived from recent domestic dog hybridisation but as having an earlier precedent, and suggest further that the dingo's phenotype has changed over time.
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Affiliation(s)
- Loukas G Koungoulos
- Department of Archaeology, School of Humanities, The University of Sydney, Sydney, Australia.
- Archaeology and Natural History, College of Asia and the Pacific, School of Culture, History and Language, The Australian National University, Canberra, Australia.
- Australian Museum Research Institute, Australian Museum, Sydney, Australia.
| | - Ardern Hulme-Beaman
- Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK
| | - Melanie Fillios
- Department of Archaeology, School of Humanities, Arts and Social Sciences, The University of New England, Armidale, Australia
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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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McAuliffe K. A comparative test of inequity aversion in domestic dogs (Canis familiaris) and dingoes (Canis dingo). PLoS One 2021; 16:e0255885. [PMID: 34550973 PMCID: PMC8457503 DOI: 10.1371/journal.pone.0255885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/26/2021] [Indexed: 11/18/2022] Open
Abstract
Despite much recent empirical work on inequity aversion in nonhuman species, many questions remain about its distribution across taxa and the factors that shape its evolution and expression. Past work suggests that domestic dogs (Canis familiaris) and wolves (Canis lupus) are averse to inequitable resource distributions in contexts that call upon some degree of training such as 'give paw' and 'buzzer press' tasks. However, it is unclear whether inequity aversion appears in other canid species and in other experimental contexts. Using a novel inequity aversion task that does not require specific training, this study helps address these gaps by investigating inequity aversion in domestic dogs and a closely related but non-domesticated canid, the dingo (Canis dingo). Subjects were presented with equal and unequal reward distributions and given the opportunity to approach or refuse to approach allocations. Measures of interest were (1) subjects' refusal to approach when getting no food; (2) approach latency; and (3) social referencing. None of these measures differed systematically across the inequity condition and control conditions in either dogs or dingoes. These findings add to the growing literature on inequity aversion in canids, providing data from a new species and a new experimental context. Additionally, they raise questions about the experimental features that must be in place for inequity aversion to appear in canids.
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Affiliation(s)
- Katherine McAuliffe
- Department of Psychology and Neuroscience, Boston College, Chestnut Hill, Massachusetts, United States of America
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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5
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Conroy GC, Lamont RW, Bridges L, Stephens D, Wardell-Johnson A, Ogbourne SM. Conservation concerns associated with low genetic diversity for K'gari-Fraser Island dingoes. Sci Rep 2021; 11:9503. [PMID: 33947920 PMCID: PMC8097078 DOI: 10.1038/s41598-021-89056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
The dingo population on world heritage-listed K'gari-Fraser Island (K'gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K'gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K'gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.
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Affiliation(s)
- G C Conroy
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia. .,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
| | - R W Lamont
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - L Bridges
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - D Stephens
- Zoological Genetics, Inglewood, Adelaide, SA, 5133, Australia
| | - A Wardell-Johnson
- Senior Professional Fellow, Curtin University, Bentley, WA, Australia
| | - S M Ogbourne
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania. J Hum Genet 2016; 62:343-353. [PMID: 27904152 DOI: 10.1038/jhg.2016.147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022]
Abstract
Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.
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15
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Cairns KM, Wilton AN. New insights on the history of canids in Oceania based on mitochondrial and nuclear data. Genetica 2016; 144:553-565. [PMID: 27640201 DOI: 10.1007/s10709-016-9924-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022]
Abstract
How and when dingoes arrived in Oceania poses a fascinating question for scientists with interest in the historical movements of humans and dogs. The dingo holds a unique position as top terrestrial predator of Australia and exists in a wild state. In the first geographical survey of genetic diversity in the dingo using whole mitochondrial genomes, we analysed 16,428 bp in 25 individuals from five separate populations. We also investigated 13 nuclear loci to compare with the mitochondrial population history patterns. Phylogenetic analyses based upon mitochondrial DNA and nuclear DNA support the hypothesis that there are at least two distinct populations of dingo, one of which occurs in the northwest and the other in the southeast of the continent. Conservative molecular dating based upon mitochondrial DNA suggest that the lineages split approximately 8300 years before present, likely outside Australia but within Oceania. The close relationship between dingoes and New Guinea Singing Dogs suggests that plausibly dingoes spread into Australia via the land bridge between Papua New Guinea and Australia although seafaring introductions cannot be rejected. The geographical distribution of these divergent lineages suggests there were multiple independent dingo immigrations. Importantly, the observation of multiple dingo populations suggests the need for revision of existing conservation and management programs that treat dingoes as a single homogeneous population.
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Affiliation(s)
- Kylie M Cairns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Alan N Wilton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
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16
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Behrendorff L, Leung LKP, McKinnon A, Hanger J, Belonje G, Tapply J, Jones D, Allen BL. Insects for breakfast and whales for dinner: the diet and body condition of dingoes on Fraser Island (K'gari). Sci Rep 2016; 6:23469. [PMID: 27009879 PMCID: PMC4806299 DOI: 10.1038/srep23469] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/08/2016] [Indexed: 11/24/2022] Open
Abstract
Top-predators play stabilising roles in island food webs, including Fraser Island, Australia. Subsidising generalist predators with human-sourced food could disrupt this balance, but has been proposed to improve the overall health of the island’s dingo (Canis lupus dingo) population, which is allegedly ‘starving’ or in ‘poor condition’. We assess this hypothesis by describing the diet and health of dingoes on Fraser Island from datasets collected between 2001 and 2015. Medium-sized mammals (such as bandicoots) and fish were the most common food items detected in dingo scat records. Stomach contents records revealed additional information on diet, such as the occurrence of human-sourced foods. Trail camera records highlighted dingo utilisation of stranded marine fauna, particularly turtles and whales. Mean adult body weights were higher than the national average, body condition scores and abundant-excessive fat reserves indicated a generally ideal-heavy physical condition, and parasite loads were low and comparable to other dingo populations. These data do not support hypotheses that Fraser Island dingoes have restricted diets or are in poor physical condition. Rather, they indicate that dingoes on Fraser Island are capable of exploiting a diverse array of food sources which contributes to the vast majority of dingoes being of good-excellent physical condition.
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Affiliation(s)
- Linda Behrendorff
- The University of Queensland, School of Agriculture and Food Sciences, Gatton, Queensland 4343, Australia.,Queensland Parks and Wildlife Service, Department of National Parks, Sport and Racing, Fraser Island, Queensland 4581, Australia
| | - Luke K-P Leung
- The University of Queensland, School of Agriculture and Food Sciences, Gatton, Queensland 4343, Australia
| | - Allan McKinnon
- Department of Environmental Heritage Protection, Threatened Species Unit, Moggill, Queensland 4070, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology, Toorbul, Queensland 4510, Australia
| | - Grant Belonje
- Fraser Coast Veterinary Services, Maryborough, Queensland 4650, Australia
| | - Jenna Tapply
- Queensland Parks and Wildlife Service, Department of National Parks, Sport and Racing, Fraser Island, Queensland 4581, Australia
| | - Darryl Jones
- Griffith University, Environmental Futures Research Institute, Nathan, Queensland 4111, Australia
| | - Benjamin L Allen
- The University of Southern Queensland, Institute for Agriculture and the Environment, Toowoomba, Queensland 4350, Australia
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17
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Dwyer PD, Minnegal M. Wild dogs and village dogs in New Guinea: were they different? AUSTRALIAN MAMMALOGY 2016. [DOI: 10.1071/am15011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent accounts of wild-living dogs in New Guinea argue that these animals qualify as an ‘evolutionarily significant unit’ that is distinct from village dogs, have been and remain genetically isolated from village dogs and merit taxonomic recognition at, at least, subspecific level. These accounts have paid little attention to reports concerning village dogs. This paper reviews some of those reports, summarises observations from the interior lowlands of Western Province and concludes that: (1) at the time of European colonisation, wild-living dogs and most, if not all, village dogs of New Guinea comprised a single though heterogeneous gene pool; (2) eventual resolution of the phylogenetic relationships of New Guinean wild-living dogs will apply equally to all or most of the earliest New Guinean village-based dogs; and (3) there remain places where the local village-based population of domestic dogs continues to be dominated by individuals whose genetic inheritance can be traced to precolonisation canid forebears. At this time, there is no firm basis from which to assign a unique Linnaean name to dogs that live as wild animals at high altitudes of New Guinea.
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18
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Spencer PBS, Yurchenko AA, David VA, Scott R, Koepfli KP, Driscoll C, O'Brien SJ, Menotti-Raymond M. The Population Origins and Expansion of Feral Cats in Australia. J Hered 2015; 107:104-14. [PMID: 26647063 DOI: 10.1093/jhered/esv095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris).
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Affiliation(s)
- Peter B S Spencer
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond).
| | - Andrey A Yurchenko
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Victor A David
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Rachael Scott
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Klaus-Peter Koepfli
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Carlos Driscoll
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Stephen J O'Brien
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
| | - Marilyn Menotti-Raymond
- From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond)
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Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ. Antiquity and diversity of aboriginal Australian Y-chromosomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:367-81. [DOI: 10.1002/ajpa.22886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Kaye N. Ballantyne
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Mannis van Oven
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Duncan Taylor
- Forensic Science South Australia; 21 Divett Place Adelaide SA 5000 Australia
- School of Biological Sciences; Flinders University; Adelaide SA 5001 Australia
| | - Stephen Wilcox
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Rust Turkalov
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Roland A.H. van Oorschot
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
| | | | - Lesley Williams
- Department of Communities; Child Safety and Disability Services, Queensland Government; Brisbane QLD Australia
| | - Manfred Kayser
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Robert J. Mitchell
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
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Ardalan A, Oskarsson MCR, van Asch B, Rabakonandriania E, Savolainen P. African origin for Madagascan dogs revealed by mtDNA analysis. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140552. [PMID: 26064658 PMCID: PMC4453261 DOI: 10.1098/rsos.140552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/17/2015] [Indexed: 06/04/2023]
Abstract
Madagascar was one of the last major land masses to be inhabited by humans. It was initially colonized by Austronesian speaking Indonesians 1500-2000 years ago, but subsequent migration from Africa has resulted in approximately equal genetic contributions from Indonesia and Africa, and the material culture has mainly African influences. The dog, along with the pig and the chicken, was part of the Austronesian Neolithic culture, and was furthermore the only domestic animal to accompany humans to every continent in ancient times. To illuminate Madagascan cultural origins and track the initial worldwide dispersal of dogs, we here investigated the ancestry of Madagascan dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared it with that from potential ancestral populations in Island Southeast Asia (n=219) and sub-Saharan Africa (n=493). We found that 90% of the Madagascan dogs carried a haplotype that was also present in sub-Saharan Africa and that the remaining lineages could all be attributed to a likely origin in Africa. By contrast, only 26% of Madagascan dogs shared haplotypes with Indonesian dogs, and one haplotype typical for Austronesian dogs, carried by more than 40% of Indonesian and Polynesian dogs, was absent among the Madagascan dogs. Thus, in contrast to the human population, Madagascan dogs seem to trace their origin entirely from Africa. These results suggest that dogs were not brought to Madagascar by the initial Austronesian speaking colonizers on their transoceanic voyage, but were introduced at a later stage, together with human migration and cultural influence from Africa.
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Affiliation(s)
- Arman Ardalan
- Department of Gene Technology, KTH–Royal Institute of Technology, Science for Life Laboratory, Solna 171 21, Sweden
- Division of Animal Biotechnology and Genomics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Mattias C. R. Oskarsson
- Department of Gene Technology, KTH–Royal Institute of Technology, Science for Life Laboratory, Solna 171 21, Sweden
| | - Barbara van Asch
- IPATIMUP, Rua Dr Roberto Frias s/n, Porto 4200–465, Portugal
- Department of Genetics, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7601, South Africa
| | - Elisabeth Rabakonandriania
- Département de Biologie et Écologie Végétales, Faculté des Sciences Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Peter Savolainen
- Department of Gene Technology, KTH–Royal Institute of Technology, Science for Life Laboratory, Solna 171 21, Sweden
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21
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Ongoing unraveling of a continental fauna: decline and extinction of Australian mammals since European settlement. Proc Natl Acad Sci U S A 2015; 112:4531-40. [PMID: 25675493 DOI: 10.1073/pnas.1417301112] [Citation(s) in RCA: 414] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The highly distinctive and mostly endemic Australian land mammal fauna has suffered an extraordinary rate of extinction (>10% of the 273 endemic terrestrial species) over the last ∼200 y: in comparison, only one native land mammal from continental North America became extinct since European settlement. A further 21% of Australian endemic land mammal species are now assessed to be threatened, indicating that the rate of loss (of one to two extinctions per decade) is likely to continue. Australia's marine mammals have fared better overall, but status assessment for them is seriously impeded by lack of information. Much of the loss of Australian land mammal fauna (particularly in the vast deserts and tropical savannas) has been in areas that are remote from human population centers and recognized as relatively unmodified at global scale. In contrast to general patterns of extinction on other continents where the main cause is habitat loss, hunting, and impacts of human development, particularly in areas of high and increasing human population pressures, the loss of Australian land mammals is most likely due primarily to predation by introduced species, particularly the feral cat, Felis catus, and European red fox, Vulpes vulpes, and changed fire regimes.
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22
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Moreno E. Retrospective and prospective perspectives on zoonotic brucellosis. Front Microbiol 2014; 5:213. [PMID: 24860561 PMCID: PMC4026726 DOI: 10.3389/fmicb.2014.00213] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 04/23/2014] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Brucella are pathogenic bacteria exceedingly well adapted to their hosts. The bacterium is transmitted by direct contact within the same host species or accidentally to secondary hosts, such as humans. Human brucellosis is strongly linked to the management of domesticated animals and ingestion of their products. Since the domestication of ungulates and dogs in the Fertile Crescent and Asia in 12000 and 33000 ya, respectively, a steady supply of well adapted emergent Brucella pathogens causing zoonotic disease has been provided. Likewise, anthropogenic modification of wild life may have also impacted host susceptibility and Brucella selection. Domestication and human influence on wild life animals are not neutral phenomena. Consequently, Brucella organisms have followed their hosts’ fate and have been selected under conditions that favor high transmission rate. The “arm race” between Brucella and their preferred hosts has been driven by genetic adaptation of the bacterium confronted with the evolving immune defenses of the host. Management conditions, such as clustering, selection, culling, and vaccination of Brucella preferred hosts have profound influences in the outcome of brucellosis and in the selection of Brucella organisms. Countries that have controlled brucellosis systematically used reliable smooth live vaccines, consistent immunization protocols, adequate diagnostic tests, broad vaccination coverage and sustained removal of the infected animals. To ignore and misuse tools and strategies already available for the control of brucellosis may promote the emergence of new Brucella variants. The unrestricted use of low-efficacy vaccines may promote a “false sense of security” and works towards selection of Brucella with higher virulence and transmission potential.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional Heredia, Costa Rica ; Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica San José, Costa Rica
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23
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Crowther MS, Fillios M, Colman N, Letnic M. An updated description of the
A
ustralian dingo (
C
anis dingo
M
eyer, 1793). J Zool (1987) 2014. [DOI: 10.1111/jzo.12134] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- M. S. Crowther
- School of Biological Sciences University of Sydney Sydney NSW Australia
| | - M. Fillios
- Department of Archaeology University of Sydney Sydney NSW Australia
| | - N. Colman
- Hawkesbury Institute for the Environment University of Western Sydney Penrith NSW Australia
| | - M. Letnic
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
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Crapon de Caprona MD, Savolainen P. Extensive Phenotypic Diversity among South Chinese Dogs. ACTA ACUST UNITED AC 2013. [DOI: 10.5402/2013/621836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We describe here a broad diversity in phenotype among dogs in southern China’s rural areas, previously relatively unknown outside of China. These dogs display a much broader spectrum of diversity than is observed for the Indian Pariah Dog and the Australian Dingo, which are of a more uniform type and popularly thought to be typical for South Asian dogs and to represent the primitive morphology of the earliest domestic dogs. We show here that the village dog population of southern China harbors a broad diversity of morphological features, for color, body structure and size, coat texture, ear, and tail set, that are otherwise typically associated with the wide variety of Western dog breeds and assumed to be the result of intense selective breeding. The diversity of southern China’s dogs is cast in the light of mtDNA and Y-chromosome DNA studies showing that the genetic diversity is distinctly higher in southern East Asia than in the rest of the world, indicating that this was the geographical origins of today’s dog. These data suggest that the diverse morphologies of European dogs may have been formed from genetic “building blocks" still present in the dog population of rural southern China.
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Affiliation(s)
| | - Peter Savolainen
- Division of Gene Technology, School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
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Interpreting the evidence for middle Holocene gene flow from India to Australia. Proc Natl Acad Sci U S A 2013; 110:E2948. [PMID: 23754366 DOI: 10.1073/pnas.1306505110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Newsome TM, Ballard GA, Dickman CR, Fleming PJS, Howden C. Anthropogenic resource subsidies determine space use by Australian arid zone dingoes: an improved resource selection modelling approach. PLoS One 2013; 8:e63931. [PMID: 23750191 PMCID: PMC3667862 DOI: 10.1371/journal.pone.0063931] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/09/2013] [Indexed: 11/19/2022] Open
Abstract
Dingoes (Canis lupus dingo) were introduced to Australia and became feral at least 4,000 years ago. We hypothesized that dingoes, being of domestic origin, would be adaptable to anthropogenic resource subsidies and that their space use would be affected by the dispersion of those resources. We tested this by analyzing Resource Selection Functions (RSFs) developed from GPS fixes (locations) of dingoes in arid central Australia. Using Generalized Linear Mixed-effect Models (GLMMs), we investigated resource relationships for dingoes that had access to abundant food near mine facilities, and for those that did not. From these models, we predicted the probability of dingo occurrence in relation to anthropogenic resource subsidies and other habitat characteristics over ∼ 18,000 km(2). Very small standard errors and subsequent pervasively high P-values of results will become more important as the size of data sets, such as our GPS tracking logs, increases. Therefore, we also investigated methods to minimize the effects of serial and spatio-temporal correlation among samples and unbalanced study designs. Using GLMMs, we accounted for some of the correlation structure of GPS animal tracking data; however, parameter standard errors remained very small and all predictors were highly significant. Consequently, we developed an alternative approach that allowed us to review effect sizes at different spatial scales and determine which predictors were sufficiently ecologically meaningful to include in final RSF models. We determined that the most important predictor for dingo occurrence around mine sites was distance to the refuse facility. Away from mine sites, close proximity to human-provided watering points was predictive of dingo dispersion as were other landscape factors including palaeochannels, rocky rises and elevated drainage depressions. Our models demonstrate that anthropogenically supplemented food and water can alter dingo-resource relationships. The spatial distribution of such resources is therefore critical for the conservation and management of dingoes and other top predators.
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Affiliation(s)
- Thomas M Newsome
- Institute of Wildlife Research, School of Biological Sciences, Heydon-Laurence Building, University of Sydney, New South Wales, Australia.
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Sacks BN, Brown SK, Stephens D, Pedersen NC, Wu JT, Berry O. Y Chromosome Analysis of Dingoes and Southeast Asian Village Dogs Suggests a Neolithic Continental Expansion from Southeast Asia Followed by Multiple Austronesian Dispersals. Mol Biol Evol 2013; 30:1103-18. [DOI: 10.1093/molbev/mst027] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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