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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] [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. SIGNIFICANCE A long-standing question in conservation genetics is whether long-term isolation and elevated levels of inbreeding always leads to inevitable population extinction. Here we conduct the first-ever whole-genome analysis of a population of dingoes living in long-term isolation on an island off the coast of Australia (K'gari). We show that these animals are beset by very low genetic diversity, likely the result of extensive inbreeding, and an elevated number of deleterious homozygotes. However, our results suggest that these dingoes are likely purging highly deleterious alleles, which may have allowed them to persist long term despite their extremely small population (<200 individuals).
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2
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Koungoulos LG, Balme J, O’Connor S. Dingoes, companions in life and death: The significance of archaeological canid burial practices in Australia. PLoS One 2023; 18:e0286576. [PMID: 37862353 PMCID: PMC10588905 DOI: 10.1371/journal.pone.0286576] [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: 03/14/2023] [Accepted: 05/18/2023] [Indexed: 10/22/2023] Open
Abstract
The dingo, also known as the Australian native dog, was introduced in the late Holocene. Dingoes were primarily wild animals but a number resided in Aboriginal people's camps. Traditionally, these individuals were taken from wild litters before weaning and raised by Aboriginal people. It is generally believed that these dingoes were not directly provided for, and upon sexual maturity, returned to reproduce in the wild. However, some died while in the company of people and, were buried in occupation sites. This Australian practice parallels the burial of domestic dogs in many regions of the Asia-Pacific and beyond but has attracted very little research. We explore the historical and archaeological evidence for dingo burial, examining its different forms, chronological and geographic distribution, and cultural significance. Dingoes were usually buried in the same manner as Aboriginal community members and often in areas used for human burial, sometimes alongside people. This practice probably occurred from the time of their introduction until soon after European colonisation. We present a case study of dingo burials from Curracurrang Rockshelter (NSW) which provides insights into the lives of ancient tame dingoes, and suggests that domestication and genetic continuity between successive camp-dwelling generations may have occurred prior to European contact.
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Affiliation(s)
- Loukas George Koungoulos
- School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Jane Balme
- School of Social Sciences, University of Western Australia, Crawley, Australia
| | - Sue O’Connor
- School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australia
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3
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Cairns KM, Crowther MS, Parker HG, Ostrander EA, Letnic M. Genome-wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes. Mol Ecol 2023; 32:4133-4150. [PMID: 37246949 PMCID: PMC10524503 DOI: 10.1111/mec.16998] [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: 10/10/2022] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 05/30/2023]
Abstract
Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to interspecific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. But there exists a concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here, we apply genome-wide single-nucleotide polymorphism (SNP) genotyping to a set of 402 wild and captive dingoes collected from across Australia and then carry out comparisons to domestic dogs. We then perform ancestry modelling and biogeographic analyses to characterise population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes. Our work challenges previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in south-eastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policymakers to assess and inform dingo management policy and legislation moving forwards.
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Affiliation(s)
- Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mathew S. Crowther
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
| | - Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mike Letnic
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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4
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Taylor P, Swan M, Sitters H, Smith A, Di Stefano J. Small mammals reduce activity during high moon illumination under risk of predation by introduced predators. Sci Rep 2023; 13:10532. [PMID: 37386037 PMCID: PMC10310734 DOI: 10.1038/s41598-023-37166-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Predation influences prey survival and drives evolution of anti-predator behaviour. Anti-predator strategies by prey are stimulated by direct encounters with predators, but also by exposure to indicators of risk such as moonlight illumination and vegetation cover. Many prey species will suffer increased risk on moonlit nights, but risk may be reduced by the presence of dense vegetation. Determining the role of vegetation in reducing perceived risk is important, especially given predictions of increased global wildfire, which consumes vegetation and increases predation. We used remote cameras in southeastern Australia to compare support for the predation risk and habitat-mediated predation risk hypotheses. We examined the influence of moonlight and understorey cover on seven 20-2500 g mammalian prey species and two introduced predators, red foxes and feral cats. Activity of all prey species reduced by 40-70% with increasing moonlight, while one species (bush rat) reduced activity in response to increasing moonlight more sharply in low compared to high understorey cover. Neither predator responded to moonlight. Our findings supported the predation risk hypothesis and provided limited support for the habitat-mediated predation risk hypothesis. For prey, perceived costs of increased predation risk on moonlit nights outweighed any benefits of a brighter foraging environment.
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Affiliation(s)
- P Taylor
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, 4 Water Street, Creswick, VIC, 3363, Australia
- NSW Department of Primary Industries, Vertebrate Pest Research Unit, 1447 Forest Road, Orange, NSW, 2800, Australia
| | - M Swan
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, 4 Water Street, Creswick, VIC, 3363, Australia.
| | - H Sitters
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, 4 Water Street, Creswick, VIC, 3363, Australia
| | - A Smith
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, 4 Water Street, Creswick, VIC, 3363, Australia
| | - J Di Stefano
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, 4 Water Street, Creswick, VIC, 3363, Australia
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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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6
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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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7
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Genetic Structure of the Ca Rater Mallorquí Dog Breed Inferred by Microsatellite Markers. Animals (Basel) 2022; 12:ani12202733. [PMID: 36290119 PMCID: PMC9597762 DOI: 10.3390/ani12202733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2022] Open
Abstract
Ca Rater Mallorquí is a dog breed from the Island of Mallorca (Spain) traditionally used as a hunting and ratting dog to prevent disease spread and economic losses related to rodent activities on farms. However, the census data shows a population decline that should be addressed by implementing a conservation program. The first step to implementing a conservation plan is knowing the genetic situation of the Ca Rater Mallorquí population. Therefore, we aimed to genetically characterise the breed in our study. We analysed 33 microsatellites recommended by the International Society of Animal Genetics (ISAG) in 77 samples. Data were obtained from 13 samples of Balearic, Spanish, and international dog breeds to study the genetic diversity among breeds. The population did not significantly deviate from the Hardy-Weinberg equilibrium with heterozygosity (Ho) of 0.655 and expected heterozygosity (He) of 0.685. The Wright's fixation indices, the Factorial Correspondence Analysis (FCA), a dendrogram representing Reynolds genetic distance between populations, and the pairwise FST values establish the Ca Rater Mallorquí as an independent breed distinct from the Balearic, Spanish, and international breeds.
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8
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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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9
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Genome-Wide SNPs Detect Hybridisation of Marsupial Gliders ( Petaurus breviceps breviceps × Petaurus norfolcensis) in the Wild. Genes (Basel) 2021; 12:genes12091327. [PMID: 34573311 PMCID: PMC8467023 DOI: 10.3390/genes12091327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Petaurus breviceps and Petaurus norfolcensis have produced hybrids in captivity, however there are no reported cases of Petaurus hybridisation in the wild. This study uses morphological data, mitochondrial DNA, and nuclear genome-wide SNP markers to confirm P. breviceps breviceps × P. norfolcensis hybridisation within their natural range on the central coast of New South Wales, Australia. Morphological data identified a potential hybrid that was confirmed with next-generation sequencing technology and 10,111 genome-wide SNPs. Both STRUCTURE and NewHybrid analyses identified the hybrid as a P. norfolcensis backcross, which suggests an initial F1 hybrid was fertile. The mitochondrial DNA matched that of a P. b. breviceps, indicating that a P. b. breviceps female initially mated with a P. norfolcensis male to produce a fertile female offspring. Our study is an important example of how genome-wide SNPs can be used to identify hybrids where the distribution of congeners overlaps. Hybridisation between congeners is likely to become more frequent as climate changes and habitats fragment, resulting in increased interactions and competition for resources and mates.
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10
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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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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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Abstract
New Guinea singing dogs (NGSD) are distinctive among the Canidae because of their unique and characteristic vocalization, isolated habitat, and status as a rare representative of wild dogs. Their scarcity, combined with the knowledge that none have been captured or exported since the late 1970s, supports the hypothesis that NGSD are extinct in the wild. We have analyzed the nuclear genome of the first dogs captured from the highlands of Papua in approximately 50 y. We provide DNA-based evidence for an ancestral relationship between highland wild dogs (HWD) and captive NGSD suggesting that the founding population of the NGSD is not, in fact, extinct and that HWD should be resourced for conservation efforts to rebuild this unique canid population. New Guinea singing dogs (NGSD) are identifiable by their namesake vocalizations, which are unlike any other canid population. Their novel behaviors and potential singular origin during dog domestication make them an attractive, but elusive, subject for evolutionary and conservation study. Although once plentiful on the island of New Guinea (NG), they were presumed to currently exist only in captivity. This conclusion was based on the lack of sightings in the lowlands of the island and the concurrent expansion of European- and Asian-derived dogs. We have analyzed the first nuclear genomes from a canid population discovered during a recent expedition to the highlands of NG. The extreme altitude (>4,000 m) of the highland wild dogs’ (HWD) observed range and confirmed vocalizations indicate their potential to be a wild NGSD population. Comparison of single-nucleotide polymorphism genotypes shows strong similarity between HWD and the homogeneous captive NGSD, with the HWD showing significantly higher genetic diversity. Admixture analyses and estimation of shared haplotypes with phylogenetically diverse populations also indicates the HWD is a novel population within the distinct evolutionary lineage of Oceanic canids. Taken together, these data indicate the HWD possesses a distinct potential to aid in the conservation of NGSD both in the wild and under human care.
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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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15
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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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16
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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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17
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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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