1
|
Atağ G, Kaptan D, Yüncü E, Başak Vural K, Mereu P, Pirastru M, Barbato M, Leoni GG, Güler MN, Er T, Eker E, Yazıcı TD, Kılıç MS, Altınışık NE, Çelik EA, Morell Miranda P, Dehasque M, Floridia V, Götherström A, Bilgin CC, Togan İ, Günther T, Özer F, Hadjisterkotis E, Somel M. Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages. Genome Biol Evol 2024; 16:evae090. [PMID: 38670119 PMCID: PMC11109821 DOI: 10.1093/gbe/evae090] [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: 01/15/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
Collapse
Affiliation(s)
- Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Paolo Mereu
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Monica Pirastru
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Mario Barbato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | | | - Merve Nur Güler
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Tuğçe Er
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Elifnaz Eker
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Tunca Deniz Yazıcı
- Graduate School for Evolution, Ecology and Systematics, Ludwig Maximillian University of Munich, Munich, Germany
| | - Muhammed Sıddık Kılıç
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | | | - Ecem Ayşe Çelik
- Department of Settlement Archeology, Middle East Technical University, Ankara, Turkey
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Marianne Dehasque
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Viviana Floridia
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
| | - Cemal Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Eleftherios Hadjisterkotis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| |
Collapse
|
2
|
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).
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Stephens D, Fleming PJS, Sawyers E, Mayr TP. An isolated population reveals greater genetic structuring of the Australian dingo. Sci Rep 2022; 12:19105. [PMID: 36352001 PMCID: PMC9646726 DOI: 10.1038/s41598-022-23648-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022] Open
Abstract
The Australian dingo is a recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed 34 microsatellite markers using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual level. The broader southern Australia sample (n = 1138) comprised mostly hybrid animals, with 30% considered pure dingoes. All western Victorian individuals (n = 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and low genetic diversity on all measures tested. Based upon our characterisation of this unusual mainland population, we advise against assuming homogeneity of dingoes across the continent.
Collapse
Affiliation(s)
| | - Peter J. S. Fleming
- grid.1680.f0000 0004 0559 5189Vertebrate Pest Research Unit, NSW Department of Primary Industries, 1447 Forest Road, Orange, NSW 2800 Australia ,grid.1020.30000 0004 1936 7371Ecosystem Management, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia ,grid.1048.d0000 0004 0473 0844Institute for Agriculture and the Environment, Centre for Sustainable Agricultural Systems, University of Southern Queensland, Toowoomba, QLD 4350 Australia
| | - Emma Sawyers
- grid.1680.f0000 0004 0559 5189Vertebrate Pest Research Unit, NSW Department of Primary Industries, 1447 Forest Road, Orange, NSW 2800 Australia ,Vertebrate Pest Research Unit, NSW Department of Primary Industries, 10 Valentine Ave, Parramatta, NSW 2150 Australia
| | - Tim P. Mayr
- grid.452205.40000 0000 9561 2798Department of Environment, Land, Water and Planning, 308-390 Koorlong Ave, Irymple, VIC 3498 Australia
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
Collapse
Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
| |
Collapse
|
10
|
Vaux F, Bohn S, Hyde JR, O'Malley KG. Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation. Evol Appl 2021; 14:1343-1364. [PMID: 34025772 PMCID: PMC8127716 DOI: 10.1111/eva.13202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double-digest restriction site-associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross-hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.
Collapse
Affiliation(s)
- Felix Vaux
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Sandra Bohn
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - John R. Hyde
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceLa JollaCAUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
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.
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
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]
|
16
|
McIntyre JK, Wolf LL, Sacks BN, Koibur J, Brisbin Jr IL. A population of free-living highland wild dogs in Indonesian Papua. AUSTRALIAN MAMMALOGY 2020. [DOI: 10.1071/am18039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A 10-day rapid assessment has confirmed a small population of indigenous wild-living dogs in the highlands of Papua Province, Indonesia. The goal of the assessment was to observe, census, assess health and reproductive status, and collect biological samples or other data for this understudied canid. Trail cameras and DNA hair traps were deployed and baited with scent attractants, and game calls were used to elicit vocal responses or lure the dogs within observation range. Adults and pups of both sexes as well as a den were documented in 149 photographs. DNA testing of scat samples confirmed a canid origin with a close relationship to other oceanic canids including NGSD (New Guinea Singing Dog) and dingoes.
Collapse
|
17
|
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]
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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]
|
20
|
Marinov M, Teofanova D, Gadjev D, Radoslavov G, Hristov P. Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin. PeerJ 2018; 6:e5060. [PMID: 29967734 PMCID: PMC6026455 DOI: 10.7717/peerj.5060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak, n = 34; Bulgarian Scenthound Dog: Gonche, n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs.
Collapse
Affiliation(s)
- Miroslav Marinov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Denitsa Teofanova
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Dimitar Gadjev
- Agricultural and Stockbreeding Experimental Station, Agricultural Academy, Smolyan, Bulgaria
| | - Georgi Radoslavov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Byosiere SE, Espinosa J, Smith BP. The function of play bows in Canis lupus and its variants: a comparison of dingo (Canis lupus dingo), dog (Canis lupus familiaris) and wolf puppies (Canis lupus). BEHAVIOUR 2018. [DOI: 10.1163/1568539x-00003495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Play bows represent a common, highly stereotyped behaviour across the genus Canis. However, much of what we know is limited to the wolf and its domestic derivative, the domestic dog. Here we continue to look at the function of play bows among subspecies/variants of Canis lupus by including the dingo. Comparing dingoes to wolves and dogs may provide further insight into the impact of domestication on play behaviour. We analysed play bows in three-to-six month old dingo puppies and compared the results to previous studies of wolves and dogs. The function of play bows in dingoes appears consistent with those observed in dogs and wolf puppies. However, subtle intraspecific differences (such as the frequency and duration of play bows, and vocalizations during play) were apparent, and warrant further investigation in the genus Canis, as well as the Family Canidae more broadly.
Collapse
Affiliation(s)
- Sarah-Elizabeth Byosiere
- aSchool of Psychology and Public Health, La Trobe University, P.O. Box 199, Bendigo VIC 3552, Australia
| | - Julia Espinosa
- bDepartment of Psychology, University of Toronto, 100 St George Street, Toronto, ON, Canada M5S 3G3
| | - Bradley P. Smith
- cAppleton Institute, Central Queensland University, 44 Greenhill Road, Wayville, SA 5034, Australia
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Smith BP, Lucas TA, Norris RM, Henneberg M. Brain size/body weight in the dingo (Canis dingo): comparisons with domestic and wild canids. AUST J ZOOL 2017. [DOI: 10.1071/zo17040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Endocranial volume was measured in a large sample (n = 128) of free-ranging dingoes (Canis dingo) where body size was known. The brain/body size relationship in the dingoes was compared with populations of wild (Family Canidae) and domestic canids (Canis familiaris). Despite a great deal of variation among wild and domestic canids, the brain/body size of dingoes forms a tight cluster within the variation of domestic dogs. Like dogs, free-ranging dingoes have paedomorphic crania; however, dingoes have a larger brain and are more encephalised than most domestic breeds of dog. The dingo’s brain/body size relationship was similar to those of other mesopredators (medium-sized predators that typically prey on smaller animals), including the dhole (Cuon alpinus) and the coyote (Canis latrans). These findings have implications for the antiquity and classification of the dingo, as well as the impact of feralisation on brain size. At the same time, it highlights the difficulty in using brain/body size to distinguish wild and domestic canids.
Collapse
|