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Souilmi Y, Wasef S, Williams MP, Conroy G, Bar I, Bover P, Dann J, Heiniger H, Llamas B, Ogbourne S, Archer M, Ballard JWO, Reed E, Tobler R, Koungoulos L, Walshe K, Wright JL, Balme J, O’Connor S, Cooper A, Mitchell KJ. Ancient genomes reveal over two thousand years of dingo population structure. Proc Natl Acad Sci U S A 2024; 121:e2407584121. [PMID: 38976766 PMCID: PMC11287250 DOI: 10.1073/pnas.2407584121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Sally Wasef
- Ancient DNA Facility, Defence Genomics, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, QLD4059, Australia
- Innovation Division, Forensic Science Queensland, Queensland Health, Coopers Plains, QLD4108, Australia
| | - Matthew P. Williams
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Department of Biology, The Pennsylvania State University, State College, PA16802
| | - Gabriel Conroy
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD4111, Australia
| | - Pere Bover
- Fundación Agencia Aragonesa para la Investigacióny el Desarrollo (ARAID), Zaragoza50018, Spain
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA)-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza50009, Spain
| | - Jackson Dann
- Grützner Laboratory of Comparative Genomics, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Holly Heiniger
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, ActonACT2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA5000, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Michael Archer
- Earth and Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales Sydney, SydneyNSW2052, Australia
| | - J. William O. Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC3052, Australia
| | - Elizabeth Reed
- Ecology and Evolutionary Biology, School of Biological Sciences, The University of Adelaide, AdelaideSA5005, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Acton, ACT2601, Australia
| | - Loukas Koungoulos
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW2010, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Keryn Walshe
- School of Anthropology and Archaeology, University of Auckland, Auckland1010, New Zealand
| | - Joanne L. Wright
- Queensland Department of Education, Kelvin Grove State College, Kelvin Grove, QLD4059, Australia
| | - Jane Balme
- School of Social Sciences, University of Western Australia, Crawley, WA6009, Australia
| | - Sue O’Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Alan Cooper
- Gulbali Institute, Charles Sturt University, Albury, NSW2640, Australia
| | - Kieren J. Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- Manaaki Whenua—Landcare Research, Lincoln, Canterbury7608, New Zealand
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2
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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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The impact of environmental factors on the evolution of brain size in carnivorans. Commun Biol 2022; 5:998. [PMID: 36130990 PMCID: PMC9492690 DOI: 10.1038/s42003-022-03748-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022] Open
Abstract
The reasons why some animals have developed larger brains has long been a subject of debate. Yet, it remains unclear which selective pressures may favour the encephalization and how it may act during evolution at different taxonomic scales. Here we studied the patterns and tempo of brain evolution within the order Carnivora and present large-scale comparative analysis of the effect of ecological, environmental, social, and physiological variables on relative brain size in a sample of 174 extant carnivoran species. We found a complex pattern of brain size change between carnivoran families with differences in both the rate and diversity of encephalization. Our findings suggest that during carnivorans’ evolution, a trade-off have occurred between the cognitive advantages of acquiring a relatively large brain allowing to adapt to specific environments, and the metabolic costs of the brain which may constitute a disadvantage when facing the need to colonize new environments. The brain size of carnivores has evolved to balance a trade-off between increased cognitive function and increased metabolic cost.
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Abstract
The reasons why some animals have developed larger brains has long been a subject of debate. Yet, it remains unclear which selective pressures may favour the encephalization and how it may act during evolution at different taxonomic scales. Here we studied the patterns and tempo of brain evolution within the order Carnivora and present large-scale comparative analysis of the effect of ecological, environmental, social, and physiological variables on relative brain size in a sample of 174 extant carnivoran species. We found a complex pattern of brain size change between carnivoran families with differences in both the rate and diversity of encephalization. Our findings suggest that during carnivorans' evolution, a trade-off have occurred between the cognitive advantages of acquiring a relatively large brain allowing to adapt to specific environments, and the metabolic costs of the brain which may constitute a disadvantage when facing the need to colonize new environments.
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5
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The Role of Socialisation in the Taming and Management of Wild Dingoes by Australian Aboriginal People. Animals (Basel) 2022; 12:ani12172285. [PMID: 36078005 PMCID: PMC9454437 DOI: 10.3390/ani12172285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The dingo (Canis dingo) is a wild-living canid endemic to mainland Australia; the descendent of an early lineage of dog introduced thousands of years ago to the continent, where it was isolated from further introductions of domestic canines until European colonisation began in 1788. Dingoes are notoriously difficult to maintain in captivity and owing to their predatory nature it is also known that they can pose a serious risk to children. Yet, written records and oral histories indicate that Aboriginal people in mainland Australia routinely practiced the rearing and keeping of dingoes in a tame state within their home communities and domestic spaces. This paper reviews historical and archaeological evidence for the management of wild and captive dingoes by Indigenous communities, revealing a substantial divide between the nature and outcomes of these interactions between historical/pre-contact Aboriginal societies and those in contemporary Australia. It is concluded that this special human-wild canid relationship has implications for the understanding of the domestication of dogs from wolves during the Late Pleistocene. Abstract Historical sources and Indigenous oral traditions indicate that Australian Aboriginal people commonly reared and kept the wild-caught pups of dingoes (C. dingo) as tamed companion animals. A review of the available evidence suggests Indigenous communities employed an intense socialisation process that forged close personal bonds between humans and their tame dingoes from an early age. This was complemented by oral traditions which passed down awareness of the dangers to children posed by wild or unfamiliar dingoes, and which communicated the importance of treating dingoes with respect. Together, these practices resulted in what can be interpreted as substantially altered behaviours in tamed dingoes, which, despite their naturally high prey drive, were not considered a serious threat to children and were thus able to be maintained as companion animals in the long term. This relationship is of importance for understanding the original domestication of the dog, as it demonstrates a means by which careful and deliberate socialisation by foragers could both manage risks to children’s safety posed by keeping wild canids in the domestic realm and retain them well into reproductive maturity—both issues which have been highlighted as obstacles to the domestication of dogs from wolves.
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Ballard JWO, Gardner C, Ellem L, Yadav S, Kemp RI. Eye contact and sociability data suggests that Australian dingoes were never domesticated. Curr Zool 2022; 68:423-432. [PMID: 36090142 PMCID: PMC9450177 DOI: 10.1093/cz/zoab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Dogs were the first animal to become domesticated by humans, and they represent a classic model system for unraveling the processes of domestication. We compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog (GSD) breeds. Australian dingoes arrived in Australia 5,000-8,000 BP, and there is debate whether they were domesticated before their arrival. The Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process, while GSDs are a breed dog selected from existing domestic dogs in the late 1800s. We conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each canid. We found 75% of dingoes made eye contact in each phase. In contrast, 86% of Basenjis and 96% of GSDs made eye contact. Dingoes also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called actively. Sociability, quantified as a canid coming within 1 m of the experimenter, was lowest for dingoes and highest for GSDs. For sociability duration, dingoes spent less time within 1 m of the experimenter than either breed dog. When compared with previous studies, these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in Australia. However, it remains possible that the accumulation of mutations since colonization has obscured historical behaviors, and dingoes now exist in a feralized retamed cycle. Additional morphological and genetic data are required to resolve this conundrum.
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Affiliation(s)
- J William O Ballard
- Department of Ecology, Environment, and Evolution, Latrobe University, Melbourne, VIC 3086, Australia
- Department of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Chloe Gardner
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Richard I Kemp
- School of Psychology, UNSW Sydney, Sydney, NSW 2052, Australia
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Before Azaria: A Historical Perspective on Dingo Attacks. Animals (Basel) 2022; 12:ani12121592. [PMID: 35739928 PMCID: PMC9219548 DOI: 10.3390/ani12121592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
This paper investigates the origin of the once popular belief in Australian society that wild dingoes do not attack humans. To address this problem, a digital repository of archived newspaper articles and other published texts written between 1788 and 1979 were searched for references to dingoes attacking non-Indigenous people. A total of 52 accounts spanning the period between 1804 and 1928 was identified. A comparison of these historical accounts with the details of modern dingo attacks suggests that at least some of the former are credible. The paper also examined commonly held attitudes towards dingoes in past Australian society based on historical print media articles and other records. Early chroniclers of Australian rural life and culture maintained that dingoes occasionally killed and ate humans out of a predatory motivation. By the early decades of the 20th century, however, an opposing view of this species had emerged: namely, that dingoes were timid animals that continued to pose a danger to livestock, but never to people. This change in the cultural image of dingoes can possibly be linked to more than a century of lethal dingo control efforts greatly reducing the frequency of human–dingo interactions in the most populous parts of the country. This intensive culling may also have expunged the wild genetic pool of dingoes that exhibited bold behaviour around people and/or created a dingo population that was largely wary of humans.
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8
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Field MA, Yadav S, Dudchenko O, Esvaran M, Rosen BD, Skvortsova K, Edwards RJ, Keilwagen J, Cochran BJ, Manandhar B, Bustamante S, Rasmussen JA, Melvin RG, Chernoff B, Omer A, Colaric Z, Chan EKF, Minoche AE, Smith TPL, Gilbert MTP, Bogdanovic O, Zammit RA, Thomas T, Aiden EL, Ballard JWO. The Australian dingo is an early offshoot of modern breed dogs. SCIENCE ADVANCES 2022; 8:eabm5944. [PMID: 35452284 PMCID: PMC9032958 DOI: 10.1126/sciadv.abm5944] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/09/2022] [Indexed: 06/11/2023]
Abstract
Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.
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Affiliation(s)
- Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD 4878, Australia
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Meera Esvaran
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Blake J. Cochran
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bikash Manandhar
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
| | - Richard G. Melvin
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, Duluth, MN 55812, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth and Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Arina Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eva K. F. Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle, NSW 2300, Australia
| | - Andre E. Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Timothy P. L. Smith
- U.S. Meat Animal Research Center, Agricultural Research Service, USDA, Rd 313, Clay Center, NE 68933, USA
| | - M. Thomas P. Gilbert
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Erez L. Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical 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 University, Pudong 201210, China
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J. William O. Ballard
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, VIC 3086, Australia
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC 3052, Australia
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9
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The Social Lives of Free-Ranging Cats. Animals (Basel) 2022; 12:ani12010126. [PMID: 35011232 PMCID: PMC8749887 DOI: 10.3390/ani12010126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the diversity of social situations in which cats live, the degree to which free-ranging cats (FRCs) are social is still debated. The aim of this review is to explore the literature on the social behavior of FRCs. A search of two major databases revealed that observations of intraspecies and interspecies social interactions have been conducted. The intraspecific social dynamics of FRCs differ based on group of cats surveyed. Some groups display strong social bonds and preferential affiliations, while other groups are more loosely associated and display little to no social interaction. Factors impacting FRC conspecific interactions include cat body size, cat social rank, cat individuality, cat age, relationship to conspecific (kin/familiar), cat sex, level of human caretaking, presence of food, the health of the individual, or sexual status of conspecifics. Interspecies interactions also occur with humans and wildlife. The human’s sex and the weather conditions on the day of interaction have been shown to impact FRC social behavior. Interactions with wildlife were strongly linked to the timing of cat feeding events. These findings support the idea that FRCs are “social generalists” who display flexibility in their social behavior. The social lives of FRCs exist, are complex, and deserve further study.
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Niego A, Benítez-Burraco A. Are feralization and domestication truly mirror processes? ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2021.1975314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amy Niego
- PhD Program, Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain (E-mail: )
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11
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Metabolomics shows the Australian dingo has a unique plasma profile. Sci Rep 2021; 11:5245. [PMID: 33664285 PMCID: PMC7933249 DOI: 10.1038/s41598-021-84411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 01/02/2023] Open
Abstract
Dingoes occupy a wide range of the Australian mainland and play a crucial role as an apex predator with a generalist omnivorous feeding behaviour. Dingoes are ecologically, phenotypically and behaviourally distinct from modern breed dogs and have not undergone artificial selection since their arrival in Australia. In contrast, humans have selected breed dogs for novel and desirable traits. First, we examine whether the distinct evolutionary histories of dingoes and domestic dogs has lead to differences in plasma metabolomes. We study metabolite composition differences between dingoes (n = 15) and two domestic dog breeds (Basenji n = 9 and German Shepherd Dog (GSD) n = 10). Liquid chromatography mass spectrometry, type II and type III ANOVA with post-hoc tests and adjustments for multiple comparisons were used for data evaluation. After accounting for within group variation, 62 significant metabolite differences were detected between dingoes and domestic dogs, with the majority of differences in protein (n = 14) and lipid metabolites (n = 12), mostly lower in dingoes. Most differences were observed between dingoes and domestic dogs and fewest between the domestic dog breeds. Next, we collect a second set of data to investigate variation between pure dingoes (n = 10) and dingo-dog hybrids (n = 10) as hybridisation is common in regional Australia. We detected no significant metabolite differences between dingoes and dingo-dog hybrids after Bonferroni correction. However, power analysis showed that increasing the sample size to 15 could result in differences in uridine 5′-diphosphogalactose (UDPgal) levels related to galactose metabolism. We suggest this may be linked to an increase in Amylase 2B copy number in hybrids. Our study illustrates that the dingo metabolome is significantly different from domestic dog breeds and hybridisation is likely to influence carbohydrate metabolism.
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Shipman P. What the dingo says about dog domestication. Anat Rec (Hoboken) 2020; 304:19-30. [PMID: 33103861 PMCID: PMC7756258 DOI: 10.1002/ar.24517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 01/27/2023]
Abstract
Worldwide, dogs (Canis familiaris) are certainly the most common domesticate (900 million according to the World Atlas) and are sometimes used as a proxy for human presence. Dogs were the first and therefore arguably most important species ever to be domesticated. It is widely accepted that the domestic dog is a descendent of Pleistocene gray wolves (Canis lupus), possibly of a population now extinct. How can an extant canid, the dingo (Canis dingo or Canis familiaris), whose status as a species and as a domesticate is controversial, improve our understanding of the ancient process of domesticating the dog? Here I review anatomical, behavioral, biogeographic, and molecular evidence on the appropriate status of dingoes in a historical context. Dingoes are now the major apex predator in Australia aside from humans. Different sources of evidence have suggested different times of arrival in Greater Australia for humans and canids and different degrees of intimacy or domestication between humans and canids. Just as domestic dogs are often accorded near‐human status, dingoes have special relationships with human families, but reproductively and behaviorally they remain independent. In sum, traits of the dingo reflect its lupine ancestry, a certain degree of accommodation to human company, and unique adaptations to the demands of its habitat. Emphasizing that domestication is a long‐term process, not an event, helps clarify the ambiguous status of dingoes.
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Affiliation(s)
- Pat Shipman
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, USA
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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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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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