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Leeb T. Special Issue: "Canine Genetics 2". Genes (Basel) 2023; 14:1930. [PMID: 37895280 PMCID: PMC10606197 DOI: 10.3390/genes14101930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Wolves were the first animal species to become domesticated by humans, approximately 30,000-50,000 years ago. Human-directed dog breeding over thousands of generations has generated more than 350 recognized breeds displaying surprisingly different phenotypes with respect to morphology, behavior and disease predispositions. The domestication of wolves and the subsequent breeding of dogs can be viewed as one of humankind's oldest and largest genetic experiments and provides us with unique opportunities for research. Dogs have not only become human's best friend but were also described as geneticists' best friend in a past issue of Science. In recognition of the importance of canine genetics, this Special Issue, entitled "Canine Genetics 2", was compiled. It represents a sequel to the former Special Issue "Canine Genetics", which was published in 2019. During the last 15 years, the canine community has heavily relied on a reference genome derived from the female Boxer Tasha. "Canine Genetics 2" includes an article describing a greatly improved version of this important community resource. This Special Issue further contains several reports related to monogenic or complex inherited diseases in dogs. Finally, important aspects of wild canid research, genetic diversity in different populations and canine morphology were investigated.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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2
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de Alcântara LP, Santana JA, Clark Xavier RG, Tinoco HP, Coelho CM, Dos Santos DO, Santos RL, Nogueira de Carvalho MP, Silveira Silva RO. ANTIMICROBIAL SUSCEPTIBILITY OF STAPHYLOCOCCUS SPP. ISOLATED FROM FELIDS AND CANIDS IN BELO HORIZONTE ZOO, BRAZIL. J Zoo Wildl Med 2023; 54:584-592. [PMID: 37817625 DOI: 10.1638/2022-0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2023] [Indexed: 10/12/2023] Open
Abstract
The epidemiology of Staphylococcus spp. has become a major concern among humans and animals due to increasing antimicrobial resistance and frequent reports of infection. Despite the importance of animals as reservoirs for staphylococci, little is known about the epidemiology of Staphylococcus spp. in most nondomestic species, including canids and felids. This study evaluated the frequency, distribution, and patterns of antimicrobial resistance of staphylococcal species isolated from captive felids and canids from Belo Horizonte Zoo, Brazil. Rectal, oral, and nasal swabs from apparently healthy maned wolves (Chrysocyon brachyurus, n= 7), a lion (Panthera leo, n = 1), jaguars (Panthera onca, n = 3), and one swab of a cougar (Puma concolor) with an ear infection were streaked onto mannitol salt agar. Colonies identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, polymerase chain reaction for the Staphylococcus intermedius group (SIG), and 16S rRNA gene sequencing. Isolates were subjected to antimicrobial susceptibility tests and Staphylococcus pseudintermedius strains were subjected to multilocus sequence typing. Staphylococcus species were isolated from 24 of the 34 samples (70.6%). Among the isolated strains, S. pseudintermedius and Staphylococcus felis were the most frequent species (41.7 and 25%, respectively). Five novel sequence types were identified among the S. pseudintermedius isolates. Resistance to tetracycline (7/24, 29.2%) or penicillin (6/23, 26.1%) was significantly higher than the other antimicrobial agents tested (P < 0.05). One isolate, Staphylococcus nepalensis, was positive for mecA and resistant to five antimicrobials, and was thus classified as multidrug-resistant. The present work suggests that maned wolves are natural hosts of SIG and also reports the isolation of S. felis in sick and healthy, captive, nondomestic carnivores. The isolated staphylococci were susceptible to most classes of antimicrobials tested. However, the multidrug-resistance capability of an S. nepalensis strain reinforces the hypothesis that felids and canids act as reservoirs of pathogens with antimicrobial resistance.
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Affiliation(s)
| | - Jordana Almeida Santana
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil, 31270-901
| | | | - Herlandes Penha Tinoco
- Municipal Parks and Zoobotanic Foundation of Belo Horizonte, Belo Horizonte, MG, Brazil, 31365-450
| | - Carlyle Mendes Coelho
- Municipal Parks and Zoobotanic Foundation of Belo Horizonte, Belo Horizonte, MG, Brazil, 31365-450
| | | | - Renato Lima Santos
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil, 31270-901
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3
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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; 12:7086663. [PMID: 36994871 DOI: 10.1093/gigascience/giad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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
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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4
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Meiring C, Schurz H, van Helden P, Hoal E, Tromp G, Kinnear C, Kleynhans L, Glanzmann B, van Schalkwyk L, Miller M, Möller M. African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity. Sci Rep 2022; 12:14979. [PMID: 36056068 PMCID: PMC9440078 DOI: 10.1038/s41598-022-19025-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.
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Affiliation(s)
- Christina Meiring
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa.
| | - Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, PO Box 241, Cape Town, 7500, South Africa
| | - Craig Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Léanie Kleynhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Louis van Schalkwyk
- Department of Agriculture, Land Reform and Rural Development, PO Box 12, Skukuza, 1350, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Soutpan Road, Pretoria, 0110, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
| | - Michele Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Private bag X1, Merriman Avenue, Stellenbosch, 7600, South Africa
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5
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Chavez DE, Gronau I, Hains T, Dikow RB, Frandsen PB, Figueiró HV, Garcez FS, Tchaicka L, de Paula RC, Rodrigues FHG, Jorge RSP, Lima ES, Songsasen N, Johnson WE, Eizirik E, Koepfli KP, Wayne RK. Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids. Proc Natl Acad Sci U S A 2022; 119:e2205986119. [PMID: 35969758 PMCID: PMC9407222 DOI: 10.1073/pnas.2205986119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.
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Affiliation(s)
- Daniel E. Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya 46150, Israel
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Henrique V. Figueiró
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Fabrício S. Garcez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Ligia Tchaicka
- Rede de Biodiversidade e Biotecnologia da Amazônia, Curso de Pós-Graduação em Recursos Aquáticos e Pesca, Universidade Estadual do Maranhão, São Luis, 2016-8100, Brazil
| | - Rogério C. de Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, 12952-011, Atibaia, Brazil
| | - Flávio H. G. Rodrigues
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rodrigo S. P. Jorge
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado, Instituto Chico Mendes de Conservação da Biodiversidade, Brasilia, 70670-350, Brazil
| | - Edson S. Lima
- Private address, Nova Xavantina, MT, 78690-000, Brazil
| | - Nucharin Songsasen
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Warren E. Johnson
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, 12945-010, Brazil
- Instituto Nacional de Ciência e Tecnologia em Ecologia Evolução Conservação da Biodiverside, Universidade Federal de GoiásGoiânia, 74690-900, Brazil
| | - Klaus-Peter Koepfli
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
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6
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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. Sci Adv 2022; 8:eabm5944. [PMID: 35452284 PMCID: PMC9032958 DOI: 10.1126/sciadv.abm5944] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Taron UH, Paijmans JLA, Barlow A, Preick M, Iyengar A, Drăgușin V, Vasile Ș, Marciszak A, Roblíčková M, Hofreiter M. Ancient DNA from the Asiatic Wild Dog ( Cuon alpinus) from Europe. Genes (Basel) 2021; 12:144. [PMID: 33499169 PMCID: PMC7911384 DOI: 10.3390/genes12020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/11/2023] Open
Abstract
The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.
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Affiliation(s)
- Ulrike H. Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Arati Iyengar
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Virgil Drăgușin
- Emil Racoviţă Institute of Speleology, Romanian Academy, 31 Frumoasă Street, 010986 Bucharest, Romania;
- Research Institute of the University of Bucharest, Earth, Environmental and Life Sciences Division, Panduri 90–92, 050663 Bucharest, Romania
| | - Ștefan Vasile
- Department of Geology, Faculty of Geology and Geophysics, University of Bucharest, 1 Nicolae Bălcescu Avenue, 010041 Bucharest, Romania;
| | - Adrian Marciszak
- Department of Paleozoology, Faculty of Biological Sciences, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland;
| | - Martina Roblíčková
- Moravian Museum, Anthropos Institute, Zelný trh 6, 65937 Brno, Czech Republic;
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
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8
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Letko A, Minor KM, Friedenberg SG, Shelton GD, Salvador JP, Mandigers PJJ, Leegwater PAJ, Winkler PA, Petersen-Jones SM, Stanley BJ, Ekenstedt KJ, Johnson GS, Hansen L, Jagannathan V, Mickelson JR, Drögemüller C. A CNTNAP1 Missense Variant Is Associated with Canine Laryngeal Paralysis and Polyneuropathy. Genes (Basel) 2020; 11:E1426. [PMID: 33261176 PMCID: PMC7761076 DOI: 10.3390/genes11121426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Laryngeal paralysis associated with a generalized polyneuropathy (LPPN) most commonly exists in geriatric dogs from a variety of large and giant breeds. The purpose of this study was to discover the underlying genetic and molecular mechanisms in a younger-onset form of this neurodegenerative disease seen in two closely related giant dog breeds, the Leonberger and Saint Bernard. Neuropathology of an affected dog from each breed showed variable nerve fiber loss and scattered inappropriately thin myelinated fibers. Using across-breed genome-wide association, haplotype analysis, and whole-genome sequencing, we identified a missense variant in the CNTNAP1 gene (c.2810G>A; p.Gly937Glu) in which homozygotes in both studied breeds are affected. CNTNAP1 encodes a contactin-associated protein important for organization of myelinated axons. The herein described likely pathogenic CNTNAP1 variant occurs in unrelated breeds at variable frequencies. Individual homozygous mutant LPPN-affected Labrador retrievers that were on average four years younger than dogs affected by geriatric onset laryngeal paralysis polyneuropathy could be explained by this variant. Pathologic changes in a Labrador retriever nerve biopsy from a homozygous mutant dog were similar to those of the Leonberger and Saint Bernard. The impact of this variant on health in English bulldogs and Irish terriers, two breeds with higher CNTNAP1 variant allele frequencies, remains unclear. Pathogenic variants in CNTNAP1 have previously been reported in human patients with lethal congenital contracture syndrome and hypomyelinating neuropathy, including vocal cord palsy and severe respiratory distress. This is the first report of contactin-associated LPPN in dogs characterized by a deleterious variant that most likely predates modern breed establishment.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - Katie M. Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA;
| | - G. Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Jill Pesayco Salvador
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Paul J. J. Mandigers
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Peter A. J. Leegwater
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Paige A. Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Simon M. Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Kari J. Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Liz Hansen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
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9
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Koupadi K, Fontani F, Ciucani MM, Maini E, De Fanti S, Cattani M, Curci A, Nenzioni G, Reggiani P, Andrews AJ, Sarno S, Bini C, Pelotti S, Caniglia R, Luiselli D, Cilli E. Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age. Genes (Basel) 2020; 11:genes11121409. [PMID: 33256122 PMCID: PMC7761486 DOI: 10.3390/genes11121409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.
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Affiliation(s)
- Kyriaki Koupadi
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of the City of Athens, Makriyianni 2-4, 11742 Athens, Greece;
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
| | - Marta Maria Ciucani
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen, Denmark;
| | - Elena Maini
- ArcheoLaBio—Research Centre for Bioarchaeology, Department of History and Cultures, University of Bologna, Via San Vitale 30, 48121 Ravenna, Italy; (E.M.); (A.C.)
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; (S.D.F.); (S.S.)
- Interdepartmental Centre “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, Via Petroni 26, 40126 Bologna, Italy
| | - Maurizio Cattani
- Department of History and Cultures, University of Bologna, Via San Vitale 30, 48121 Ravenna, Italy;
| | - Antonio Curci
- ArcheoLaBio—Research Centre for Bioarchaeology, Department of History and Cultures, University of Bologna, Via San Vitale 30, 48121 Ravenna, Italy; (E.M.); (A.C.)
| | - Gabriele Nenzioni
- Museo della Preistoria “Luigi Donini”, Via Fratelli Canova 49, 40068 San Lazzaro di Savena, BO, Italy;
| | - Paolo Reggiani
- Paleostudy, Via Martiri delle Foibe 1, 35028 Piove di Sacco, PD, Italy;
| | - Adam J. Andrews
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; (S.D.F.); (S.S.)
| | - Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; (S.D.F.); (S.S.)
| | - Carla Bini
- Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy; (C.B.); (S.P.)
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy; (C.B.); (S.P.)
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca’ Fornacetta 9, 40064 Ozzano dell’Emilia, BO, Italy;
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
- Correspondence:
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10
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Abstract
The association between phenotype and ecology is essential for understanding the environmental drivers of morphological evolution. This is a particularly challenging task when dealing with complex traits, such as the skull, where multiple selective pressures are at play and evolution might be constrained by ontogenetic and genetic factors. I integrate morphometric tools, comparative methods, and quantitative genetics to investigate how ontogenetic constraints and selection might have interacted during the evolution of the skull in extant Canidae. The results confirm that the evolution of cranial morphology was largely adaptive and molded by changes in diet composition. While the investigation of the adaptive landscape reveals two main selective lines of least resistance (one associated with size and one associated with functional shape features), rates of evolution along size were higher than those found for shape dimensions, suggesting the influence of constraints on morphological evolution. Structural modeling analyses revealed that size, which is the line of most genetic/phenotypic variation, might have acted as a constraint, negatively impacting dietary evolution. Constraints might have been overcome in the case of selection for the consumption of large prey by associating strong selection along both size and shape directions. The results obtained here show that microevolutionary constraints may have played a role in shaping macroevolutionary patterns of morphological evolution.
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11
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Zhang SJ, Wang GD, Ma P, Zhang LL, Yin TT, Liu YH, Otecko NO, Wang M, Ma YP, Wang L, Mao B, Savolainen P, Zhang YP. Genomic regions under selection in the feralization of the dingoes. Nat Commun 2020; 11:671. [PMID: 32015346 PMCID: PMC6997406 DOI: 10.1038/s41467-020-14515-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 12/16/2019] [Indexed: 12/30/2022] Open
Abstract
Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.
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Affiliation(s)
- Shao-Jie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Liang-Liang Zhang
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Meng Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Ya-Ping Ma
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Peter Savolainen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China.
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12
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Smith O, Dunshea G, Sinding MHS, Fedorov S, Germonpre M, Bocherens H, Gilbert MTP. Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. PLoS Biol 2019; 17:e3000166. [PMID: 31361744 PMCID: PMC6667121 DOI: 10.1371/journal.pbio.3000166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data’s authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology. Ancient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions, ancient RNA can survive well enough to show tissue specificity even in mammalian soft tissues.
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Affiliation(s)
- Oliver Smith
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Glenn Dunshea
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S. Sinding
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, Yakutsk, Russia
| | - Mietje Germonpre
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Science, Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - M. T. P. Gilbert
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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13
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Chavez DE, Gronau I, Hains T, Kliver S, Koepfli KP, Wayne RK. Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus). Sci Rep 2019; 9:8329. [PMID: 31171819 PMCID: PMC6554312 DOI: 10.1038/s41598-019-44772-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/22/2019] [Indexed: 12/02/2022] Open
Abstract
Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.
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Affiliation(s)
- Daniel E Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), Herzliya, 46150, Israel
| | - Taylor Hains
- Environmental Science and Policy, Johns Hopkins University, Washington, D.C., 20036, USA
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Novosibirsk, 630090, Russian Federation
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C., 20008, USA
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
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14
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Tsai KL, Evans JM, Noorai RE, Starr-Moss AN, Clark LA. Novel Y Chromosome Retrocopies in Canids Revealed through a Genome-Wide Association Study for Sex. Genes (Basel) 2019; 10:genes10040320. [PMID: 31027231 PMCID: PMC6523286 DOI: 10.3390/genes10040320] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022] Open
Abstract
The lack of an annotated reference sequence for the canine Y chromosome has limited evolutionary studies, as well as our understanding of the role of Y-linked sequences in phenotypes with a sex bias. In genome-wide association studies (GWASs), we observed spurious associations with autosomal SNPs when sex was unbalanced in case-control cohorts and hypothesized that a subset of SNPs mapped to autosomes are in fact sex-linked. Using the Illumina 230K CanineHD array in a GWAS for sex, we identified SNPs that amplify in both sexes but possess significant allele frequency differences between males and females. We found 48 SNPs mapping to 14 regions of eight autosomes and the X chromosome that are Y-linked, appearing heterozygous in males and monomorphic in females. Within these 14 regions are eight genes: three autosomal and five X-linked. We investigated the autosomal genes (MITF, PPP2CB, and WNK1) and determined that the SNPs are diverged nucleotides in retrocopies that have transposed to the Y chromosome. MITFY and WNK1Y are expressed and appeared recently in the Canidae lineage, whereas PPP2CBY represents a much older insertion with no evidence of expression in the dog. This work reveals novel canid Y chromosome sequences and provides evidence for gene transposition to the Y from autosomes and the X.
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Affiliation(s)
- Kate L Tsai
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Jacquelyn M Evans
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA.
| | - Rooksana E Noorai
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC 29634, USA.
| | - Alison N Starr-Moss
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Leigh Anne Clark
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
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15
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Modi S, Mondol S, Ghaskadbi P, Hussain Z, Nigam P, Habib B. Noninvasive DNA-based species and sex identification of Asiatic wild dog ( Cuon alpinus). J Genet 2018; 97:1457-1461. [PMID: 30555094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Asiatic wild dog (Cuon alpinus) or dhole is an endangered canid with fragmented distribution in South, East and Southeast Asia. The remaining populations of this species face severe conservation challenges from anthropogenic interventions, but only limited information is available at population and demography levels. Here, we describe the novel molecular approaches for unambiguous species and sex identification from noninvasively collected dhole samples. We successfully tested these assays on 130 field-collected dhole faecal samples from the Vidarbha part of central Indian tiger landscape that resulted in 97 and 77% successrates in species and sex identification, respectively. These accurate, fast and cheap molecular approaches prove the efficacy of such methods in gathering ecological data from this elusive, endangered canid and show their application in generating population level information from noninvasive samples.
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Affiliation(s)
- Shrushti Modi
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, India.
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16
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First IVF puppies 'open the door' for the conservation of endangered canids. Vet Rec 2015; 177:612. [PMID: 26679908 DOI: 10.1136/vr.h6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Gimranov DO, Kosintsev PA, Smirnov NG. The late Neopleistocene dhole (Carnivora, Canidae, Cuon alpinus Pallas, 1811) from the Urals. Dokl Biol Sci 2015; 464:248-250. [PMID: 26530068 DOI: 10.1134/s0012496615050117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 06/05/2023]
Abstract
Morphotypic and morphometric analyses of the M2 tooth found in the Late Pleistocene deposits of the Ignatievskaya Cave (southern Urals) demonstrate that this tooth belongs to the dhole (Cuon alpinus Pallas, 1811). This is the first reliable evidence for the presence of the dhole in the Urals. Radiocarbon dating and associated theriofauna allow the tooth to be dated to the first half of the late Neopleistocene or, more precisely, to marine isotope stages (MISs) 3 and 4.
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Affiliation(s)
- D O Gimranov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russia
| | - P A Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russia
| | - N G Smirnov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russia.
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Lee EJ, Merriwether DA, Kasparov AK, Nikolskiy PA, Sotnikova MV, Pavlova EY, Pitulko VV. Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog. PLoS One 2015; 10:e0125759. [PMID: 26018528 PMCID: PMC4446326 DOI: 10.1371/journal.pone.0125759] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/26/2015] [Indexed: 11/18/2022] Open
Abstract
Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.
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Affiliation(s)
- Esther J. Lee
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, United States of America
- * E-mail:
| | - D. Andrew Merriwether
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
| | - Alexei K. Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | | | - Vladimir V. Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
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Becker PA, Miller PS, Gunther MS, Somers MJ, Wildt DE, Maldonado JE. Inbreeding avoidance influences the viability of reintroduced populations of African wild dogs (Lycaon pictus). PLoS One 2012; 7:e37181. [PMID: 22615933 PMCID: PMC3353914 DOI: 10.1371/journal.pone.0037181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 04/17/2012] [Indexed: 11/19/2022] Open
Abstract
The conservation of many fragmented and small populations of endangered African wild dogs (Lycaon pictus) relies on understanding the natural processes affecting genetic diversity, demographics, and future viability. We used extensive behavioural, life-history, and genetic data from reintroduced African wild dogs in South Africa to (1) test for inbreeding avoidance via mate selection and (2) model the potential consequences of avoidance on population persistence. Results suggested that wild dogs avoided mating with kin. Inbreeding was rare in natal packs, after reproductive vacancies, and between sibling cohorts (observed on 0.8%, 12.5%, and 3.8% of occasions, respectively). Only one of the six (16.7%) breeding pairs confirmed as third-order (or closer) kin consisted of animals that were familiar with each other, while no other paired individuals had any prior association. Computer-simulated populations allowed to experience inbreeding had only a 1.6% probability of extinction within 100 years, whereas all populations avoiding incestuous matings became extinct due to the absence of unrelated mates. Populations that avoided mating with first-order relatives became extinct after 63 years compared with persistence of 37 and 19 years for those also prevented from second-order and third-order matings, respectively. Although stronger inbreeding avoidance maintains significantly more genetic variation, our results demonstrate the potentially severe demographic impacts of reduced numbers of suitable mates on the future viability of small, isolated wild dog populations. The rapid rate of population decline suggests that extinction may occur before inbreeding depression is observed.
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Affiliation(s)
- Penny A Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Smithsonian Institution, Washington, District of Columbia, United States of America.
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Poinar H, Fiedel S, King CE, Devault AM, Bos K, Kuch M, Debruyne R. Comment on "DNA from Pre-Clovis Human Coprolites in Oregon, North America". Science 2009; 325:148; author reply 148. [PMID: 19589985 DOI: 10.1126/science.1168182] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9 Canada.
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Abstract
BACKGROUND Population densities of many species throughout the world are changing due to direct persecution as well as anthropogenic habitat modification. These changes may induce or increase the frequency of hybridization among taxa. If extensive, hybridization can threaten the genetic integrity or survival of endangered species. Three native species of the genus Canis, coyote (C. latrans), Mexican wolf (C. lupus baileyi) and red wolf (C. rufus), were historically sympatric in Texas, United States. Human impacts caused the latter two to go extinct in the wild, although they survived in captive breeding programs. Morphological data demonstrate historic reproductive isolation between all three taxa. While the red wolf population was impacted by introgressive hybridization with coyotes as it went extinct in the wild, the impact of hybridization on the Texas populations of the other species is not clear. METHODOLOGY/ PRINCIPAL FINDINGS We surveyed variation at maternally and paternally inherited genetic markers (mitochondrial control region sequence and Y chromosome microsatellites) in coyotes from Texas, Mexican wolves and red wolves from the captive breeding programs, and a reference population of coyotes from outside the historic red wolf range. Levels of variation and phylogenetic analyses suggest that hybridization has occasionally taken place between all three species, but that the impact on the coyote population is very small. CONCLUSION/SIGNIFICANCE Our results demonstrate that the factors driving introgressive hybridization in sympatric Texan Canis are multiple and complex. Hybridization is not solely determined by body size or sex, and density-dependent effects do not fully explain the observed pattern either. No evidence of hybridization was identified in the Mexican wolf captive breeding program, but introgression appears to have had a greater impact on the captive red wolves.
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Affiliation(s)
- Frank Hailer
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Center for Conservation and Evolutionary Genetics, National Zoological Park & National Museum of Natural History, Smithsonian Institution, Washington, D. C., United States of America
| | - Jennifer A. Leonard
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Center for Conservation and Evolutionary Genetics, National Zoological Park & National Museum of Natural History, Smithsonian Institution, Washington, D. C., United States of America
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Abstract
Physiological strategies that maximize reproductive success may be phylogenetically constrained or might have a plastic response to different environmental conditions. Among mammals, Canidae lend themselves to the study of these two influences on reproductive physiology because all the species studied to date have been characterized as monestrous (i.e., a single ovulatory event per breeding season), suggesting a phylogenetic effect. Greater flexibility could be associated with environments that are less seasonal, such as the tropics; however, little is known for many of the species from this region. To compensate for this lack of data, two regressions were done on the length of the reproductive season relative to the latitudinal distribution of a species: one with raw data and another with phylogenetically independent contrasts. There was a significant negative relationship, independent of phylogeny, with canids that have longer breeding seasons occurring at lower latitudes. In contrast, the pervasiveness of monestrus within Canidae appears to be phylogenetically constrained by their pairing/packing life and is most likely associated with monogamy. The persistence of the monestrous condition is supported by a captive study where a tropical canid, the fennec fox, Vulpes zerda, never exhibited polyestrous cycles despite a constant photoperiod (12L : 12D).
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Affiliation(s)
- Carolina Valdespino
- Departamento de Biodiversidad y Ecología Animal, Instituto de Ecología, A. C., Xalapa, 91070 Veracruz, Mexico.
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Abstract
The remarkable responsiveness of dog morphology to selection is a testament to the mutability of mammals. The genetic sources of this morphological variation are largely unknown, but some portion is due to tandem repeat length variation in genes involved in development. Previous analysis of tandem repeats in coding regions of developmental genes revealed fewer interruptions in repeat sequences in dogs than in the orthologous repeats in humans, as well as higher levels of polymorphism, but the fragmentary nature of the available dog genome sequence thwarted attempts to distinguish between locus-specific and genome-wide origins of this disparity. Using whole-genome analyses of the human and recently completed dog genomes, we show that dogs possess a genome-wide increase in the basal germ-line slippage mutation rate. Building on the approach that gave rise to the initial observation in dogs, we sequenced 55 coding repeat regions in 42 species representing 10 major carnivore clades and found that a genome-wide elevated slippage mutation rate is a derived character shared by diverse wild canids, distinguishing them from other Carnivora. A similarly heightened slippage profile was also detected in rodents, another taxon exhibiting high diversity and rapid evolvability. The correlation of enhanced slippage rates with major evolutionary radiations suggests that the possession of a "slippery" genome may bestow on some taxa greater potential for rapid evolutionary change.
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Affiliation(s)
- Jeffrey Laidlaw
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
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Abstract
In this issue of Cell, Murgia et al. (2006) confirm that the infectious agent of canine transmissible venereal tumor is the cancer cell itself and that the tumor is clonal in origin. Their findings have implications for understanding the relationship between genome instability and transmissible cancer and for conservation biology, canine genomics, and companion animal medicine.
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Affiliation(s)
- Bridgett M VonHoldt
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Murgia C, Pritchard JK, Kim SY, Fassati A, Weiss RA. Clonal origin and evolution of a transmissible cancer. Cell 2006; 126:477-87. [PMID: 16901782 PMCID: PMC2593932 DOI: 10.1016/j.cell.2006.05.051] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/15/2006] [Accepted: 05/25/2006] [Indexed: 01/08/2023]
Abstract
The transmissible agent causing canine transmissible venereal tumor (CTVT) is thought to be the tumor cell itself. To test this hypothesis, we analyzed genetic markers including major histocompatibility (MHC) genes, microsatellites, and mitochondrial DNA (mtDNA) in naturally occurring tumors and matched blood samples. In each case, the tumor is genetically distinct from its host. Moreover, tumors collected from 40 dogs in 5 continents are derived from a single neoplastic clone that has diverged into two subclades. Phylogenetic analyses indicate that CTVT most likely originated from a wolf or an East Asian breed of dog between 200 and 2500 years ago. Although CTVT is highly aneuploid, it has a remarkably stable genotype. During progressive growth, CTVT downmodulates MHC antigen expression. Our findings have implications for understanding genome instability in cancer, natural transplantation of allografts, and the capacity of a somatic cell to evolve into a transmissible parasite.
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Affiliation(s)
- Claudio Murgia
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - Jonathan K. Pritchard
- Department of Human Genetics, University of Chicago, CLSC–507, 920 East 58th Street, Chicago, IL 60637, USA
| | - Su Yeon Kim
- Department of Statistics, University of Chicago, CLSC–507, 920 East 58th Street, Chicago, IL 60637, USA
| | - Ariberto Fassati
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - Robin A. Weiss
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T 4JF, UK
- Contact:
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Bardeleben C, Moore RL, Wayne RK. A molecular phylogeny of the Canidae based on six nuclear loci. Mol Phylogenet Evol 2005; 37:815-31. [PMID: 16213754 DOI: 10.1016/j.ympev.2005.07.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Revised: 07/08/2005] [Accepted: 07/28/2005] [Indexed: 11/15/2022]
Abstract
We have reconstructed the phylogenetic relationships of 23 species in the dog family, Canidae, using DNA sequence data from six nuclear loci. Individual gene trees were generated with maximum parsimony (MP) and maximum likelihood (ML) analysis. In general, these individual gene trees were not well resolved, but several identical groupings were supported by more than one locus. Phylogenetic analysis with a data set combining the six nuclear loci using MP, ML, and Bayesian approaches produced a more resolved tree that agreed with previously published mitochondrial trees in finding three well-defined clades, including the red fox-like canids, the South American foxes, and the wolf-like canids. In addition, the nuclear data set provides novel indel support for several previously inferred clades. Differences between trees derived from the nuclear data and those from the mitochondrial data include the grouping of the bush dog and maned wolf into a clade with the South American foxes, the grouping of the side-striped jackal (Canis adustus) and black-backed jackal (Canis mesomelas) and the grouping of the bat-eared fox (Otocyon megalotis) with the raccoon dog (Nycteruetes procyonoides). We also analyzed the combined nuclear+mitochondrial tree. Many nodes that were strongly supported in the nuclear tree or the mitochondrial tree remained strongly supported in the nuclear+mitochondrial tree. Relationships within the clades containing the red fox-like canids and South American canids are well resolved, whereas the relationships among the wolf-like canids remain largely undetermined. The lack of resolution within the wolf-like canids may be due to their recent divergence and insufficient time for the accumulation of phylogenetically informative signal.
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Affiliation(s)
- Carolyne Bardeleben
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-1606, USA.
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Abstract
The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India.
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Affiliation(s)
- A Iyengar
- Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Pienkowska-Schelling A, Zawada M, Schelling C. A canine X chromosome painting probe applied to four canid species: close relationship of a heterochromatic-like sequence between the dog and the blue fox. J Anim Breed Genet 2005; 122 Suppl 1:54-9. [PMID: 16130457 DOI: 10.1111/j.1439-0388.2005.00509.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microdissection of chromosomes is an invaluable tool to physically isolate single chromosomes, chromosome-arms or chromosome-bands and, subsequently generate painting probes with which numerical or structural aberrations of chromosomes can be studied. In addition, such painting probes can be used to compare karyotypic relationships among mammalian species. For the present study a canine whole X chromosome painting probe was prepared by means of conventional microdissection and degenerate-oligonucleotide-primed PCR. The application of this paint to the chromosomes of the domestic dog, red fox, blue fox and Chinese raccoon dog revealed hybridization to the entire X chromosome and the pseudo-autosomal region of the Y chromosome in all four species analysed. In the blue fox the same paint revealed additional strong hybridization signals on the heterochromatic arms after low-stringent posthybridization washes. The present study indicates the existence of an ancient canid heterochromatic-like DNA sequence, which survived in the proximal part of the X chromosome of all species studied and, in addition, was involved in the formation of heterochromatic arms in the blue fox.
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Affiliation(s)
- A Pienkowska-Schelling
- Department of Animal Genetics and Breeding, Agricultural University of Poznan, Poznan, Poland
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Bardeleben C, Moore RL, Wayne RK. Isolation and Molecular Evolution of the Selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) Genes in the Dog Family, Canidae. Mol Biol Evol 2004; 22:347-59. [PMID: 15496554 DOI: 10.1093/molbev/msi022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In an effort to identify rapidly evolving nuclear sequences useful for phylogenetic analyses of closely related species, we isolated two genes transcribed by RNA polymerase III (pol III), the selenocysteine tRNA gene (TRSP) and an RNase P RNA (RPPH1) gene from the domestic dog (Canis familiaris). We focus on genes transcribed by pol III because their coding regions are small (generally 100-300 base pairs [bp]) and their essential promoter elements are located within a couple of hundred bps upstream of the coding region. Therefore, we predicted that regions flanking the coding region and outside of the promoter elements would be free of constraint and would evolve rapidly. We amplified TRSP from 23 canids and RPPH1 from 12 canids and analyzed the molecular evolution of these genes and their utility as phylogenetic markers for resolving relationships among species in Canidae. We compared the rate of evolution of the gene-flanking regions to other noncoding regions of nuclear DNA (introns) and to the mitochondrial encoded COII gene. Alignment of TRSP from 23 canids revealed that regions directly adjacent to the coding region display high sequence variability. We discuss this pattern in terms of functional mechanisms of transcription. Although the flanking regions evolve no faster than introns, both genes were found to be useful phylogenetic markers, in part, because of the synapomorphic indels found in the flanking regions. Gene trees generated from the TRSP and RPPH1 loci were generally in agreement with the published mtDNA phylogeny and are the first phylogeny of Canidae based on nuclear sequences.
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Affiliation(s)
- Carolyne Bardeleben
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
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