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Perfilyeva A, Bespalova K, Kuzovleva Y, Mussabayev R, Begmanova М, Amirgalyeva A, Vishnyakova O, Nazarenko I, Zhaxsylykova A, Yerzhan A, Perfilyeva Y, Dzhaembaeva T, Khamchukova A, Plakhov K, Torekhanov A, Djansugurova L, Zhunussova G, Bekmanov B. Genetic diversity and origin of Kazakh Tobet Dogs. Sci Rep 2024; 14:23137. [PMID: 39367220 PMCID: PMC11452641 DOI: 10.1038/s41598-024-74061-9] [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: 08/07/2024] [Accepted: 09/23/2024] [Indexed: 10/06/2024] Open
Abstract
The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.
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Affiliation(s)
- Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Kira Bespalova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan.
| | - Yelena Kuzovleva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Rustam Mussabayev
- Laboratory of Informational Processes Analysis and Modelling, Institute of Information and Computational Technologies, Almaty, 050000, Kazakhstan
| | - Мamura Begmanova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Almira Amirgalyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Olga Vishnyakova
- Department of Сynology, Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", Almaty, 050008, Kazakhstan
| | - Inna Nazarenko
- Department of Сynology, Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", Astana, 020000, Kazakhstan
| | - Assel Zhaxsylykova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Arailym Yerzhan
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Yuliya Perfilyeva
- Laboratory of Molecular Immunology and Immunobiotechnology, M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, Almaty, 050012, Kazakhstan
| | | | - Anna Khamchukova
- Laboratory of Biocenology and Hunting management, Institute of Zoology, Almaty, 050060, Kazakhstan
| | - Konstantin Plakhov
- Laboratory of Biocenology and Hunting management, Institute of Zoology, Almaty, 050060, Kazakhstan
| | - Aibyn Torekhanov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty, 050071, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
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2
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Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population. Genome Biol Evol 2024; 16:evae130. [PMID: 38913571 PMCID: PMC11221432 DOI: 10.1093/gbe/evae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
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Affiliation(s)
- Ana V Leon-Apodaca
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | - Andres del Castillo
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabriel C Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
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3
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Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic consequences of isolation and inbreeding in an island dingo population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557950. [PMID: 37745583 PMCID: PMC10516007 DOI: 10.1101/2023.09.15.557950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
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Affiliation(s)
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | | | - Gabriel C. Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, PA, USA
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Spatola GJ, Buckley RM, Dillon M, Dutrow EV, Betz JA, Pilot M, Parker HG, Bogdanowicz W, Thomas R, Chyzhevskyi I, Milinevsky G, Kleiman N, Breen M, Ostrander EA, Mousseau TA. The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone. SCIENCE ADVANCES 2023; 9:eade2537. [PMID: 36867701 PMCID: PMC9984172 DOI: 10.1126/sciadv.ade2537] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, as well as those 15 to 45 kilometers from the disaster site. Genome-wide profiles from Chernobyl, purebred and free-breeding dogs, worldwide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. Analysis of shared ancestral genome segments highlights differences in the extent and timing of western breed introgression. Kinship analysis reveals 15 families, with the largest spanning all collection sites within the radioactive exclusion zone, reflecting migration of dogs between the power plant and Chernobyl City. This study presents the first characterization of a domestic species in Chernobyl, establishing their importance for genetic studies into the effects of exposure to long-term, low-dose ionizing radiation.
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Affiliation(s)
- Gabriella J Spatola
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megan Dillon
- North Carolina State University, Raleigh NC 27695, USA
| | - Emily V Dutrow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Rachel Thomas
- North Carolina State University, Raleigh NC 27695, USA
| | | | - Gennadi Milinevsky
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- International Center of Future Science, College of Physics, Jilin University, Changchun 130012, China
| | | | - Matthew Breen
- North Carolina State University, Raleigh NC 27695, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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5
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Conroy GC, Lamont RW, Bridges L, Stephens D, Wardell-Johnson A, Ogbourne SM. Conservation concerns associated with low genetic diversity for K'gari-Fraser Island dingoes. Sci Rep 2021; 11:9503. [PMID: 33947920 PMCID: PMC8097078 DOI: 10.1038/s41598-021-89056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
The dingo population on world heritage-listed K'gari-Fraser Island (K'gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K'gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K'gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.
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Affiliation(s)
- G C Conroy
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia. .,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
| | - R W Lamont
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - L Bridges
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - D Stephens
- Zoological Genetics, Inglewood, Adelaide, SA, 5133, Australia
| | - A Wardell-Johnson
- Senior Professional Fellow, Curtin University, Bentley, WA, Australia
| | - S M Ogbourne
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
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6
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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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7
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Genetic diversity and population structure of African village dogs based on microsatellite and immunity-related molecular markers. PLoS One 2018; 13:e0199506. [PMID: 29940023 PMCID: PMC6016929 DOI: 10.1371/journal.pone.0199506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 06/10/2018] [Indexed: 11/19/2022] Open
Abstract
The village and street dogs represent a unique model of canine populations. In the absence of selective breeding and veterinary care, they are subject mostly to natural selection. Their analyses contribute to understanding general mechanisms governing the genetic diversity, evolution and adaptation. In this study, we analyzed the genetic diversity and population structure of African village dogs living in villages in three different geographical areas in Northern Kenya. Data obtained for neutral microsatellite molecular markers were compared with those computed for potentially non-neutral markers of candidate immunity-related genes. The neutral genetic diversity was similar to other comparable village dog populations studied so far. The overall genetic diversity in microsatellites was higher than the diversity of European pure breeds, but it was similar to the range of diversity observed in a group composed of many European breeds, indicating that the African population has maintained a large proportion of the genetic diversity of the canine species as a whole. Microsatellite marker diversity indicated that the entire population is subdivided into three genetically distinct, although closely related subpopulations. This genetical partitioning corresponded to their geographical separation and the observed gene flow well correlated with the communication patterns among the three localities. In contrast to neutral microsatellites, the genetic diversity in immunity-related candidate SNP markers was similar across all three subpopulations and to the European group. It seems that the genetic structure of this particular population of Kenyan village dogs is mostly determined by geographical and anthropogenic factors influencing the gene flow between various subpopulations rather than by biological factors, such as genetic contribution of original migrating populations and/or the pathogen-mediated selection. On the other hand, the study of oldest surviving dogs suggested a biological mechanism, i.e. a possible advantage of the overal heterozygosity marked by the the microsatellite loci analyzed.
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Cairns KM, Shannon LM, Koler-Matznick J, Ballard JWO, Boyko AR. Elucidating biogeographical patterns in Australian native canids using genome wide SNPs. PLoS One 2018; 13:e0198754. [PMID: 29889854 PMCID: PMC5995383 DOI: 10.1371/journal.pone.0198754] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/24/2018] [Indexed: 11/19/2022] Open
Abstract
Dingoes play a strong role in Australia's ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.
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Affiliation(s)
- Kylie M. Cairns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: ,
| | - Laura M. Shannon
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Janice Koler-Matznick
- The New Guinea Singing Dog Conservation Society, Central Point, Oregon, United States of America
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
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Corrieri L, Adda M, Miklósi Á, Kubinyi E. Companion and free-ranging Bali dogs: Environmental links with personality traits in an endemic dog population of South East Asia. PLoS One 2018; 13:e0197354. [PMID: 29870525 PMCID: PMC5988322 DOI: 10.1371/journal.pone.0197354] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/01/2018] [Indexed: 11/18/2022] Open
Abstract
Dogs living on Bali Island have been free-ranging for thousands of years. A large group of expatriates sometimes adopt Bali dogs and keep them restricted to their houses and backyards, as is typical in modern western cultures. This provides us with the unique opportunity to compare the personality traits of dogs to their lifestyle either living as human companions or as free-ranging animals, exploring at the same time the impact of demographic variables (such as age, sex, and neutered status) on personality. After controlling for internal consistency of the scales and between-observer variation, we found that free-ranging Bali dogs were rated as less active, less excitable, less aggressive towards animals, and less inclined to chase animals or humans than Bali dogs living as human companions. Among free-ranging dogs, females were found to be more excitable. Females in the whole sample were also more fearful of people. The results of this preliminary study suggest that a change in lifestyle, i.e. being adopted, and living in a confined environment has negative consequences on some canine personality traits, such as activity/excitability, aggression towards animals, and prey drive.
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Affiliation(s)
- Luca Corrieri
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | - Marco Adda
- Independent Researcher, AEC Anthrozoology Education and Canines, Naples, Italy
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Enikő Kubinyi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
- * E-mail:
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10
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Hirata D, Mano T, Abramov AV, Baryshnikov GF, Kosintsev PA, Murata K, Masuda R. Paternal phylogeographic structure of the brown bear ( Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations. ZOOLOGICAL LETTERS 2017; 3:21. [PMID: 29214050 PMCID: PMC5707830 DOI: 10.1186/s40851-017-0084-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Sex-biased dispersal is widespread among mammals, including the brown bear (Ursus arctos). Previous phylogeographic studies of the brown bear based on maternally inherited mitochondrial DNA have shown intraspecific genetic structuring around the northern hemisphere. The brown bears on Hokkaido Island, northern Japan, comprise three distinct maternal lineages that presumably immigrated to the island from the continent in three different periods. Here, we investigate the paternal genetic structure across northeastern Asia and assess the connectivity among and within intraspecific populations in terms of male-mediated gene flow. RESULTS We analyzed paternally inherited Y-chromosomal DNA sequence data and Y-linked microsatellite data of 124 brown bears from Hokkaido, the southern Kuril Islands (Kunashiri and Etorofu), Sakhalin, and continental Eurasia (Kamchatka Peninsula, Ural Mountains, European Russia, and Tibet). The Hokkaido brown bear population is paternally differentiated from, and lacked recent genetic connectivity with, the continental Eurasian and North American populations. We detected weak spatial genetic structuring of the paternal lineages on Hokkaido, which may have arisen through male-mediated gene flow among natal populations. In addition, our results suggest that the different dispersal patterns between male and female brown bears, combined with the founder effect and subsequent genetic drift, contributed to the makeup of the Etorofu Island population, in which the maternal and paternal lineages show different origins. CONCLUSIONS Brown bears on Hokkaido and the adjacent southern Kuril Islands experienced different maternal and paternal evolutionary histories. Our results indicate that sex-biased dispersal has played a significant role in the evolutionary history of the brown bear in continental populations and in peripheral insular populations, such as on Hokkaido, the southern Kuril Islands, and Sakhalin.
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Affiliation(s)
- Daisuke Hirata
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Tsutomu Mano
- Institute of Environmental Sciences, Hokkaido Research Organization, Sapporo, 080-0819 Japan
| | - Alexei V. Abramov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, 199034 Russia
| | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Russian Academy of Sciences, Ekaterinburg, 620219 Russia
| | - Koichi Murata
- College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880 Japan
| | - Ryuichi Masuda
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
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11
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Cairns KM, Brown SK, Sacks BN, Ballard JWO. Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography. Ecol Evol 2017; 7:9787-9807. [PMID: 29188009 PMCID: PMC5696388 DOI: 10.1002/ece3.3487] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/03/2017] [Accepted: 09/04/2017] [Indexed: 01/07/2023] Open
Abstract
It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.
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Affiliation(s)
- Kylie M Cairns
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Sarah K Brown
- Mammalian Ecology and Conservation Unit Veterinary Genetics Laboratory School of Veterinary Medicine University of California Davis CA USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit Veterinary Genetics Laboratory School of Veterinary Medicine University of California Davis CA USA.,Department of Population, Health and Reproduction School of Veterinary Medicine University of California Davis CA USA
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
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12
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Pires AE, Amorim IR, Borges C, Simões F, Teixeira T, Quaresma A, Petrucci‐Fonseca F, Matos J. New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula. Ecol Evol 2017; 7:4404-4418. [PMID: 28649351 PMCID: PMC5478058 DOI: 10.1002/ece3.2949] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 02/17/2017] [Accepted: 03/05/2017] [Indexed: 12/26/2022] Open
Abstract
This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.
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Affiliation(s)
- Ana Elisabete Pires
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - Isabel R. Amorim
- Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresFaculdade de Ciências Agrárias e do AmbienteAçoresPortugal
| | - Carla Borges
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Fernanda Simões
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Tatiana Teixeira
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Andreia Quaresma
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - Francisco Petrucci‐Fonseca
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - José Matos
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
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13
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Kaewmongkol G, Lukkana N, Yangtara S, Kaewmongkol S, Thengchaisri N, Sirinarumitr T, Jittapalapong S, Fenwick SG. Association of Ehrlichia canis, Hemotropic Mycoplasma spp. and Anaplasma platys and severe anemia in dogs in Thailand. Vet Microbiol 2017; 201:195-200. [PMID: 28284610 DOI: 10.1016/j.vetmic.2017.01.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 12/07/2016] [Accepted: 01/18/2017] [Indexed: 11/25/2022]
Abstract
Canine tick-borne bacteria; Ehrlichia canis, hemotropic Mycoplasma spp. and Anaplasma spp., are organisms transmitted by Rhipicephalus sanguineus ticks. However, only a few clinical studies evaluating dogs infected with these organisms and anemia condition have been published. In this study, the potential tick-borne bacteria linked to anemia were investigated in eighty-one blood samples selected from anemic dogs using a broad range nested-PCR of the 16S rRNA gene. Positive results were shown in 12/81 blood specimens (14.81%). Nucleotide sequences from the PCR products were analyzed using BLAST and resulted in identification of Ehrlichia canis (8), Candidatus Mycoplasma haematoparvum (1) and Anaplasma platys (3). Two other PCR assays were used to detect and identify the positive results of these pathogens including a specific PCR for Ehrlichia canis (gp36) and a specific nested-PCR for hemoplasma species (16S rRNA) and the phylogenetic analyses of E. canis and canine hemoplasmas were performed using these two loci. These specific PCRs revealed co-infection of E. canis and Mycoplasma haemocanis in two cases. These two male dogs had presented with jaundice, severe hemolytic anemia, severe thrombocytopenia, leukocytosis, mild azotemia and hepatitis. Ehrlichia canis was detected in a significantly greater number of severe anemia cases (PCV<15%) than moderate or mild anemia cases (PCV 16-29%) (P<0.05) and these severe anemia cases were 7-fold more at risk of having E. canis infections (odds ratio: 7.11, p=0.020). However, no statistical differences were detected between E. canis detection and degrees of thrombocytopenia or leukopenia. From the results of this study, we conclude that the severity of anemia is associated with E. canis infections rather than the severity of thrombocytopenia.
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Affiliation(s)
- Gunn Kaewmongkol
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.
| | - Nicha Lukkana
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Sarawut Yangtara
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | | | | | | | | | - Stanley G Fenwick
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Boston, USA
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14
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Pilot M, Malewski T, Moura AE, Grzybowski T, Oleński K, Ruść A, Kamiński S, Ruiz Fadel F, Mills DS, Alagaili AN, Mohammed OB, Kłys G, Okhlopkov IM, Suchecka E, Bogdanowicz W. On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia. Proc Biol Sci 2017; 282:20152189. [PMID: 26631564 DOI: 10.1098/rspb.2015.2189] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Tadeusz Malewski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
| | - Andre E Moura
- School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Skłodowskiej-Curie 9, Bydgoszcz 85-094, Poland
| | - Kamil Oleński
- Department of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 5, Olsztyn 10-711, Poland
| | - Anna Ruść
- Department of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 5, Olsztyn 10-711, Poland
| | - Stanisław Kamiński
- Department of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 5, Olsztyn 10-711, Poland
| | - Fernanda Ruiz Fadel
- School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Daniel S Mills
- School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Grzegorz Kłys
- Department of Biosystematics, University of Opole, Oleska 22, Opole 45-052, Poland
| | - Innokentiy M Okhlopkov
- Science Institute of Biological Problems Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk 677980, Russia
| | - Ewa Suchecka
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
| | - Wiesław Bogdanowicz
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
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15
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Abstract
Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.
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Affiliation(s)
- Adam H Freedman
- Informatics Group, Faculty of Arts & Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
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16
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A cryptic mitochondrial DNA link between North European and West African dogs. J Genet Genomics 2016; 44:163-170. [PMID: 28302420 DOI: 10.1016/j.jgg.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/17/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
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17
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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18
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Polymorphisms in ERAP1 and ERAP2 are shared by Caninae and segregate within and between random- and pure-breeds of dogs. Vet Immunol Immunopathol 2016; 179:46-57. [PMID: 27590425 DOI: 10.1016/j.vetimm.2016.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/01/2023]
Abstract
Specific polymorphisms in the endoplasmic reticulum amino peptidase genes ERAP1 and ERAP2, when present with certain MHC class receptor types, have been associated with increased risk for specific cancers, infectious diseases and autoimmune disorders in humans. This increased risk has been linked to distinct polymorphisms in both ERAPs and MHC class I receptors that affect the way cell-generated peptides are screened for antigenicity. The incidence of cancer, infectious disease and autoimmune disorders differ greatly among pure breeds of dogs as it does in humans and it is possible that this heightened susceptibility is also due to specific polymorphisms in ERAP1 and ERAP2. In order to determine if such polymorphisms exist, the ERAP1 and ERAP2 genes of 10 dogs of nine diverse breeds were sequenced and SNPs causing synonymous or non-synonymous amino acid changes, deletions or insertions were identified. Eight ERAP1 and 10 ERAP2 SNPs were used to create a Sequenom MassARRAY iPLEX based test panel which defined 24 ERAP1, 36 ERAP2 and 128 ERAP1/2 haplotypes. The prevalence of these haplotypes was then measured among dog, wolf, coyote, jackal and red fox populations. Some haplotypes were species specific, while others were shared across species, especially between dog, wolf, coyote and jackal. The prevalence of these haplotypes was then compared among various canid populations, and in particular between various populations of random- and pure-bred dogs. Human-directed positive selection has led to loss of ERAP diversity and segregation of certain haplotypes among various dog breeds. A phylogenetic tree generated from 45 of the most common ERAP1/2 haplotypes demonstrated three distinct clades, all of which were rooted with haplotypes either shared among species or specific to contemporary dogs, coyote and wolf.
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19
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Pedersen NC, Pooch AS, Liu H. A genetic assessment of the English bulldog. Canine Genet Epidemiol 2016; 3:6. [PMID: 27478618 PMCID: PMC4965900 DOI: 10.1186/s40575-016-0036-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/10/2016] [Indexed: 01/16/2023] Open
Abstract
Background This study examines genetic diversity among 102 registered English Bulldogs used for breeding based on maternal and paternal haplotypes, allele frequencies in 33 highly polymorphic short tandem repeat (STR) loci on 25 chromosomes, STR-linked dog leukocyte antigen (DLA) class I and II haplotypes, and the number and size of genome-wide runs of homozygosity (ROH) determined from high density SNP arrays. The objective was to assess whether the breed retains enough genetic diversity to correct the genotypic and phenotypic abnormalities associated with poor health, to allow for the elimination of deleterious recessive mutations, or to make further phenotypic changes in body structure or coat. An additional 37 English bulldogs presented to the UC Davis Veterinary Clinical Services for health problems were also genetically compared with the 102 registered dogs based on the perception that sickly English bulldogs are products of commercial breeders or puppy-mills and genetically different and inferior. Results Four paternal haplotypes, with one occurring in 93 % of dogs, were identified using six Y-short tandem repeat (STR) markers. Three major and two minor matrilines were identified by mitochondrial D-loop sequencing. Heterozygosity was determined from allele frequencies at genomic loci; the average number of alleles per locus was 6.45, with only 2.7 accounting for a majority of the diversity. However, observed and expected heterozygosity values were nearly identical, indicating that the population as a whole was in Hardy-Weinberg equilibrium (HWE). However, internal relatedness (IR) and adjusted IR (IRVD) values demonstrated that a number of individuals were the offspring of parents that were either more inbred or outbred than the population as a whole. The diversity of DLA class I and II haplotypes was low, with only 11 identified DLA class I and nine class II haplotypes. Forty one percent of the breed shared a single DLA class I and 62 % a single class II haplotype. Nineteen percent of the dogs were homozygous for the dominant DLA class I haplotype and 42 % for the dominant DLA class II haplotype. The extensive loss of genetic diversity is most likely the result of a small founder population and artificial genetic bottlenecks occurring in the past. The prominent phenotypic changes characteristic of the breed have also resulted in numerous large runs of homozygosity (ROH) throughout the genome compared to Standard Poodles, which were phenotypically more similar to indigenous-type dogs. Conclusions English bulldogs have very low genetic diversity resulting from a small founder population and artificial genetic bottlenecks. Although some phenotypic and genotypic diversity still exists within the breed, whether it is sufficient to use reverse selection to improve health, select against simple recessive deleterious traits, and/or to accommodate further genotypic/phenotypic manipulations without further decreasing existing genetic diversity is questionable.
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Affiliation(s)
- Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Ashley S Pooch
- School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Hongwei Liu
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616 USA
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20
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Janssens L, Miller R, Van Dongen S. The morphology of the mandibular coronoid process does not indicate that Canis lupus chanco is the progenitor to dogs. ZOOMORPHOLOGY 2016; 135:269-277. [PMID: 27340333 PMCID: PMC4871911 DOI: 10.1007/s00435-015-0298-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/12/2015] [Accepted: 12/30/2015] [Indexed: 12/18/2022]
Abstract
The domestication of wolves is currently under debate. Where, when and from which wolf sub-species dogs originated are being investigated both by osteoarchaeologists and geneticists. While DNA research is rapidly becoming more active and popular, morphological methods have been the gold standard in the past. But even today morphological details are routinely employed to discern archaeological wolves from dogs. One such morphological similarity between Canis lupus chanco and dogs was published in 1977 by Olsen and Olsen. This concerns the “turned back” anatomy of the dorsal part of the vertical ramus of the mandible that was claimed to be specific to domestic dogs and Chinese wolves C. lupus chanco, and “absent from other canids”. Based on this characteristic, C. lupus chanco was said to be the progenitor of Asian and American dogs, and this specific morphology has been continuously used as an argument to assign archaeological specimens, including non-Asian and non-American, to the dog clade. We challenged this statement by examining 384 dog skulls of 72 breeds and 60 skulls of four wolf sub-species. Only 20 % of dog mandibles and 80 % of C. lupus chanco showed the specific anatomy. In addition, 12 % of Canis lupus pallipes mandibles showed the “turned back” morphology. It can be concluded that the shape of the coronoid process of the mandible cannot be used as a morphological trait to determine whether a specimen belongs to a dog or as an argument in favour of chanco as the progenitor to dogs.
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Affiliation(s)
- Luc Janssens
- Department of Archaeology, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
| | - Rebecca Miller
- Service of Prehistory, University of Liège, quai Roosevelt, 1, 4000 Liège, Belgium
| | - Stefan Van Dongen
- Department of Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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21
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Frantz LAF, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 2016; 352:1228-31. [PMID: 27257259 DOI: 10.1126/science.aaf3161] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/25/2016] [Indexed: 01/19/2023]
Abstract
The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
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Affiliation(s)
- Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Maud Pionnier-Capitan
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France. CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Ophélie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Morgane Ollivier
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Angela Perri
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anne Tresset
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marilyne Duffraisse
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Finbar McCormick
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, University Road, Belfast, Northern Ireland, UK
| | - László Bartosiewicz
- Osteoarchaeological Research Laboratory, University of Stockholm, Stockholm, Sweden
| | - Erika Gál
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Éva A Nyerges
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Stéphanie Bréhard
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marjan Mashkour
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Adrian Bălăşescu
- The National Museum of Romanian History, 12 Calea Victoriei, 030026 Bucharest, Romania
| | - Benjamin Gillet
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Sandrine Hughes
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Olivier Chassaing
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Christophe Hitte
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes 1, Rennes, France
| | - Jean-Denis Vigne
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Elphinstone Road, AB24 3UF, UK. Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Catherine Hänni
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
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22
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Grigg EK, Nibblett BM, Sacks BN, Hack R, Serpell JA, Hart L. Genetic and behavioral characteristics of the St. Kitts ‘island dog’. Appl Anim Behav Sci 2016. [DOI: 10.1016/j.applanim.2016.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Genetic structure in village dogs reveals a Central Asian domestication origin. Proc Natl Acad Sci U S A 2015; 112:13639-44. [PMID: 26483491 DOI: 10.1073/pnas.1516215112] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups--a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations--including those of Vietnam, India, and Egypt-show minimal evidence of European admixture. These populations exhibit a clear gradient of short--range linkage disequilibrium consistent with a Central Asian domestication origin.
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Aarnes SG, Hagen SB, Andreassen R, Schregel J, Knappskog PM, Hailer F, Stenhouse G, Janke A, Eiken HG. Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples. Forensic Sci Int Genet 2015; 19:197-204. [PMID: 26264959 DOI: 10.1016/j.fsigen.2015.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/27/2015] [Accepted: 07/26/2015] [Indexed: 11/15/2022]
Abstract
High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9-25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2-9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics.
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Affiliation(s)
| | | | - Rune Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College, Oslo Norway
| | | | | | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | - Gordon Stenhouse
- Foothills Research Institute, 1176 Switzer Drive, Box 6330, Hinton, AB T7V 1X6, Canada
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Frankfurt am Main, Germany
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25
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Safra N, Hayward LJ, Aguilar M, Sacks BN, Westropp JL, Mohr FC, Mellersh CS, Bannasch DL. DNA Sequence Variants in the Five Prime Untranslated Region of the Cyclooxygenase-2 Gene Are Commonly Found in Healthy Dogs and Gray Wolves. PLoS One 2015; 10:e0133127. [PMID: 26244515 PMCID: PMC4526539 DOI: 10.1371/journal.pone.0133127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/24/2015] [Indexed: 01/19/2023] Open
Abstract
The aim of this study was to investigate the frequency of regional DNA variants upstream to the translation initiation site of the canine Cyclooxygenase-2 (Cox-2) gene in healthy dogs. Cox-2 plays a role in various disease conditions such as acute and chronic inflammation, osteoarthritis and malignancy. A role for Cox-2 DNA variants in genetic predisposition to canine renal dysplasia has been proposed and dog breeders have been encouraged to select against these DNA variants. We sequenced 272–422 bases in 152 dogs unaffected by renal dysplasia and found 19 different haplotypes including 11 genetic variants which had not been described previously. We genotyped 7 gray wolves to ascertain the wildtype variant and found that the wolves we analyzed had predominantly the second most common DNA variant found in dogs. Our results demonstrate an elevated level of regional polymorphism that appears to be a feature of healthy domesticated dogs.
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Affiliation(s)
- Noa Safra
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
| | | | - Miriam Aguilar
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Benjamin N. Sacks
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, California United States of America
| | - Jodi L. Westropp
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - F. Charles Mohr
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | | | - Danika L. Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
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26
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Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris. Forensic Sci Int Genet 2015. [PMID: 26218982 DOI: 10.1016/j.fsigen.2015.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To contribute to the complete mitogenome database of the species Canis lupus familiaris and shed more light on its origin, we have sequenced mitochondrial genomes of 120 modern dogs from worldwide populations. Together with all the previously published mitogenome sequences of acceptable quality, we have reconstructed a global phylogenetic tree of 555 C. l. familiaris mitogenomes and standardized haplogroup nomenclature. The phylogenetic tree presented here and available online at http://clf.mtdna.tree.cm.umk.pl/ could be further used by forensic and evolutionary geneticists as well cynologists, for data quality control and unambiguous haplogroup classification. Our in-depth phylogeographic analysis of all C. l. familiaris mitogenomes confirmed that domestic dogs may have originated in East Asia during the Mesolithic and Upper Paleolithic time periods and started to expand to other parts of the world during Neolithic times.
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27
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Brown SK, Darwent CM, Wictum EJ, Sacks BN. Using multiple markers to elucidate the ancient, historical and modern relationships among North American Arctic dog breeds. Heredity (Edinb) 2015; 115:488-95. [PMID: 26103948 DOI: 10.1038/hdy.2015.49] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 03/17/2015] [Accepted: 04/28/2015] [Indexed: 11/09/2022] Open
Abstract
Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown. During the Alaskan Gold Rush, additional sled dogs, possibly of post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky, were used in the Arctic. The genealogical relationships among and origins of these breeds are unknown. Here we use autosomal, paternal and maternal DNA markers to (1) test the hypothesis that Inuit dogs have retained their indigenous ancestry, (2) characterize their relationship to one another and to other Arctic breeds, and (3) estimate the age of North American indigenous matrilines and patrilines. On the basis of the agreement of all three markers we determined that Inuit dogs have maintained their indigenous nature, and that they likely derive from Thule dogs. In addition, we provide support for previous research that the Inuit dogs from Canada and Greenland dog should not be distinguished as two breeds. The Alaskan Husky displayed evidence of European introgression, in contrast to the Malamute and Siberian Husky, which appear to have maintained most of their ancient Siberian ancestry.
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Affiliation(s)
- S K Brown
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA.,Department of Anthropology, University of California, Davis, CA, USA
| | - C M Darwent
- Department of Anthropology, University of California, Davis, CA, USA
| | - E J Wictum
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA
| | - B N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
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28
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Fregel R, Suárez NM, Betancor E, González AM, Cabrera VM, Pestano J. Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature. Mitochondrion 2015; 22:75-84. [PMID: 25869968 DOI: 10.1016/j.mito.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/27/2014] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
Abstract
Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain.
| | - Nicolás M Suárez
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Eva Betancor
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
| | - Ana M González
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - Vicente M Cabrera
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - José Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
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29
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Cronin MA, Cánovas A, Bannasch DL, Oberbauer AM, Medrano JF. Single Nucleotide Polymorphism (SNP) Variation of Wolves (Canis lupus) in Southeast Alaska and Comparison with Wolves, Dogs, and Coyotes in North America. J Hered 2014; 106:26-36. [DOI: 10.1093/jhered/esu075] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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30
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Bidon T, Janke A, Fain SR, Eiken HG, Hagen SB, Saarma U, Hallström BM, Lecomte N, Hailer F. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages. Mol Biol Evol 2014; 31:1353-63. [PMID: 24667925 DOI: 10.1093/molbev/msu109] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.
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Affiliation(s)
- Tobias Bidon
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyGoethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Frankfurt am Main, Germany
| | - Steven R Fain
- National Fish and Wildlife Forensic Laboratory, Ashland, OR
| | - Hans Geir Eiken
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Svanvik, Norway
| | - Snorre B Hagen
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Svanvik, Norway
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Björn M Hallström
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyScience for Life Laboratory, School of Biotechnology, KTH, Stockholm, Sweden
| | - Nicolas Lecomte
- Canada Research Chair in Polar and Boreal Ecology, Department of Biology, University of Moncton, Moncton, Canada
| | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
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31
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Kopaliani N, Shakarashvili M, Gurielidze Z, Qurkhuli T, Tarkhnishvili D. Gene flow between wolf and shepherd dog populations in Georgia (Caucasus). J Hered 2014; 105:345-53. [PMID: 24622972 DOI: 10.1093/jhered/esu014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We studied the distribution of the mitochondrial DNA haplotypes and microsatellite genotypes at 8 loci in 102 gray wolves, 57 livestock guarding dogs, and 9 mongrel dogs from Georgia (Caucasus). Most of the studied dogs had mitochondrial haplotypes clustered with presumably East Asian dog lineages, and most of the studied wolves had the haplotypes clustered with European wolves, but 20% of wolves and 37% of dogs shared the same mitochondrial haplotypes. Bayesian inference with STRUCTURE software suggested that more than 13% of the studied wolves had detectable dog ancestry and more than 10% of the dogs had detectable wolf ancestry. About 2-3% of the sampled wolves and dogs were identified, with a high probability, as first-generation hybrids. These results were supported by the relatedness analysis, which showed that 10% of wolves and 20% of dogs had closest relatives from an opposite group. The results of the study suggest that wolf-dog hybridization is a common event in the areas where large livestock guarding dogs are held in a traditional way, and that gene flow between dogs and gray wolves was an important force influencing gene pool of dogs for millennia since early domestication events. This process may have been terminated 1) in areas outside the natural range of gray wolves and 2) since very recent time, when humans started to more tightly control contacts of purebred dogs.
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Affiliation(s)
- Natia Kopaliani
- the Institute of Ecology, Ilia State University, 3/5 K. Cholokashvili Ave., Tbilisi 0162, Georgia
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32
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Verscheure S, Backeljau T, Desmyter S. Reviewing population studies for forensic purposes: Dog mitochondrial DNA. Zookeys 2013:381-411. [PMID: 24453568 PMCID: PMC3890688 DOI: 10.3897/zookeys.365.5859] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/14/2013] [Indexed: 02/02/2023] Open
Abstract
The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium ; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium ; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000, Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
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33
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Reponen SEM, Brown SK, Barnett BD, Sacks BN. Genetic and morphometric evidence on a Galápagos Island exposes founder effects and diversification in the first-known (truly) feral western dog population. Mol Ecol 2013; 23:269-83. [PMID: 24261528 DOI: 10.1111/mec.12595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 11/29/2022]
Abstract
Domesticated animals that revert to a wild state can become invasive and significantly impact native biodiversity. Although dogs can be problematic locally, only the Australasian dingo is known to occur in isolation from humans. Western dogs have experienced more intense artificial selection, which potentially limits their invasiveness. However, feral dogs eradicated from Isabela Island, Galápagos in the 1980s could be the first-known exception. We used DNA and morphometric data from 92 of these dogs to test the hypotheses that (i) these dogs persisted independently of humans for up to a century and a half since descending from a handful of dogs introduced in the early 1800s, vs. (ii) similarly to other western feral dog populations, they reflected continuous recruitment of strays from human settlements on a portion of the Island. We detected one dominant maternal lineage and one dominant paternal lineage shared by the three subpopulations, along with low autosomal genetic diversity, consistent with the hypothesized common origins from a small founder population. Genetic diversity patterns among the three island subpopulations were consistent with stepping-stone founder effects, while morphometric differentiation suggested rapid phenotypic divergence, possibly due to drift and reinforced by selection corresponding to distinct microclimates and habitats on Isabela. Despite the continued presence of free-ranging dogs in the vicinity of settlements on Isabela and other Galápagos Islands, feral populations have not reestablished in remote areas since the 1980s, emphasizing the rarity of conditions necessary for feralization of modern western dogs.
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Affiliation(s)
- Sini E M Reponen
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA
| | - Sarah K Brown
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA.,Department of Anthropology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Bruce D Barnett
- Barnett Environmental, 5214 El Cemonte Ave., Davis, CA, 95618, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA.,Department of Population Health and Reproduction, University of California, One Shields Avenue/Old Davis Road, Davis, CA, 95616, USA
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34
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van Asch B, Zhang AB, Oskarsson MCR, Klütsch CFC, Amorim A, Savolainen P. Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis. Proc Biol Sci 2013; 280:20131142. [PMID: 23843389 PMCID: PMC3730590 DOI: 10.1098/rspb.2013.1142] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dogs were present in pre-Columbian America, presumably brought by early human migrants from Asia. Studies of free-ranging village/street dogs have indicated almost total replacement of these original dogs by European dogs, but the extent to which Arctic, North and South American breeds are descendants of the original population remains to be assessed. Using a comprehensive phylogeographic analysis, we traced the origin of the mitochondrial DNA lineages for Inuit, Eskimo and Greenland dogs, Alaskan Malamute, Chihuahua, xoloitzcuintli and perro sín pelo del Peru, by comparing to extensive samples of East Asian (n = 984) and European dogs (n = 639), and previously published pre-Columbian sequences. Evidence for a pre-Columbian origin was found for all these breeds, except Alaskan Malamute for which results were ambigous. No European influence was indicated for the Arctic breeds Inuit, Eskimo and Greenland dog, and North/South American breeds had at most 30% European female lineages, suggesting marginal replacement by European dogs. Genetic continuity through time was shown by the sharing of a unique haplotype between the Mexican breed Chihuahua and ancient Mexican samples. We also analysed free-ranging dogs, confirming limited pre-Columbian ancestry overall, but also identifying pockets of remaining populations with high proportion of indigenous ancestry, and we provide the first DNA-based evidence that the Carolina dog, a free-ranging population in the USA, may have an ancient Asian origin.
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35
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Wheeldon TJ, Rutledge LY, Patterson BR, White BN, Wilson PJ. Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes. Ecol Evol 2013; 3:3005-20. [PMID: 24101990 PMCID: PMC3790547 DOI: 10.1002/ece3.693] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/20/2013] [Accepted: 06/23/2013] [Indexed: 11/20/2022] Open
Abstract
Hybridization has played an important role in the evolutionary history of Canis species in eastern North America. Genetic evidence of coyote–dog hybridization based on mitochondrial DNA (mtDNA) is lacking compared to that based on autosomal markers. This discordance suggests dog introgression into coyotes has potentially been male biased, but this hypothesis has not been formally tested. Therefore, we investigated biparentally, maternally, and paternally inherited genetic markers in a sample of coyotes and dogs from southeastern Ontario to assess potential asymmetric dog introgression into coyotes. Analysis of autosomal microsatellite genotypes revealed minimal historical and contemporary admixture between coyotes and dogs. We observed only mutually exclusive mtDNA haplotypes in coyotes and dogs, but we observed Y-chromosome haplotypes (Y-haplotypes) in both historical and contemporary coyotes that were also common in dogs. Species-specific Zfy intron sequences of Y-haplotypes shared between coyotes and dogs confirmed their homology and indicated a putative origin from dogs. We compared Y-haplotypes observed in coyotes, wolves, and dogs profiled in multiple studies, and observed that the Y-haplotypes shared between coyotes and dogs were either absent or rare in North American wolves, present in eastern coyotes, but absent in western coyotes. We suggest the eastern coyote has experienced asymmetric genetic introgression from dogs, resulting from predominantly historical hybridization with male dogs and subsequent backcrossing of hybrid offspring with coyotes. We discuss the temporal and spatial dynamics of coyote–dog hybridization and the conditions that may have facilitated the introgression of dog Y-chromosomes into coyotes. Our findings clarify the evolutionary history of the eastern coyote.
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Affiliation(s)
- Tyler J Wheeldon
- Environmental and Life Sciences Graduate Program, Trent University Peterborough, ON, Canada, K9J 7B8
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Li Y, vonHoldt BM, Reynolds A, Boyko AR, Wayne RK, Wu DD, Zhang YP. Artificial Selection on Brain-Expressed Genes during the Domestication of Dog. Mol Biol Evol 2013; 30:1867-76. [DOI: 10.1093/molbev/mst088] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds. PLoS One 2013; 8:e60015. [PMID: 23573227 PMCID: PMC3616054 DOI: 10.1371/journal.pone.0060015] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022] Open
Abstract
The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.
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Affiliation(s)
- Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.
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Sacks BN, Brown SK, Stephens D, Pedersen NC, Wu JT, Berry O. Y Chromosome Analysis of Dingoes and Southeast Asian Village Dogs Suggests a Neolithic Continental Expansion from Southeast Asia Followed by Multiple Austronesian Dispersals. Mol Biol Evol 2013; 30:1103-18. [DOI: 10.1093/molbev/mst027] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Pedersen N, Liu H, Theilen G, Sacks B. The effects of dog breed development on genetic diversity and the relative influences of performance and conformation breeding. J Anim Breed Genet 2012; 130:236-48. [PMID: 23679949 DOI: 10.1111/jbg.12017] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/02/2012] [Indexed: 12/22/2022]
Abstract
Genetic diversity was compared among eight dog breeds selected primarily for conformation (Standard Poodle, Italian Greyhound and show English Setter), conformation and performance (Brittany), predominantly performance (German Shorthaired and Wirehaired Pointers) or solely performance (field English Setter and Red Setter). Modern village dogs, which better reflect ancestral genetic diversity, were used as the standard. Four to seven maternal and one to two Y haplotypes were found per breed, with one usually dominant. Diversity of maternal haplotypes was greatest in village dogs, intermediate in performance breeds and lowest in conformation breeds. Maternal haplotype sharing occurred across all breeds, while Y haplotypes were more breed specific. Almost all paternal haplotypes were identified among village dogs, with the exception of the dominant Y haplotype in Brittanys, which has not been identified heretofore. The highest heterozygosity based on 24 autosomal microsatellites was found in village dogs and the lowest in conformation (show) breeds. Principal coordinate analysis indicated that conformation-type breeds were distinct from breeds heavily used for performance, the latter clustering more closely with village dogs. The Brittany, a well-established dual show and field breed, was also genetically intermediate between the conformation and performance breeds. The number of DLA-DRB1 alleles varied from 3 to 10 per breed with extensive sharing. SNPs across the wider DLA region were more frequently homozygous in all pure breeds than in village dogs. Compared with their village dog relatives, all modern breed dogs exhibit reduced genetic diversity. Genetic diversity was even more reduced among breeds under selection for show/conformation.
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Affiliation(s)
- N Pedersen
- Koret Foundation Center for Veterinary Genetics of the Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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Chen R, Irwin DM, Zhang YP. Differences in selection drive olfactory receptor genes in different directions in dogs and wolf. Mol Biol Evol 2012; 29:3475-84. [PMID: 22683813 DOI: 10.1093/molbev/mss153] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The olfactory receptor (OR) gene family is the largest gene family found in mammalian genomes. It is known to evolve through a birth-and-death process. Here, we characterized the sequences of 16 segregating OR pseudogenes in the samples of the wolf and the Chinese village dog (CVD) and compared them with the sequences from dogs of different breeds. Our results show that the segregating OR pseudogenes in breed dogs are under strong purifying selection, while evolving neutrally in the CVD, and show a more complicated pattern in the wolf. In the wolf, we found a trend to remove deleterious polymorphisms and accumulate nondeleterious polymorphisms. On the basis of protein structure of the ORs, we found that the distribution of different types of polymorphisms (synonymous, nonsynonymous, tolerated, and untolerated) varied greatly between the wolf and the breed dogs. In summary, our results suggest that different forms of selection have acted on the segregating OR pseudogenes in the CVD since domestication, breed dogs after breed formation, and ancestral wolf population, which has driven the evolution of these genes in different directions.
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Affiliation(s)
- Rui Chen
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Pedersen NC, Liu H, McLaughlin B, Sacks BN. Genetic characterization of healthy and sebaceous adenitis affected Standard Poodles from the United States and the United Kingdom. ACTA ACUST UNITED AC 2012; 80:46-57. [PMID: 22512808 DOI: 10.1111/j.1399-0039.2012.01876.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The degree of heterogeneity associated with geographic origin and sebaceous adenitis (SA) status in Standard Poodles from the United States (US) and the United Kingdom (UK) was assessed. Healthy and SA-affected Standard Poodles from the US and the UK shared a major mitochondrial DNA (mtDNA) haplotype and a single Y chromosome haplotype. However, minor mtDNA haplotypes and frequencies were somewhat different between US and UK dogs and were significantly less associated with SA than major haplotypes across both populations. The US and UK populations exhibited recent divergence from a common gene pool, based on allele frequencies of 24 highly polymorphic short tandem repeats and principle coordinates and cluster analyses of genotype frequencies. However, there was no differentiation between SA affected and unaffected dogs. Over 90% of US and UK Poodles shared a common dog leukocyte antigen (DLA) class II haplotype, but showed some differentiation in minor haplotype frequency. No difference was observed in haplotype heterozygosity between SA affected and unaffected dogs from the same country and no disease association for SA was found within the DLA region by a high density single nucleotide polymorphism (SNP) scan. Zygosity mapping in the DLA region of Poodles indicated much lower site-specific diversity than in an outbred population of street dogs from Bali, Indonesia, reflecting the degree that breed associated historical bottlenecks have reduced diversity in a polymorphic region of the genome. This study shows possible pitfalls in more extensive genome-wide association studies, such as case and control numbers, population stratification, the involvement of multiple genes, and/or the possibility that SA susceptibility is fixed or nearly fixed within the breed, which can reduce power to detect genetic associations.
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Affiliation(s)
- N C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
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