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Deakin S, Coltman DW. Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep ( Ovis canadensis canadensis). PeerJ 2024; 12:e16946. [PMID: 38426129 PMCID: PMC10903336 DOI: 10.7717/peerj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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2
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Polinas M, Cacciotto C, Zobba R, Antuofermo E, Burrai GP, Pirino S, Pittau M, Alberti A. Ovine papillomaviruses: Diversity, pathogenicity, and evolution. Vet Microbiol 2024; 289:109955. [PMID: 38160507 DOI: 10.1016/j.vetmic.2023.109955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/14/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
The family Papillomaviridae includes a plethora of viral species infecting virtually all vertebrates excluding amphibians, with astonishing impact on human and animal health. Although more than 250 species have been described in humans, the total number of papillomaviruses (PVs) discovered in animals does not reach up to this number. In animals, PV infections are mostly asymptomatic or can cause variable clinical conditions ranging from self-limiting papillomas and other cutaneous and mucosal benign lesions to cancer. Most of animal PV types have been discovered in cattle, dogs, horses, and cats with other farm host species remaining overlooked. In particular, the number of PV types so far identified in sheep is limited. This paper comprehensively reviews ovine PVs features, including viral taxonomy and evolution; genome organization; viral tropism and pathogenesis; macroscopical features and histopathological patterns, as well as available diagnostics tools. Data are critically presented and discussed in terms of impact on veterinary and public health. The development of future dedicated research is also discussed.
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Affiliation(s)
- Marta Polinas
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy
| | - Carla Cacciotto
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy; Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy
| | - Rosanna Zobba
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy; Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy
| | - Elisabetta Antuofermo
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy; Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy
| | - Giovanni Pietro Burrai
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy; Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy
| | - Salvatore Pirino
- Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy
| | - Marco Pittau
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy; Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy
| | - Alberto Alberti
- Dipartimento di Medicina Veterinaria, Università degli studi di Sassari, Italy; Mediterranean Center for Disease Control, Università degli studi di Sassari, Italy.
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3
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Mereu P, Pirastru M, Sanna D, Bassu G, Naitana S, Leoni GG. Phenotype transition from wild mouflon to domestic sheep. Genet Sel Evol 2024; 56:1. [PMID: 38166592 PMCID: PMC10763062 DOI: 10.1186/s12711-023-00871-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
The domestication of animals started around 12,000 years ago in the Near East region. This "endless process" is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today's domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.
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Affiliation(s)
- Paolo Mereu
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100, Sassari, Italy
| | - Monica Pirastru
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100, Sassari, Italy.
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100, Sassari, Italy
| | - Giovanni Bassu
- Agenzia FoReSTAS, Regione autonoma della Sardegna, 09123, Cagliari, Italy
| | - Salvatore Naitana
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100, Sassari, Italy
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4
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Whiting JC, Bleich VC, Bowyer RT, Epps CW. Restoration of bighorn sheep: History, successes, and remaining conservation issues. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1083350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Mammals are imperiled worldwide, primarily from habitat loss or modification, and exhibit downward trends in their populations and distributions. Likewise, large-bodied herbivores have undergone a collapse in numbers and are at the highest extinction risk of all mammals. Bighorn sheep (Ovis canadensis) are among those large-bodied herbivores that possess a slow-paced life history, suffer from debilitating diseases, and have experienced range contractions across their historical distribution since the late 1800s. Translocations and reintroductions of these mountain ungulates are key aspects of restoration and often are used to re-establish populations in historical habitat or to supplement declining herds. Millions of US dollars and much effort by state and federal natural resource agencies, as well as public and private organizations, have been expended to restore bighorn sheep. Despite those efforts, translocated populations of bighorn sheep have not always been successful. We assessed restoration of bighorn sheep to provide insights in the context of conservation of populations of bighorn sheep, because this management tool is a frequently used to re-establish populations. We focused briefly on past efforts to restore bighorn sheep populations and followed with updates on the value of habitat enhancements, genetic issues, the importance of ecotypic or phenotypic adaptations when restoring populations, predation, and disease transmission. We also raised issues and posed questions that have potential to affect future decisions regarding the restoration of bighorn sheep. This information will help conservationists improve the success of conserving these iconic large mammals.
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5
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Cheng H, Zhang Z, Wen J, Lenstra JA, Heller R, Cai Y, Guo Y, Li M, Li R, Li W, He S, Wang J, Shao J, Song Y, Zhang L, Billah M, Wang X, Liu M, Jiang Y. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep. PLoS Genet 2023; 19:e1010615. [PMID: 36821549 PMCID: PMC9949681 DOI: 10.1371/journal.pgen.1010615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/13/2023] [Indexed: 02/24/2023] Open
Abstract
The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.
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Affiliation(s)
- Hong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenrong Li
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Sangang He
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Jintao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Junjie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuxuan Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Masum Billah
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingjun Liu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
- * E-mail: (ML); (YJ)
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- * E-mail: (ML); (YJ)
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6
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Li X, He SG, Li WR, Luo LY, Yan Z, Mo DX, Wan X, Lv FH, Yang J, Xu YX, Deng J, Zhu QH, Xie XL, Xu SS, Liu CX, Peng XR, Han B, Li ZH, Chen L, Han JL, Ding XZ, Dingkao R, Chu YF, Wu JY, Wang LM, Zhou P, Liu MJ, Li MH. Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation. Genome Res 2022; 32:gr.276769.122. [PMID: 35948368 PMCID: PMC9528982 DOI: 10.1101/gr.276769.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022]
Abstract
Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.
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Affiliation(s)
- Xin Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - San-Gang He
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Wen-Rong Li
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ze Yan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Dong-Xin Mo
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ji Yang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ya-Xi Xu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Juan Deng
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang-Hui Zhu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Chen-Xi Liu
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Xin-Rong Peng
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Bin Han
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Zhong-Hui Li
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Lei Chen
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Xue-Zhi Ding
- MOA Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture (MOA), Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Renqing Dingkao
- Institute of Animal Science and Veterinary Medicine, Gannan Tibetan Autonomous Prefecture, Hezuo, 747000, China
| | - Yue-Feng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jin-Yan Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Li-Min Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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7
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Flesch E, Graves T, Thomson J, Proffitt K, Garrott R. Average kinship within bighorn sheep populations is associated with connectivity, augmentation, and bottlenecks. Ecosphere 2022. [DOI: 10.1002/ecs2.3972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Elizabeth Flesch
- Fish and Wildlife Ecology and Management Program, Ecology Department Montana State University Bozeman Montana USA
| | - Tabitha Graves
- Glacier Field Station U.S. Geological Survey West Glacier Montana USA
| | - Jennifer Thomson
- Animal and Range Sciences Department Montana State University Bozeman Montana USA
| | | | - Robert Garrott
- Fish and Wildlife Ecology and Management Program, Ecology Department Montana State University Bozeman Montana USA
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8
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Her C, Rezaei HR, Hughes S, Naderi S, Duffraisse M, Mashkour M, Naghash HR, Bălășescu A, Luikart G, Jordan S, Özüt D, Kence A, Bruford MW, Tresset A, Vigne JD, Taberlet P, Hänni C, Pompanon F. Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros. Anim Genet 2022; 53:452-459. [PMID: 35288946 DOI: 10.1111/age.13191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).
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Affiliation(s)
- Charlotte Her
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Hamid-Reza Rezaei
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Environmental Sciences Department, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Saeid Naderi
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Department of Environment, Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - Marilyne Duffraisse
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marjan Mashkour
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Hamid-Reza Naghash
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Adrian Bălășescu
- Department of Bioarchaeology, 'Vasile Pârvan' Institute of Archaeology, Romanian Academy, Bucharest, Romania
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, Montana, USA
| | - Steve Jordan
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Deniz Özüt
- Biology Department, Middle East Technical University, Ankara, Turkey
| | - Aykut Kence
- Biology Department, Middle East Technical University, Ankara, Turkey
| | | | - Anne Tresset
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Jean-Denis Vigne
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Pierre Taberlet
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway
| | - Catherine Hänni
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - François Pompanon
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
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9
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Santos SHD, Peery RM, Miller JM, Dao A, Lyu FH, Li X, Li MH, Coltman DW. Ancient hybridization patterns between bighorn and thinhorn sheep. Mol Ecol 2021; 30:6273-6288. [PMID: 34845798 DOI: 10.1111/mec.16136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Whole-genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.
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Affiliation(s)
- Sarah H D Santos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anh Dao
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Feng-Hua Lyu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences (CAS), Beijing, China
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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10
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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11
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Upadhyay M, Kunz E, Sandoval-Castellanos E, Hauser A, Krebs S, Graf A, Blum H, Dotsev A, Okhlopkov I, Shakhin A, Bagirov V, Brem G, Fries R, Zinovieva N, Medugorac I. Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep. Mol Ecol 2021; 30:6701-6717. [PMID: 34534381 DOI: 10.1111/mec.16184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F4 -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | | | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | | | - Alexey Shakhin
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Vugar Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, VMU, Vienna, Austria
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - Natalia Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
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12
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Mitochondrial DNA Analysis Clarifies Taxonomic Status of the Northernmost Snow Sheep ( Ovis nivicola) Population. Life (Basel) 2021; 11:life11030252. [PMID: 33803851 PMCID: PMC8003287 DOI: 10.3390/life11030252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/18/2022] Open
Abstract
Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.
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13
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Flesch EP, Graves TA, Thomson JM, Proffitt KM, White PJ, Stephenson TR, Garrott RA. Evaluating wildlife translocations using genomics: A bighorn sheep case study. Ecol Evol 2020; 10:13687-13704. [PMID: 33391673 PMCID: PMC7771163 DOI: 10.1002/ece3.6942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/12/2020] [Accepted: 09/25/2020] [Indexed: 01/10/2023] Open
Abstract
Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.
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Affiliation(s)
- Elizabeth P. Flesch
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
| | - Tabitha A. Graves
- Northern Rocky Mountain Science CenterU.S. Geological SurveyWest GlacierMTUSA
| | | | | | - P. J. White
- Yellowstone Center for ResourcesNational Park ServiceMammothWYUSA
| | - Thomas R. Stephenson
- Sierra Nevada Bighorn Sheep Recovery ProgramCalifornia Department of Fish and WildlifeBishopCAUSA
| | - Robert A. Garrott
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
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14
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Derouiche L, Irzagh A, Rahmouni R, Tahri R, Hadjeloum M, Bouhadad R, Fernandes C. Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini). Gene 2020; 739:144510. [PMID: 32109559 DOI: 10.1016/j.gene.2020.144510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.
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Affiliation(s)
- Louiza Derouiche
- LBEIG, Population Genetics & Conservation Unit, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, Bab Ezzouar, 16111, Algiers, Algeria.
| | - Ahmed Irzagh
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Saad Dahlab de Blida, route de Soumâa, BP 270, 09000 Blida, Algeria
| | - Rafiq Rahmouni
- Réserve de Chasse de Tlemcen, Direction Générale des Forêts (DGF), Boulevard de Lala Sitti, Tlemcen, Algeria
| | | | - Mohamed Hadjeloum
- Bureau de la Gestion et Protection de la Faune, Direction Générale des Forêts (DGF), Algiers, Algeria
| | - Rachid Bouhadad
- LBEIG, Population Genetics & Conservation Unit, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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15
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Genetic structure of Mycoplasma ovipneumoniae informs pathogen spillover dynamics between domestic and wild Caprinae in the western United States. Sci Rep 2019; 9:15318. [PMID: 31653889 PMCID: PMC6814754 DOI: 10.1038/s41598-019-51444-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/30/2019] [Indexed: 01/24/2023] Open
Abstract
Spillover diseases have significant consequences for human and animal health, as well as wildlife conservation. We examined spillover and transmission of the pneumonia-associated bacterium Mycoplasma ovipneumoniae in domestic sheep, domestic goats, bighorn sheep, and mountain goats across the western United States using 594 isolates, collected from 1984 to 2017. Our results indicate high genetic diversity of M. ovipneumoniae strains within domestic sheep, whereas only one or a few strains tend to circulate in most populations of bighorn sheep or mountain goats. These data suggest domestic sheep are a reservoir, while the few spillovers to bighorn sheep and mountain goats can persist for extended periods. Domestic goat strains form a distinct clade from those in domestic sheep, and strains from both clades are found in bighorn sheep. The genetic structure of domestic sheep strains could not be explained by geography, whereas some strains are spatially clustered and shared among proximate bighorn sheep populations, supporting pathogen establishment and spread following spillover. These data suggest that the ability to predict M. ovipneumoniae spillover into wildlife populations may remain a challenge given the high strain diversity in domestic sheep and need for more comprehensive pathogen surveillance.
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16
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Sim Z, Coltman DW. Heritability of Horn Size in Thinhorn Sheep. Front Genet 2019; 10:959. [PMID: 31681413 PMCID: PMC6797622 DOI: 10.3389/fgene.2019.00959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/09/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic basis of fitness-related trait variation has long been of great interest to evolutionary biologists. Secondary sexual characteristics, such as horns in bovids, are particularly intriguing since they can be potentially affected by both natural and sexual selection. Until recently, however, the study of fitness-related quantitative trait variation in wild species has been hampered by a lack of genomic resources, pedigree, and/or phenotype data. Recent innovations in genomic technologies have enabled wildlife researchers to perform marker-based relatedness estimation and acquire adequate loci density, enabling both the “top-down” approach of quantitative genetics and the “bottom-up” approach of association studies to describe the genetic basis of fitness-related traits. Here we combine a cross species application of the OvineHD BeadChip and horn measurements (horn length, base circumference, and volume) from harvested thinhorn sheep to examine the heritability and to perform a genome-wide single-nucleotide polymorphism association study of horn size in the species. Thinhorn sheep are mountain ungulates that reside in the mountainous regions of northwestern North America. Thinhorn sheep males grow massive horns that determine the social rank and mating success. We found horn length, base circumference, and volume to be moderately heritable and two loci to be suggestively associated with horn length.
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Affiliation(s)
- Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Fish and Wildlife Forensic Unit, Alberta Fish and Wildlife Enforcement Branch, Government of Alberta, Edmonton, AB, Canada
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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17
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Dotsev AV, Deniskova TE, Okhlopkov IM, Mészáros G, Sölkner J, Reyer H, Wimmers K, Brem G, Zinovieva NA. Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep ( Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia). Ecol Evol 2018; 8:8000-8010. [PMID: 30250679 PMCID: PMC6144981 DOI: 10.1002/ece3.4350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 01/01/2023] Open
Abstract
Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1,121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge-Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographic pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population-TIK, and maximum values were observed in the most southern population-SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH, and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the Late Pleistocene glaciations of Verkhoyansk Range.
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Affiliation(s)
- Arsen V. Dotsev
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
| | | | - Gabor Mészáros
- Division of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Johann Sölkner
- Division of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Henry Reyer
- Institute of Genome BiologyLeibniz Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Klaus Wimmers
- Institute of Genome BiologyLeibniz Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
- Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine (VMU)ViennaAustria
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
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18
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Abstract
We report here the complete mitochondrial genome sequence of a Rocky Mountain bighorn sheep (Ovis canadensis) in the United States. The circular genome has a size of 16,466 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes.
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19
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Flesch EP, Rotella JJ, Thomson JM, Graves TA, Garrott RA. Evaluating sample size to estimate genetic management metrics in the genomics era. Mol Ecol Resour 2018; 18:1077-1091. [PMID: 29856123 DOI: 10.1111/1755-0998.12898] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/29/2022]
Abstract
Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross-species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra- and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effective approach to ensure rigour in estimating genomic kinship and population differentiation.
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Affiliation(s)
| | - Jay J Rotella
- Ecology Department, Montana State University, Bozeman, Montana
| | - Jennifer M Thomson
- Animal and Range Sciences Department, Montana State University, Bozeman, Montana
| | - Tabitha A Graves
- U.S. Geological Survey Glacier Field Station, Northern Rocky Mountain Science Center, West Glacier, Montana
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20
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Deniskova TE, Dotsev AV, Okhlopkov IM, Bagirov VA, Kramarenko AS, Brem G, Zinovieva NA. Characteristics of the Genetic Structure of Snow Sheep (Ovis nivicola lydekkeri) of the Verkhoyansk Mountain Chain. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418030031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Miller JM, Festa-Bianchet M, Coltman DW. Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium ® HD SNP BeadChip. PeerJ 2018; 6:e4364. [PMID: 29473002 PMCID: PMC5817937 DOI: 10.7717/peerj.4364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Current affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Medvedev DG, Dotsev AV, Okhlopkov IM, Deniskova TE, Reyer H, Wimmers K, Brem G, Bagirov VA, Zinovieva NA. Genetic characteristics of Kodar snow sheep using SNP markers. CONTEMP PROBL ECOL+ 2017. [DOI: 10.1134/s1995425517060099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Tore G, Cacciotto C, Anfossi AG, Dore GM, Antuofermo E, Scagliarini A, Burrai GP, Pau S, Zedda MT, Masala G, Pittau M, Alberti A. Host cell tropism, genome characterization, and evolutionary features of OaPV4, a novel Deltapapillomavirus identified in sheep fibropapilloma. Vet Microbiol 2017; 204:151-158. [DOI: 10.1016/j.vetmic.2017.04.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
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Mitochondrial DNA D-Loop diversity and evolutionary relationship of wild Punjab Urial sheep ( Ovis vignei punjabiensis ) with closely related taxa. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Deniskova TE, Okhlopkov IM, Sermyagin AA, Gladyr' EA, Bagirov VA, Sölkner J, Mamaev NV, Brem G, Zinov'eva NA. Whole genome SNP scanning of snow sheep (Ovis nivicola). DOKL BIOCHEM BIOPHYS 2016; 469:288-93. [PMID: 27599514 DOI: 10.1134/s1607672916040141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 11/23/2022]
Abstract
This is the first report performing the whole genome SNP scanning of snow sheep (Ovis nivicola). Samples of snow sheep (n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations.
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Affiliation(s)
- T E Deniskova
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia.
| | - I M Okhlopkov
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia.,Institute of Biological Problems of Cryolithozone, Siberian Branch, Russian Academy of Sciences, ul. Lenina 41, Yakutsk, 677980, Russia
| | - A A Sermyagin
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| | - E A Gladyr'
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| | - V A Bagirov
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| | - J Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Augasse 2-6, Vienna, A-1090, Austria
| | - N V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch, Russian Academy of Sciences, ul. Lenina 41, Yakutsk, 677980, Russia
| | - G Brem
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Veterinärplatz, Vienna, A-1210, Austria
| | - N A Zinov'eva
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
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26
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Roffler GH, Amish SJ, Smith S, Cosart T, Kardos M, Schwartz MK, Luikart G. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate. Mol Ecol Resour 2016; 16:1147-64. [PMID: 27327375 DOI: 10.1111/1755-0998.12560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/04/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022]
Abstract
Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5' and 3' untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositan and bayescan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.
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Affiliation(s)
- Gretchen H Roffler
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508, USA.,Wildlife Biology Program, Department of Ecosystem Sciences and Conservation, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Stephen J Amish
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Seth Smith
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ted Cosart
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Marty Kardos
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.,Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden
| | - Michael K Schwartz
- Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden.,US Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, 800 E. Beckwith Ave., Missoula, MT, 59801, USA
| | - Gordon Luikart
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.,Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
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Buchalski MR, Sacks BN, Gille DA, Penedo MCT, Ernest HB, Morrison SA, Boyce WM. Phylogeographic and population genetic structure of bighorn sheep ( Ovis canadensis ) in North American deserts. J Mammal 2016; 97:823-838. [PMID: 29899578 PMCID: PMC5993094 DOI: 10.1093/jmammal/gyw011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Fossil data are ambiguous regarding the evolutionary origin of contemporary desert bighorn sheep ( Ovis canadensis subspecies). To address this uncertainty, we conducted phylogeographic and population genetic analyses on bighorn sheep subspecies found in southwestern North America. We analyzed 515 base pairs of mtDNA control region sequence and 39 microsatellites in 804 individuals from 58 locations. Phylogenetic analyses revealed 2 highly divergent clades concordant with Sierra Nevada ( O. c. sierrae ) and Rocky Mountain ( O. c. canadensis ) bighorn and showed that these 2 subspecies both diverged from desert bighorn prior to or during the Illinoian glaciation (~315-94 thousand years ago [kya]). Desert bighorn comprised several more recently diverged haplogroups concordant with the putative Nelson ( O. c. nelsoni ), Mexican ( O. c. mexicana ), and Peninsular ( O. c. cremnobates ) subspecies. Corresponding estimates of effective splitting times (~17-3 kya), and haplogroup ages (~85-72 kya) placed the most likely timeframe for divergence among desert bighorn subspecies somewhere within the last glacial maximum. Median-joining haplotype network and Bayesian skyline analyses both indicated that desert bighorn collectively comprised a historically large and haplotype-diverse population, which subsequently lost much of its diversity through demographic decline. Using microsatellite data, discriminant analysis of principle components (DAPC) and Bayesian clustering analyses both indicated genetic structure concordant with the geographic distribution of 3 desert subspecies. Likewise, microsatellite and mitochondrial-based FST comparisons revealed significant fixation indices among the desert bighorn genetic clusters. We conclude these desert subspecies represent ancient lineages likely descended from separate Pleistocene refugial populations and should therefore be managed as distinct taxa to preserve maximal biodiversity. Los datos de fósiles sobre el origen evolutivo de las ovejas del desierto ( Ovis canadensis subespecies) contemporáneas son ambiguos. Para dilucidar esta incertidumbre, llevamos a cabo análisis filogeográficos y de genética de poblaciones entre cinco subespecies de ovejas del suroccidente de Norteamérica. Analizamos 515 pb de secuencia de la región control del ADN mitocondrial y 39 microsatélites en 804 ovejas de 58 localidades. Los análisis filogenéticos revelaron 2 clados altamente divergentes concordantes con ovejas de la Sierra Nevada ( O. c. sierrae ) y de las Montañas Rocosas ( O. c. canadensis ), y demostraron que estas dos subespecies divergieron antes o durante la glaciación de Illinois (315,000-94,000 años). Las ovejas del desierto formaron varios haplogrupos recientemente derivados concordantes con las subespecies de Nelson ( O. c. nelsoni ), México ( O. c. mexicana ) y peninsular ( O. c. cremnobates ). Las estimaciones correspondientes al tiempo de separación efectiva (17,000-3,000 años) y edades de haplogrupos (85,000-72,000 años) son los plazos más probables para las divergencias entre subespecies de ovejas del desierto dentro de la última glaciación máxima. Análisis de redes de haplotipos de unión de medias y análisis bayesianos de líneas de horizonte indicaron que las ovejas del desierto formaron una población históricamente grande y diversa en términos de haplotipos, que luego perdieron gran parte de su diversidad a través de un descenso demográfico. Utilizando datos de microsatélites los análisis DAPC y TESS indicaron agrupamiento genético concordante con la distribución geográfica actual de las tres subespecies. Asimismo, comparaciones de FST con datos de microsatélites y mitocondriales revelaron índices de fijación significativos entre los grupos genéticos de ovejas del desierto. Concluimos que estas subespecies de ovejas del desierto representan linajes antiguos que probablemente descienden de poblaciones de distintos refugios del Pleistoceno, y que por lo tanto deben ser manejadas como taxones distintos para preservar su biodiversidad máxima.
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The First Mitogenome of the Cyprus Mouflon (Ovis gmelini ophion): New Insights into the Phylogeny of the Genus Ovis. PLoS One 2015; 10:e0144257. [PMID: 26636977 PMCID: PMC4670089 DOI: 10.1371/journal.pone.0144257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Sheep are thought to have been one of the first livestock to be domesticated in the Near East, thus playing an important role in human history. The current whole mitochondrial genome phylogeny for the genus Ovis is based on: the five main domestic haplogroups occurring among sheep (O. aries), along with molecular data from two wild European mouflons, three urials, and one argali. With the aim to shed some further light on the phylogenetic relationship within this genus, the first complete mitochondrial genome sequence of a Cypriot mouflon (O. gmelini ophion) is here reported. Phylogenetic analyses were performed using a dataset of whole Ovis mitogenomes as well as D-loop sequences. The concatenated sequence of 28 mitochondrial genes of one Cypriot mouflon, and the D-loop sequence of three Cypriot mouflons were compared to sequences obtained from samples representatives of the five domestic sheep haplogroups along with samples of the extant wild and feral sheep. The sample included also individuals from the Mediterranean islands of Sardinia and Corsica hosting remnants of the first wave of domestication that likely went then back to feral life. The divergence time between branches in the phylogenetic tree has been calculated using seven different calibration points by means of Bayesian and Maximum Likelihood inferences. Results suggest that urial (O. vignei) and argali (O. ammon) diverged from domestic sheep about 0.89 and 1.11 million years ago (MYA), respectively; and dates the earliest radiation of domestic sheep common ancestor at around 0.3 MYA. Additionally, our data suggest that the rise of the modern sheep haplogroups happened in the span of time between six and 32 thousand years ago (KYA). A close phylogenetic relationship between the Cypriot and the Anatolian mouflon carrying the X haplotype was detected. The genetic distance between this group and the other ovine haplogroups supports the hypothesis that it may be a new haplogroup never described before. Furthermore, the updated phylogenetic tree presented in this study determines a finer classification of ovine species and may help to classify more accurately new mitogenomes within the established haplogroups so far identified.
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Kardos M, Luikart G, Bunch R, Dewey S, Edwards W, McWilliam S, Stephenson J, Allendorf FW, Hogg JT, Kijas J. Whole‐genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep. Mol Ecol 2015; 24:5616-32. [DOI: 10.1111/mec.13415] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 09/23/2015] [Accepted: 09/28/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Marty Kardos
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
- Evolutionary Biology Centre Uppsala University SE‐75236 Uppsala Sweden
| | - Gordon Luikart
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
- Division of Biological Sciences Flathead Lake Biological Station Fish and Wildlife Genomics Group University of Montana Polson MT 59860 USA
| | - Rowan Bunch
- CSIRO Agriculture 306 Carmody Road St Lucia Brisbane Qld 4067 Australia
| | - Sarah Dewey
- Grand Teton National Park Moose WY 83012 USA
| | - William Edwards
- Wyoming Game and Fish Department Wildlife Disease Laboratory Laramie WY 82070 USA
| | - Sean McWilliam
- CSIRO Agriculture 306 Carmody Road St Lucia Brisbane Qld 4067 Australia
| | | | - Fred W. Allendorf
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
| | - John T. Hogg
- Montana Conservation Science Institute Missoula MT 59803 USA
| | - James Kijas
- CSIRO Agriculture 306 Carmody Road St Lucia Brisbane Qld 4067 Australia
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Guerrini M, Forcina G, Panayides P, Lorenzini R, Garel M, Anayiotos P, Kassinis N, Barbanera F. Molecular DNA identity of the mouflon of Cyprus (Ovis orientalis ophion, Bovidae): Near Eastern origin and divergence from Western Mediterranean conspecific populations. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1046409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Monica Guerrini
- Dipartimento di Biologia, Unità di Zoologia e Antropologia, Via A. Volta 4, 56126 Pisa, Italy
| | - Giovanni Forcina
- Dipartimento di Biologia, Unità di Zoologia e Antropologia, Via A. Volta 4, 56126 Pisa, Italy
| | | | - Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Via Tancia 21, 02100 Rieti, Italy
| | - Mathieu Garel
- Office National de la Chasse et de la Faune Sauvage, Centre National d'Études et de Recherche Appliquée Faune de Montagne, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | | | | | - Filippo Barbanera
- Dipartimento di Biologia, Unità di Zoologia e Antropologia, Via A. Volta 4, 56126 Pisa, Italy
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Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015; 16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023] Open
Abstract
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1618-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - David W Coltman
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
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Demirci S, Koban Baştanlar E, Dağtaş ND, Pişkin E, Engin A, Özer F, Yüncü E, Doğan ŞA, Togan İ. Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep. PLoS One 2013; 8:e81952. [PMID: 24349158 PMCID: PMC3859546 DOI: 10.1371/journal.pone.0081952] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 10/18/2013] [Indexed: 01/10/2023] Open
Abstract
In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E. To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations. Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).
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Affiliation(s)
- Sevgin Demirci
- The Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Evren Koban Baştanlar
- Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
| | - Nihan Dilşad Dağtaş
- The Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Evangelia Pişkin
- Department of Settlement Archaeology, Middle East Technical University, Ankara, Turkey
| | - Atilla Engin
- Department of Archaeology, Cumhuriyet University, Sivas, Turkey
| | - Füsun Özer
- The Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- The Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Şükrü Anıl Doğan
- The Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- The Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- * E-mail:
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Garcia-Etxebarria K, Jugo BM. Evolutionary history of bovine endogenous retroviruses in the Bovidae family. BMC Evol Biol 2013; 13:256. [PMID: 24256121 PMCID: PMC3879100 DOI: 10.1186/1471-2148-13-256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 11/11/2013] [Indexed: 01/28/2023] Open
Abstract
Background Endogenous retroviruses (ERVs) are genomic elements of retroviral origin that are present in the genomes of almost all vertebrates. In cattle, more than 13,000 elements related to ERVs have been detected, and based on the pol gene, 24 families or groups of bovine ERVs have been described. However, information about ERVs in other bovids and the presence of families of related bovine ERVs in different species of the Bovidae family is scarce. Results The 24 families of bovine ERVs previously detected in cattle (Bos taurus) were also detected in zebus (Bos indicus) and yaks (Bos grunniens). In addition, six new families, named BoERV25 to BoERV30, were detected in the three Bos species. Five more ruminant species were screened for related ERVs: 26 families were detected in these species, but four families (BoERV24, BoERV26, BoERV28 and BoERV29) were specific to cattle, zebus, yaks and buffalo. An analysis of the homology of the ERVs of cattle, zebus and yaks revealed that the level of LTR divergence was similar between ERVs from cattle and zebus but was less similar between with ERVs from cattle and yaks. In addition, purifying selection was detected in the genes and retroviral regions of clusters of ERVs of cattle, zebus and yaks. Conclusions In this work, the 24 ERV families previously identified in cattle were also found in two other species in the Bos genus. In addition, six new bovine ERV families were detected. Based on LTR divergence, the most recently inserted families are from Class II. The divergence of the LTR, used as an indirect estimate of the ERV insertion time, seemed to be influenced by the differences in genome evolution since the divergence of the species. In addition, purifying selection could be acting on clusters of ERVs from different species.
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Affiliation(s)
| | - Begoña M Jugo
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), 644 Postakutxa, E-48080 Bilbao, Spain.
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Kalmykov NP. The most ancient finding of mountain sheep (mammalia, artiodactyla: Ovis) in the holarctic (Western Transbaikalia). DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2013; 448:25-27. [PMID: 23479013 DOI: 10.1134/s0012496613010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Indexed: 06/01/2023]
Affiliation(s)
- N P Kalmykov
- Russian Academy of Sciences, Rostov-on-Don, Russia
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Palma-Irizarry M, Damian-Matsumura P, Betancourt M, Romo S, Perales G, Lagunas-Martínez A, Madrid-Marina MV, Mejía O, Ducolomb Y. Identification of novel variants of interferon-tau gene in Bighorn sheep (Ovis canadensis mexicana), Pelibuey sheep (Ovis aries) and its expression in hybrid blastocysts (Ovis canadensis × Ovis aries). CANADIAN JOURNAL OF ANIMAL SCIENCE 2012. [DOI: 10.4141/cjas2011-023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Palma-Irizarry, M., Damian-Matsumura, P., Betancourt, M., Romo, S., Perales, G., Lagunas-Martínez, A., Madrid-Marina, M. V., Mejía, O. and Ducolomb, Y. 2012. Identification of novel variants of interferon-tau gene in Bighorn sheep ( Ovis canadensis mexicana ), Pelibuey sheep ( Ovis aries ) and its expression in hybrid blastocysts ( Ovis canadensis×Ovis aries ). Can. J. Anim. Sci. 92: 275–283. The major signal for maternal recognition of pregnancy (MRP) in ruminants is interferon-tau (IFNT). Four novel sequences of the IFNT gene were isolated from genomic DNA obtained from blood samples of Bighorn, Pelibuey or the hybrid ewes. The deduced amino acid sequence of the hybrid ewe showed 100% identity with one Bighorn sheep IFNT sequence, suggesting that this sequence was inherited from Bighorn sheep. The high degree of identity between Pelibuey and Bighorn sheep sequences could be a possible explanation for the successful MRP in some Bighorn hybrid pregnancies. In vivo and in vitro domestic sheep (Ovis aries) and hybrid sheep (Ovis aries×Ovis canadensis) blastocysts were obtained, and IFNT expression was measured by semiquantitative RT-PCR. In vivo and in vitro hybrid blastocysts showed lower expression of IFNT when compared with domestic blastocysts. In conclusion this study showed that there exists an effect of hybridization on IFNT expression and this can affect the MRP.
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Affiliation(s)
- M. Palma-Irizarry
- UAM-I, Av San Rafael Atlixco No. 186, Col. Vicentina Del. Iztapalapa México D.F. C.P. 09340. México
| | - P. Damian-Matsumura
- Departamento de Biología de la Reproducción UAM-I, Av San Rafael Atlixco No.186, Col. Vicentina Del. Iztapalapa México D.F. C.P. 09340. México
| | - M. Betancourt
- Departamento de Ciencias de la Salud UAM-I, Av San Rafael Atlixco No.186, Col. Vicentina Del. Iztapalapa México D.F. C.P. 09340. México
| | - S. Romo
- FES Cuautitlán-UNAM. Km 2.5 Carretera Cuautitlán–Teoloyucan, Cuautitlán Izcalli, Edo de México. C.P. 54714. México
| | - G. Perales
- Lab. Virología Molecular CISEI-INSP. Universidad No. 655, Col. Santa María Ahuacatitlán, Cerrada los Pinos y Caminera. Cuernavaca, Edo de Morelos. C.P. 62100. México
| | - A. Lagunas-Martínez
- Lab. Virología Molecular CISEI-INSP. Universidad No. 655, Col. Santa María Ahuacatitlán, Cerrada los Pinos y Caminera. Cuernavaca, Edo de Morelos. C.P. 62100. México
| | - M. V. Madrid-Marina
- Lab. Virología Molecular CISEI-INSP. Universidad No. 655, Col. Santa María Ahuacatitlán, Cerrada los Pinos y Caminera. Cuernavaca, Edo de Morelos. C.P. 62100. México
| | - O. Mejía
- CEIEPO FMVZ-UNAM. Km 53.1 Carretera Federal México-Cuernavaca, Municipio de Huitzilac. Tres Marías. Edo de Morelos. C.P. 62515. México
| | - Y. Ducolomb
- Departamento de Ciencias de la Salud UAM-I, Av San Rafael Atlixco No.186, Col. Vicentina Del. Iztapalapa México D.F. C.P. 09340. México
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Haynes GD, Latch EK. Identification of novel single nucleotide polymorphisms (SNPs) in deer (Odocoileus spp.) using the BovineSNP50 BeadChip. PLoS One 2012; 7:e36536. [PMID: 22590559 PMCID: PMC3348150 DOI: 10.1371/journal.pone.0036536] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 04/09/2012] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are growing in popularity as a genetic marker for investigating evolutionary processes. A panel of SNPs is often developed by comparing large quantities of DNA sequence data across multiple individuals to identify polymorphic sites. For non-model species, this is particularly difficult, as performing the necessary large-scale genomic sequencing often exceeds the resources available for the project. In this study, we trial the Bovine SNP50 BeadChip developed in cattle (Bos taurus) for identifying polymorphic SNPs in cervids Odocoileus hemionus (mule deer and black-tailed deer) and O. virginianus (white-tailed deer) in the Pacific Northwest. We found that 38.7% of loci could be genotyped, of which 5% (n = 1068) were polymorphic. Of these 1068 polymorphic SNPs, a mixture of putatively neutral loci (n = 878) and loci under selection (n = 190) were identified with the FST-outlier method. A range of population genetic analyses were implemented using these SNPs and a panel of 10 microsatellite loci. The three types of deer could readily be distinguished with both the SNP and microsatellite datasets. This study demonstrates that commercially developed SNP chips are a viable means of SNP discovery for non-model organisms, even when used between very distantly related species (the Bovidae and Cervidae families diverged some 25.1−30.1 million years before present).
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Affiliation(s)
- Gwilym D. Haynes
- Department of Biological Sciences, Behavioral and Molecular Ecology Research Group, University of Wisconsin – Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Emily K. Latch
- Department of Biological Sciences, Behavioral and Molecular Ecology Research Group, University of Wisconsin – Milwaukee, Milwaukee, Wisconsin, United States of America
- * E-mail:
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Miller JM, Malenfant RM, Moore SS, Coltman DW. Short reads, circular genome: skimming solid sequence to construct the bighorn sheep mitochondrial genome. ACTA ACUST UNITED AC 2011; 103:140-6. [PMID: 21948953 DOI: 10.1093/jhered/esr104] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As sequencing technology improves, an increasing number of projects aim to generate full genome sequence, even for nonmodel taxa. These projects may be feasibly conducted at lower read depths if the alignment can be aided by previously developed genomic resources from a closely related species. We investigated the feasibility of constructing a complete mitochondrial (mt) genome without preamplification or other targeting of the sequence. Here we present a full mt genome sequence (16,463 nucleotides) for the bighorn sheep (Ovis canadensis) generated though alignment of SOLiD short-read sequences to a reference genome. Average read depth was 1240, and each base was covered by at least 36 reads. We then conducted a phylogenomic analysis with 27 other bovid mitogenomes, which placed bighorn sheep firmly in the Ovis clade. These results show that it is possible to generate a complete mitogenome by skimming a low-coverage genomic sequencing library. This technique will become increasingly applicable as the number of taxa with some level of genome sequence rises.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
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Deng T, Wang X, Fortelius M, Li Q, Wang Y, Tseng ZJ, Takeuchi GT, Saylor JE, Säilä LK, Xie G. Out of Tibet: Pliocene woolly rhino suggests high-plateau origin of Ice Age megaherbivores. Science 2011; 333:1285-8. [PMID: 21885780 DOI: 10.1126/science.1206594] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Ice Age megafauna have long been known to be associated with global cooling during the Pleistocene, and their adaptations to cold environments, such as large body size, long hair, and snow-sweeping structures, are best exemplified by the woolly mammoths and woolly rhinos. These traits were assumed to have evolved as a response to the ice sheet expansion. We report a new Pliocene mammal assemblage from a high-altitude basin in the western Himalayas, including a primitive woolly rhino. These new Tibetan fossils suggest that some megaherbivores first evolved in Tibet before the beginning of the Ice Age. The cold winters in high Tibet served as a habituation ground for the megaherbivores, which became preadapted for the Ice Age, successfully expanding to the Eurasian mammoth steppe.
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Affiliation(s)
- Tao Deng
- Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
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Poissant J, Davis CS, Malenfant RM, Hogg JT, Coltman DW. QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep. Heredity (Edinb) 2011; 108:256-63. [PMID: 21847139 DOI: 10.1038/hdy.2011.69] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Dissecting the genetic architecture of fitness-related traits in wild populations is key to understanding evolution and the mechanisms maintaining adaptive genetic variation. We took advantage of a recently developed genetic linkage map and phenotypic information from wild pedigreed individuals from Ram Mountain, Alberta, Canada, to study the genetic architecture of ecologically important traits (horn volume, length, base circumference and body mass) in bighorn sheep. In addition to estimating sex-specific and cross-sex quantitative genetic parameters, we tested for the presence of quantitative trait loci (QTLs), colocalization of QTLs between bighorn sheep and domestic sheep, and sex × QTL interactions. All traits showed significant additive genetic variance and genetic correlations tended to be positive. Linkage analysis based on 241 microsatellite loci typed in 310 pedigreed animals resulted in no significant and five suggestive QTLs (four for horn dimension on chromosomes 1, 18 and 23, and one for body mass on chromosome 26) using genome-wide significance thresholds (Logarithm of odds (LOD) >3.31 and >1.88, respectively). We also confirmed the presence of a horn dimension QTL in bighorn sheep at the only position known to contain a similar QTL in domestic sheep (on chromosome 10 near the horns locus; nominal P<0.01) and highlighted a number of regions potentially containing weight-related QTLs in both species. As expected for sexually dimorphic traits involved in male-male combat, loci with sex-specific effects were detected. This study lays the foundation for future work on adaptive genetic variation and the evolutionary dynamics of sexually dimorphic traits in bighorn sheep.
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Affiliation(s)
- J Poissant
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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40
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Robinson TJ, Ropiquet A. Examination of Hemiplasy, Homoplasy and Phylogenetic Discordance in Chromosomal Evolution of the Bovidae. Syst Biol 2011; 60:439-50. [DOI: 10.1093/sysbio/syr045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Terence J. Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - Anne Ropiquet
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
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Meadows JRS, Hiendleder S, Kijas JW. Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel. Heredity (Edinb) 2010; 106:700-6. [PMID: 20940734 DOI: 10.1038/hdy.2010.122] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Five haplogroups have been identified in domestic sheep through global surveys of mitochondrial (mt) sequence variation, however these group classifications are often based on small fragments of the complete mtDNA sequence; partial control region or the cytochrome B gene. This study presents the complete mitogenome from representatives of each haplogroup identified in domestic sheep, plus a sample of their wild relatives. Comparison of the sequence successfully resolved the relationships between each haplogroup and provided insight into the relationship with wild sheep. The five haplogroups were characterised as branching independently, a radiation that shared a common ancestor 920,000 ± 190,000 years ago based on protein coding sequence. The utility of various mtDNA components to inform the true relationship between sheep was also examined with Bayesian, maximum likelihood and partitioned Bremmer support analyses. The control region was found to be the mtDNA component, which contributed the highest amount of support to the tree generated using the complete data set. This study provides the nucleus of a mtDNA mitogenome panel, which can be used to assess additional mitogenomes and serve as a reference set to evaluate small fragments of the mtDNA.
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Affiliation(s)
- J R S Meadows
- CSIRO Livestock Industries, St Lucia, Queensland, Australia
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Poissant J, Hogg JT, Davis CS, Miller JM, Maddox JF, Coltman DW. Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep. BMC Genomics 2010; 11:524. [PMID: 20920197 PMCID: PMC3091677 DOI: 10.1186/1471-2164-11-524] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 09/28/2010] [Indexed: 12/23/2022] Open
Abstract
Background The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corresponding sets of molecular markers that are sufficiently large. We took advantage of two long-term field studies of pedigreed individuals and genomic resources originally developed for domestic sheep (Ovis aries) to construct a linkage map for bighorn sheep, Ovis canadensis. We then assessed variability in genomic structure and recombination rates between bighorn sheep populations and sheep species. Results Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals. Conclusions We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the elevated mean recombination rate observed in domestic sheep, our results suggest that it is a characteristic of Ovis species. However, domestication may have played a role in altering patterns of heterochiasmy. Finally, we found that interval-specific patterns of sexual dimorphism were preserved among closely related Ovis species, possibly due to the conserved position of these intervals relative to the centromeres and telomeres. This study exemplifies how transferring genomic resources from domesticated species to close wild relative can benefit evolutionary ecologists while providing insights into the evolution of genomic structure and recombination rates of domesticated species.
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Affiliation(s)
- Jocelyn Poissant
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Miller JM, Poissant J, Kijas JW, Coltman DW. A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Mol Ecol Resour 2010; 11:314-22. [PMID: 21429138 DOI: 10.1111/j.1755-0998.2010.02918.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of genomic resources for wild species is still in its infancy. However, cross-species utilization of technologies developed for their domestic counterparts has the potential to unlock the genomes of organisms that currently lack genomic resources. Here, we apply the OvineSNP50 BeadChip, developed for domestic sheep, to two related wild ungulate species: the bighorn sheep (Ovis canadensis) and the thinhorn sheep (Ovis dalli). Over 95% of the domestic sheep markers were successfully genotyped in a sample of fifty-two bighorn sheep while over 90% were genotyped in two thinhorn sheep. Pooling the results from both species identified 868 single-nucleotide polymorphisms (SNPs), 570 were detected in bighorn sheep, while 330 SNPs were identified in thinhorn sheep. The total panel of SNPs was able to discriminate between the two species, assign population of origin for bighorn sheep and detect known relationship classes within one population of bighorn sheep. Using an informative subset of these SNPs (n=308), we examined the extent of genome-wide linkage disequilibrium (LD) within one population of bighorn sheep and found that high levels of LD persist over 4 Mb.
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Affiliation(s)
- J M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae). Mol Phylogenet Evol 2009; 54:315-26. [PMID: 19897045 DOI: 10.1016/j.ympev.2009.10.037] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 10/19/2009] [Accepted: 10/29/2009] [Indexed: 11/23/2022]
Abstract
New insights for the systematic and evolution of the wild sheep are provided by molecular phylogenies inferred from Maximum parsimony, Bayesian, Maximum likelihood, and Neighbor-Joining methods. The phylogeny of the wild sheep was based on cytochrome b sequences of 290 samples representative of most of the sub-species described in the genus Ovis. The result was confirmed by a combined tree based on cytochrome b and nuclear sequences for 79 Ovis samples representative of the robust clades established with mitochondrial data. Urial and mouflon, which are either considered as a single or two separate species, form two monophyletic groups (O. orientalis and O. vignei). Their hybrids appear in one or the other group, independently from their geographic origin. The European mouflon O. musimon is clearly in the O. orientalis clade. The others species, O. dalli, O. canadensis, O. nivicola, and O. ammon are monophyletic. The results support an Asiatic origin of the genus Ovis, followed by a migration to North America through North-Eastern Asia and the Bering Strait and a diversification of the genus in Eurasia less than 3 million years ago. Our results show that the evolution of the genus Ovis is a striking example of successive speciation events occurring along the migration routes propagating from the ancestral area.
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45
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Meadows JRS, Kijas JW. Re-sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes. Anim Genet 2009; 40:119-23. [DOI: 10.1111/j.1365-2052.2008.01799.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bulazel KV, Ferreri GC, Eldridge MDB, O'Neill RJ. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol 2008; 8:R170. [PMID: 17708770 PMCID: PMC2375000 DOI: 10.1186/gb-2007-8-8-r170] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 08/20/2007] [Indexed: 11/12/2022] Open
Abstract
The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes. Background It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos). Results The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks. Conclusion These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny.
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Affiliation(s)
- Kira V Bulazel
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
| | - Gianni C Ferreri
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
| | - Mark DB Eldridge
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
- Molecular Biology, Australian Museum, College St, Sydney, NSW 2010, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
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Arnaud F, Caporale M, Varela M, Biek R, Chessa B, Alberti A, Golder M, Mura M, Zhang YP, Yu L, Pereira F, DeMartini JC, Leymaster K, Spencer TE, Palmarini M. A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses. PLoS Pathog 2008; 3:e170. [PMID: 17997604 PMCID: PMC2065879 DOI: 10.1371/journal.ppat.0030170] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 09/26/2007] [Indexed: 11/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of the host germline transmitted vertically from generation to generation. It is hypothesized that some ERVs are used by the host as restriction factors to block the infection of pathogenic retroviruses. Indeed, some ERVs efficiently interfere with the replication of related exogenous retroviruses. However, data suggesting that these mechanisms have influenced the coevolution of endogenous and/or exogenous retroviruses and their hosts have been more difficult to obtain. Sheep are an interesting model system to study retrovirus-host coevolution because of the coexistence in this animal species of two exogenous (i.e., horizontally transmitted) oncogenic retroviruses, Jaagsiekte sheep retrovirus and Enzootic nasal tumor virus, with highly related and biologically active endogenous retroviruses (enJSRVs). Here, we isolated and characterized the evolutionary history and molecular virology of 27 enJSRV proviruses. enJSRVs have been integrating in the host genome for the last 5–7 million y. Two enJSRV proviruses (enJS56A1 and enJSRV-20), which entered the host genome within the last 3 million y (before and during speciation within the genus Ovis), acquired in two temporally distinct events a defective Gag polyprotein resulting in a transdominant phenotype able to block late replication steps of related exogenous retroviruses. Both transdominant proviruses became fixed in the host genome before or around sheep domestication (∼ 9,000 y ago). Interestingly, a provirus escaping the transdominant enJSRVs has emerged very recently, most likely within the last 200 y. Thus, we determined sequentially distinct events during evolution that are indicative of an evolutionary antagonism between endogenous and exogenous retroviruses. This study strongly suggests that endogenization and selection of ERVs acting as restriction factors is a mechanism used by the host to fight retroviral infections. The genome of all vertebrates is heavily colonized by “endogenous” retroviruses (ERVs). ERVs derive from retrovirus infections of the germ cells of the host during evolution, leading to permanent integration of the viral genome into the host DNA. Because ERVs are integrated in the host genome, they are transmitted to subsequent generations like any other host gene. The function of endogenous retroviruses is not completely clear, but some ERVs can block the replication cycle of horizontally transmitted “exogenous” pathogenic retroviruses. These observations lead to the hypothesis that ERVs have protected the host during evolution against incoming pathogenic retroviruses. Here, by characterizing the evolutionary history and molecular virology of a particular group of endogenous betaretroviruses of sheep (enJSRVs) we show a fascinating series of events unveiling the endless struggle between host and retroviruses. In particular, we discovered that: (i) two enJSRV loci that entered the host genome before speciation within the genus Ovis (∼ 3 million y ago) acquired, after their integration, a mutated defective viral protein capable of blocking exogenous related retroviruses; (ii) both these transdominant enJSRV loci became fixed in the host genome before or around sheep domestication (∼ 10,000 y ago); (iii) the invasion of the sheep genome by ERVs of the JSRV/enJSRVs group is still in progress; and (iv) new viruses have recently emerged (less than 200 y ago) that can escape the transdominant enJSRV loci. This study strongly suggests that endogenization and selection of ERVs acting as restriction factors is a mechanism used by the host to fight retroviral infections.
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Affiliation(s)
- Frederick Arnaud
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
| | - Marco Caporale
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
| | - Mariana Varela
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
| | - Roman Biek
- Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland
| | - Bernardo Chessa
- Sezione di Malattie Infettive del Dipartimento di Patologia e Clinica Veterinaria, University of Sassari, Sassari, Italy
| | - Alberto Alberti
- Sezione di Malattie Infettive del Dipartimento di Patologia e Clinica Veterinaria, University of Sassari, Sassari, Italy
| | - Matthew Golder
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
| | - Manuela Mura
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
| | - Ya-ping Zhang
- State Key Laboratory of Genetic Resources, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
| | - Filipe Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - James C DeMartini
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kreg Leymaster
- United States Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Thomas E Spencer
- Center for Animal Biotechnology and Genomics, Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - Massimo Palmarini
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
- * To whom correspondence should be addressed. E-mail:
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Meadows JRS, Cemal I, Karaca O, Gootwine E, Kijas JW. Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics 2006; 175:1371-9. [PMID: 17194773 PMCID: PMC1840082 DOI: 10.1534/genetics.106.068353] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Archaeozoological evidence indicates that sheep were first domesticated in the Fertile Crescent. To search for DNA sequence diversity arising from previously undetected domestication events, this survey examined nine breeds of sheep from modern-day Turkey and Israel. A total of 2027 bp of mitochondrial DNA (mtDNA) sequence from 197 sheep revealed a total of 85 haplotypes and a high level of genetic diversity. Six individuals carried three haplotypes, which clustered separately from the known ovine mtDNA lineages A, B, and C. Analysis of genetic distance, mismatch distribution, and comparisons with wild sheep confirmed that these represent two additional mtDNA lineages denoted D and E. The two haplogroup E sequences were found to link the previously identified groups A and C. The single haplogroup D sequence branched with the eastern mouflon (Ovis orientalis), urial (O. vignei), and argali (O. ammon) sheep. High sequence diversity (K = 1.86%, haplogroup D and O. orientalis) indicates that the wild progenitor of this domestic lineage remains unresolved. The identification in this study of evidence for additional domestication events adds to the emerging view that sheep were recruited from wild populations multiple times in the same way as for other livestock species such as goat, cattle, and pig.
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