Genome-Wide Insights into Intraspecific Taxonomy and Genetic Diversity of Argali (Ovis ammon)
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Published:2023-05-05
Issue:5
Volume:15
Page:627
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ISSN:1424-2818
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Container-title:Diversity
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language:en
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Short-container-title:Diversity
Author:
Dotsev Arsen1ORCID, Koshkina Olga1ORCID, Kharzinova Veronika1ORCID, Deniskova Tatiana1ORCID, Reyer Henry2ORCID, Kunz Elisabeth3, Mészáros Gábor4ORCID, Shakhin Alexey1, Petrov Sergey1, Medvedev Dmitry5, Kuksin Alexander6, Bat-Erdene Ganchimeg57, Munkhtsog Bariushaa8, Bagirov Vugar1, Wimmers Klaus2ORCID, Sölkner Johann8, Medugorac Ivica3, Zinovieva Natalia1ORCID
Affiliation:
1. L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia 2. Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany 3. Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, 80539 Munich, Germany 4. Institute of Livestock Sciences, University of Natural Resources and Life Sciences (BOKU), 1180 Vienna, Austria 5. Department of Game Management and Bioecology, Irkutsk State University of Agriculture, 664038 Molodezhny, Russia 6. Tuva Institute for the Integrated Development of Natural Resources of the Siberian Branch of the Russian Academy of Sciences, 667007 Kyzyl, Russia 7. Khovd Branch School of National University of Mongolia, Jargalant 67301, Mongolia 8. Irbis Mongolia Center, Ulaanbaatar 13380, Mongolia
Abstract
Argali (Ovis ammon), the largest species among all wild sheep, is native to mountainous regions of Central and East Asia, spreading mainly throughout such countries as Tajikistan, Kyrgyzstan, Kazakhstan, Afghanistan, Mongolia, Russia and China. Intraspecific taxonomy of argali remains unclear, and currently, most researchers recognize up to nine subspecies. The aim of our work was to investigate the phylogenetic relationship between populations of O. ammon based on genome-wide SNP analysis. Five subspecies, Altai (O. a. ammon) (n = 6), Gobi (O. a. darwini) (n = 5), Pamir (O. a. polii) (n = 12), Tian Shan (O.a. karelini) (n = 15) and Kyzylkum (O. a. severtzovi) (n = 4), were genotyped using Illumina OvineHD BeadChip. In addition, complete mitogenome sequences from 30 of those samples were obtained. After quality control procedures, 65,158 SNPs were selected for the subsequent analyses. Neighbor-Net dendrogram and principal component analysis (PCA) revealed that the five subspecies could be grouped into four clusters. It was shown that a population from Altai formed a cluster with Gobi subspecies. The highest pairwise FST genetic distance was between O. a. ammon and O. a. severtzovi (0.421) and the lowest were between O. a. polii and O.a. karelini (0.083) and between O. a. ammon and O. a. darwini (0.040) subspecies. Genetic diversity was higher in Central Asian argali as compared to East Asian populations. O. a. severtzovi had an admixed origin and consisted of two genetic components—73.5 ± 0.2% of O. a. polli and 26.5 ± 0.2% of urial (O. vignei). TreeMix analysis revealed a migration event from urial to O. a. severtzovi argali. The analysis of complete mitogenomes supported the results based on whole-genome genotyping. Considering that all the mtDNA sequences of O. a severtzovi belonged to O. ammon and not to O. vignei, we concluded that gene flow in this group was associated with urial males. As this is only the first work on intraspecific taxonomy and genetic diversity of argali based on genome-wide SNP genotyping and the analysis of complete mitogenomes, we suggest that more genetic studies are needed to clarify the status of Gobi and Tian Shan argali.
Subject
Nature and Landscape Conservation,Agricultural and Biological Sciences (miscellaneous),Ecological Modeling,Ecology
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