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全基因组 SNP 基因分型揭示了野生和家养山羊的祖先和近期渗入。

Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats.

机构信息

Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany.

出版信息

Mol Ecol. 2024 Jan;33(1):e17190. doi: 10.1111/mec.17190. Epub 2023 Nov 1.

DOI:10.1111/mec.17190
PMID:37909668
Abstract

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.

摘要

在现今（BP）前 10000 年左右，山羊被人类驯化，人类将山羊远运至它们野生祖先——羱羊的活动范围之外。这使得家山羊与许多野生山羊物种（如野山羊和盘羊）接触，导致家山羊和野生山羊之间发生基因渗入。为了研究这一点，同时阐明野生和家养山羊的分类地位，我们分析了来自 14 个分类单元的 613 个样本的全基因组 SNP 数据，包括绵羊、绵羊、瑞士、奥地利、德国和斯洛文尼亚的野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、野山羊、

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Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats.全基因组 SNP 基因分型揭示了野生和家养山羊的祖先和近期渗入。
Mol Ecol. 2024 Jan;33(1):e17190. doi: 10.1111/mec.17190. Epub 2023 Nov 1.
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Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of bezoar (Capra aegagurus).线粒体DNA研究表明，家山羊（Capra hircus）在基因上受到两种捻角山羊（Capra aegagurus）亚种的影响。
Biochem Genet. 2001 Jun;39(5-6):145-54. doi: 10.1023/a:1010266207735.
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Bezoar (Capra aegagrus) is a matriarchal candidate for ancestor of domestic goat (Capra hircus): evidence from the mitochondrial DNA diversity.羱羊（Capra aegagrus）是家山羊（Capra hircus）祖先的母系候选者：来自线粒体DNA多样性的证据。
Biochem Genet. 1997 Oct;35(9-10):315-26. doi: 10.1023/a:1021869704889.
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Evidence for introgressive hybridization of captive markhor (Capra falconeri) with domestic goat: cautions for reintroduction.圈养捻角山羊（Capra falconeri）与家山羊渐渗杂交的证据：对重新引入的警示
Biochem Genet. 2008 Apr;46(3-4):216-26. doi: 10.1007/s10528-008-9145-y. Epub 2008 Jan 29.
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Characteristics of the Allele Pool and the Genetic Differentiation of Goats of Different Breeds and their Wild Relatives by Str-Markers.利用 STR 标记研究不同品种和野生亲缘山羊的等位基因池特征及其遗传分化。
Arch Razi Inst. 2021 Nov 30;76(5):1351-1362. doi: 10.22092/ari.2021.355684.1709. eCollection 2021 Nov.
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Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica).伊比利亚羱羊（Capra pyrenaica）中隐藏的 MHC 遗传多样性。
BMC Genet. 2018 May 8;19(1):28. doi: 10.1186/s12863-018-0616-9.
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Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies.山羊属（哺乳纲，偶蹄目）的进化史：线粒体DNA与Y染色体系统发育之间的不一致
Mol Phylogenet Evol. 2006 Sep;40(3):739-49. doi: 10.1016/j.ympev.2006.04.002. Epub 2006 Apr 18.
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Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.完整线粒体基因组揭示了驯化对山羊母系变异的影响。
BMC Genomics. 2015 Dec 29;16:1115. doi: 10.1186/s12864-015-2342-2.
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Mitochondrial DNA diversity of Pakistani goats.巴基斯坦山羊的线粒体DNA多样性
Anim Genet. 2003 Dec;34(6):417-21. doi: 10.1046/j.0268-9146.2003.01040.x.
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Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.野山羊（Capra aegagrus）的参考基因组及山羊品种测序为山羊驯化的基因基础提供了见解。
BMC Genomics. 2015 Jun 5;16(1):431. doi: 10.1186/s12864-015-1606-1.

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1
Integrating SNP data to reveal the adaptive selection features of goat populations in extreme environments.整合单核苷酸多态性数据以揭示极端环境中山羊群体的适应性选择特征。
BMC Genomics. 2025 Jun 2;26(1):553. doi: 10.1186/s12864-025-11743-2.
2
Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations.非洲和欧洲牛群全基因组局部祖源及杂交的功能后果
Heredity (Edinb). 2025 Jan;134(1):49-63. doi: 10.1038/s41437-024-00734-w. Epub 2024 Nov 8.
3
The goat pan-genome reveals patterns of gene loss during domestication.
山羊泛基因组揭示了驯化过程中的基因丢失模式。
J Anim Sci Biotechnol. 2024 Oct 5;15(1):132. doi: 10.1186/s40104-024-01092-7.
4
Structural variant landscapes reveal convergent signatures of evolution in sheep and goats.结构变异景观揭示了绵羊和山羊进化的趋同特征。
Genome Biol. 2024 Jun 6;25(1):148. doi: 10.1186/s13059-024-03288-6.