Data from: Conservation of a domestic metapopulation structured into related and partly admixed strains

Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronised maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenisation process. This study collected and evaluated samples, data and genome-wide information and developed genome-assisted cross-border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semi-private alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.

遗传多样性保护是行星边界（planetary boundaries）概念中最紧迫的挑战之一。在此背景下，本研究聚焦于一个本土未选育、高度混杂的驯化集合种群（metapopulation）的遗传多样性。本研究利用中等密度单核苷酸多态性（SNP）芯片，对来自60个不同牛品种的1828个个体进行了遗传分析。其中，14个布沙牛（Buša）类群构成了包含350个个体的集合种群，其余46个品种则作为全球牛种群的参照样本。遗传分析结果显示，这一几乎未经过选育、分化程度较低的布沙牛集合种群，为该全球普通牛（taurine）种群贡献了高达52.6%的中性等位基因多样性。因此，亟需对这一高度碎片化的驯化集合种群开展协同保护：该种群分布于多个国家，缺乏完善的保护基础设施，且因全球遗传同质化进程中的持续回交替换而面临极高的灭绝风险。本研究收集并评估了样本、数据及全基因组信息，同时提出了依托基因组学的跨境保护方案。为检测并维持该集合种群类群的遗传完整性，本研究设计并应用了一种复合检测方法，该方法整合了基于加性遗传关系、最近邻图以及半私有等位基因分布的六项指标。每项指标均可提供关于过往混杂事件的独特信息维度，为混杂异常个体的检测提供了客观且高效的工具。本研究提出的保护方法与实践经验，可轻松适配于驯化物种或其他由人工繁育、圈养或处于其他人类管控模式下的集合种群的类似保护项目。