The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.

中文翻译：

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希腊和塞浦路斯土著牛种群的基因组多样性和种群结构。

由于社会经济原因，地理上的孤立以及与商业品种的杂交，来自希腊和塞浦路斯的土著牛群数量已减少，目前处于灭绝的危险中。这项研究代表了对来自希腊大陆和希腊群岛的10个本地牛种群和来自塞浦路斯的一个种群的首次全基因组全分析，并将它们与104种国际品种进行比较，使用了46,000多个单核苷酸多态性（SNP）。我们估计了遗传多样性的几个参数（例如，杂合性和等位基因多样性），这些参数表明与内陆种群相比，岛上种群的遗传多样性严重丧失，这主要是由于近年来种群数量的减少和近亲繁殖。与其余地理品种组相比，这种高度的近交状况也导致了希腊和塞浦路斯牛群内更高的遗传分化。有监督和无监督的聚类分析表明，希腊土著品种的系统发育模式与其地理起源和关于与安纳托利亚或巴尔干起源的品种杂交的历史信息一致。塞浦路斯的牛显示出较高的祖先血统。希腊小岛上的人口位于吉尔（Gir）和外Ya牛（Yak）定义的树的根部附近，而大陆品种与布沙（Buša）具有相同的历史起源。无监督聚类和D统计分析为从安纳托利亚到阿尔卑斯山南麓的几乎所有调查过的当地牛品种，以及沿亚平宁半岛到南部的大多数牛品种的Bos indicus渗入提供了有力支持。阿尔卑斯山的山麓小丘。所有经过调查的塞浦路斯和希腊品种都表现出复杂的镶嵌基因组，这是近邻和分隔良好的品种之间历史和近期混合事件的结果。虽然某些内地品种对遗传多样性库的贡献似乎很重要，但由于遗传漂移，一些岛屿和零散的内地品种却遭受人口规模的严重下降和等位基因的损失。