Data_Sheet_1_Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands.pdf

Many ungulate populations have a complex history of isolation and translocation. Consequently, ungulate populations may have experienced substantial reductions in the level of overall gene flow, yet simultaneously have augmented levels of long-distance gene flow. To investigate the effect of this dual anthropogenic effect on the genetic landscape of ungulates, we genotyped 35K SNPs in 47 red deer (Cervus elaphus) of Netherlands, including putative autochthonous relic populations as well as allochthonous populations established in private estates and rewilding areas. We applied FST and ordination analyses to determine the meta-population genetic structure and thereby the occurrence of hybridization. At population level, we investigated levels of inbreeding through individual-based diversity measures, including Runs of Homozygosity. We documented that both spatial genetic structure and within-population genetic variation differed markedly from patterns assumed from present-day abundance and distribution. Notwithstanding the small spatial scale, red deer populations formed distinct genetic clusters, and some had higher genetic similarity to distant than to nearby populations. Moreover, the putative autochthonous relic deer populations had much reduced levels of polymorphism and multi-locus heterozygosity, despite relatively large current population sizes. Accordingly, genomes of these deer contained a high proportion of long (>5 Mb) Runs of Homozygosity. Whereas the observed high levels of inbreeding warrant defragmentation measures, the presence of adjacent autochthonous and allochthonous genetic stocks imply that facilitation of gene flow would cause genetic homogenization. Such distortions of the genetic landscape of ungulates creates management dilemmas that cannot be properly anticipated without baseline genetic monitoring.

诸多有蹄类动物种群均拥有复杂的隔离与易位历史。受此影响，这类种群的整体基因流水平可能大幅降低，但与此同时长距离基因流的水平却有所提升。为探究这种双重人为影响对有蹄类动物遗传格局的作用，我们对荷兰境内47只马鹿（Cervus elaphus）进行了35,000个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNP）的基因分型，样本涵盖推定的本土孑遗种群，以及在私人庄园和再野化区域中建立的外来种群。我们采用遗传分化系数（Fixation Index, FST）与排序分析方法，解析其集合种群遗传结构，进而判断杂交事件的发生情况。在种群层面，我们通过基于个体的多样性指标（包括纯合子片段（Runs of Homozygosity, ROH））探究了近交水平。研究发现，空间遗传结构与种群内遗传变异均与基于当前种群数量和分布所推测的模式存在显著差异。尽管空间尺度较小，马鹿种群仍形成了独立的遗传聚类群，部分种群与远距离种群的遗传相似性反而高于邻近种群。此外，尽管当前种群规模相对较大，但推定的本土孑遗马鹿种群的多态性与多位点杂合度水平均大幅降低。因此，这些马鹿的基因组中含有极高比例的长片段（>5 Mb）纯合子片段。鉴于观测到的高水平近交，亟需采取种群碎片化修复措施；但邻近的本土与外来遗传种群的存在意味着，促进基因流将会引发遗传同质化。这种有蹄类动物遗传格局的扭曲会引发管理困境，若不开展基线遗传监测，便无法对这类困境进行合理预判。