Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole‐genome sequences of 30 caribou (Rangifer tarandus ) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes. Caribou are split into four subspecies and 11 extant conservation units, known as designatable units (DUs), in Canada. Using genomes from all four subspecies and six DUs, we undertake demographic reconstruction and confirm two previously inferred instances of parallel evolution in the woodland subspecies and uncover an additional instance of parallelism of the eastern migratory ecotype. Detailed investigations reveal introgression in the woodland subspecies, with introgressed regions found spread throughout the genomes encompassing both neutral and functional sites. Our investigations using whole genomes highlight the difficulties in unequivocally demonstrating parallelism through adaptive introgression in nonmodel species with complex demographic histories, with standing variation and introgression both potentially involved. Additionally, the impact of parallelism and introgression on conservation policy for management units needs to be considered in general, and the caribou designations will need amending in light of our results. Uncovering and decoupling parallelism and differential patterns of introgression will become prevalent with the availability of comprehensive genomic data from nonmodel species, and we highlight the need to incorporate this into conservation unit designations.

中文翻译：

---

渐渗和生态平行性在描述种内保护单位中的作用。

通过选择新的突变，遗传变异或适应性渗入可以实现平行进化。发现并行性和渗入种群会使受威胁物种的管理复杂化，因为并行性可能影响到保护单位的指定，而且法律通常不考虑混合种群。我们检查了30个北美驯鹿（Rangifer tarandus）的高覆盖全基因组序列），来自北美和格陵兰岛（代表不同的种内谱系），以调查平行性和渗入水平对生态型形成的贡献。在加拿大，驯鹿分为四个亚种和11个现存的保护单位，称为可指定单位（DUs）。使用来自所有四个亚种和六个DU的基因组，我们进行了人口统计学重建，并确认了两个先前推断的林地亚种平行进化实例，并揭示了东部迁徙生态型的另一个平行实例。详细的调查显示，林地亚种有渗入性，发现渗入区域遍布整个基因组，包括中性和功能性位点。我们使用全基因组的研究突显了在具有复杂人口统计学历史的非模型物种中，通过适应性渗入明确地证明平行性的困难，而站立变异和渗入都可能涉及。此外，通常需要考虑并行性和渗透性对管理单位保护政策的影响，根据我们的结果，需要对驯鹿的名称进行修改。随着来自非模型物种的全面基因组数据的获得，发现和解脱平行性和渗入的差异模式将变得普遍，我们强调必须将其纳入保护单位名称。潜在的变异和基因渗入都可能涉及。此外，通常需要考虑并行性和渗透性对管理单位保护政策的影响，根据我们的结果，需要对驯鹿的名称进行修改。随着来自非模型物种的全面基因组数据的获得，发现和解脱平行性和渗入的差异模式将变得普遍，我们强调必须将其纳入保护单位名称。潜在的变异和基因渗入都可能涉及。此外，通常需要考虑并行性和渗透性对管理单位保护政策的影响，根据我们的结果，需要对驯鹿的名称进行修改。随着来自非模型物种的全面基因组数据的获得，发现和解脱平行性和渗入的差异模式将变得普遍，我们强调必须将其纳入保护单位名称。