CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.
Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
Syst Biol. 2021 Apr 15;70(3):593-607. doi: 10.1093/sysbio/syaa088.
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].
杂交通常可能是适应变异的重要来源，但在辐射的系统发育背景下，很少评估基因渐渗的程度和长期影响。野兔（Lepus）是一个广泛分布的哺乳动物辐射群，有 32 个现存物种，具有显著的生态适应性和反复的混合。为了了解在 Lepus 多样化过程中基因渐渗杂交的相关性，我们分析了来自 15 种野兔（每个物种 1-4 个个体）的全外显子组序列（61.7Mb），这些野兔跨越了该属的全球分布范围，并选择了两个外群。尽管存在广泛的系统发育分歧，我们还是使用了一个并系发生框架来推断物种关系和分化时间。我们发现物种之间存在高水平的等位基因共享，这表明这反映了广泛的不完全谱系分选和时间分层杂交。我们的研究结果表明，在 Lepus 辐射的所有阶段都存在反复的基因渐渗，包括末次冰期以来现存物种之间的近期基因流，以及自野兔谱系起源以来就存在的普遍的古老基因渐渗。我们表明，北半球物种之间的古老杂交导致了潜在适应高度季节性环境的共享变异，包括参与昼夜节律调节、色素沉着和体温调节的基因。我们的研究结果说明了古老杂交的遗传遗产如何在辐射中持续存在，留下了共享遗传变异的持久特征，这可能有助于适应。[适应；古老的基因渐渗；杂交；Lepus；系统基因组学。]
