In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring the boundaries between a single, large metapopulation-level lineage and multiple independent species. Here we explore this model of species formation in the Eastern Red-backed Salamander (Plethodon cinereus), a widespread terrestrial vertebrate with at least six divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, we applied phylogenomic and population genomic approaches to investigate patterns of divergence, gene flow, and secondary contact. Genomic data broadly match most mitochondrial groups but reveal mitochondrial introgression and extensive admixture at several contact zones. While species delimitation analyses in BPP supported five lineages of P. cinereus, genealogical divergence indices (gdi) were highly sensitive to the inclusion of admixed samples and the geographic representation of candidate species, with increasing support for multiple species when removing admixed samples or limiting sampling to a single locality per group. An analysis of morphometric data revealed differences in body size and limb proportions among groups, with a reduction of forelimb length among warmer and drier localities consistent with increased fossoriality. We conclude that P. cinereus is a single species, but one with highly structured component lineages of various degrees of independence.

中文翻译：

---

集合种群的限制：分布广泛的陆生蝾螈（Plethodon cinereus）的谱系分裂


在替代物种的形成中，分歧主要是由于异域异域时期和基因流动受限造成的。广泛存在的物种拥有差异化的、地理上不同的亚谱系，为了解物种形成的常见模式提供了一个窗口，即一个物种起源、分布在整个景观中，然后分裂成多个单位。然而，早期的谱系通常缺乏阻止它们在二次接触时融合的生殖障碍，从而模糊了单个大型集合种群水平谱系和多个独立物种之间的界限。在这里，我们探索了东部红背蝾螈（Plethodon cinereus）的物种形成模型，这是一种分布广泛的陆生脊椎动物，在其分布范围内至少有六个不同的线粒体进化枝。使用锚定的混合富集数据，我们应用系统发育学和群体基因组方法来研究分歧、基因流和二次接触的模式。基因组数据与大多数线粒体群体大致匹配，但揭示了线粒体渗入和几个接触区的广泛混合。虽然 BPP 中的物种界定分析支持 P. cinereus 的五个谱系，但谱系分歧指数 (GDI) 对混合样本的包含和候选物种的地理代表性高度敏感，在去除混合样本或限制采样时，对多个物种的支持增加每个组的一个位置。对形态测量数据的分析揭示了各组之间身体尺寸和四肢比例的差异，在温暖和干燥的地区，前肢长度减少与化石增加一致。我们的结论是 P. cinereus 是一个单一物种，但具有不同独立程度的高度结构化的组成谱系。