Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding i) species-level diversity, ii) hybridization and admixture, and iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named linea...

暗无肺螈类（Dusky Salamanders）隶属于Desmognathus属，目前仅正式记述有22个现生物种。然而近期基于线粒体与核基因的估算研究显示，依托生态地理采样可识别出多达49个候选物种。既往研究还表明，该类群各支系间存在复杂的杂交演化历史。其他类群的相关研究提示，忽略遗传混合（admixture）可能会对系统发育推断（phylogenetic inference）及基于聚类的物种界定（clustering-based species-delimitation）工作造成干扰。本研究的数据集涵盖了来自全部49个候选物种的896份Desmognathus属标本的233个锚定杂交富集（Anchored Hybrid Enrichment, AHE）基因座测序数据，旨在检验三项假设：其一为物种水平多样性相关假设，其二为杂交与遗传混合相关假设，其三为系统发育推断受误导的相关假设。通过结合基因流分析的系统发育与群体聚类分析方法，本研究在系统基因组数据集中支持至少47个候选物种的有效性，其中部分物种为本次研究首次正式定名，其余则为此前已命名支系的组合……