Phylogenomics and species delimitation for effective conservation of manta and devil rays

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation, and law enforcement strategies

务实的生物多样性保护工作，有赖于划分具有生物学意义的保护单元。蝠鲼科（Mobulidae）物种在全球范围内均受威胁，但其形态相似性及近年一系列分类学修订，阻碍了有效保护策略的制定。本研究采集覆盖地理与分类学代表性的蝠鲼科样本，获取全基因组范围的单核苷酸多态性（SNP）数据，以重构系统发育关系，并基于通用谱系物种概念（general lineage concept）评估物种边界。研究证实，由多类独立数据支撑的暂定物种单元均为独立演化的支系，并在墨西哥湾海域发现了有力证据，支持存在一种疑似新种的蝠鲼。此外，本研究发现了大量不完全谱系分选现象，表明快速物种形成与祖先种群的留存遗传变异共同导致了蝠鲼科内的系统发育不确定性。最后，本研究在地理隔离的种群中发现了丰富的隐存多样性，表明部分物种需要开展物种层级以下的管理工作。综上，本研究为分子遗传物种界定提供了一套适用于诸多面临保护关切的广布类群的研究框架，并凸显了基因组数据在支撑高效管理、保护及执法策略方面的应用潜力。