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.