3RAD Phylogenetics and Population Genomics of Elimia melanoides sensu lato and related species

Freshwater gastropods are among the most imperiled organisms globally, and taxonomic uncertainty remains a major obstacle to their conservation. Elimia melanoides (Conrad, 1834), previously presumed extinct, was rediscovered in the Black Warrior River drainage of Alabama, prompting renewed interest in its conservation status. However, persistent taxonomic uncertainty has hindered listing under the U.S. Endangered Species Act. We used integrative taxonomy, including extensive field sampling, 3RAD-based phylogenomics, and morphological analysis of museum specimens, to resolve the taxonomy of E. melanoides sensu lato. Our molecular phylogenetic analyses revealed that E. melanoides, as currently conceived, comprises three distinct lineages: E. melanoides sensu stricto, E. hydeii (in part), and E. turgida, which we restore from synonymy. Comparison to historical museum specimens indicates that the extant lineage currently identified as E. melanoides is not conspecific with the taxon described as Anculosa melanoides by Conrad. We propose to follow prevailing usage and retain the name Elimia melanoides for the extinct taxon described by Conrad. There is no available name for the extant taxon, which we describe here as Elimia mintoni n. sp. Population genomic analyses reveal high genetic structure in E. mintoni n. sp. and E. hydeii, especially in headwater populations, while E. turgida shows no structure across its narrow range but maintains high genetic diversity. These findings have urgent conservation implications: E. mintoni n. sp. and E. turgida are valid, range-restricted species with low redundancy and representation. Our study underscores the necessity of taxonomic resolution for accurate biodiversity assessments and effective conservation planning.