Population Genomic Divergence Reveals Uncertainties in Species Identification of Cave‐Dwelling Isopods

Biodiversity conservation is advancing, though much of nature remains unexplored. Subterranean environments hold a significant portion of the world’s biodiversity, yet cave biology still largely relies on morphology for species delimitation. The lack of genomics research hinders the resolution of taxonomic classifications and the reconstruction of species evolutionary history. Here, we examined genetic diversity in seven cave‐dwelling Monolistra isopod species throughout the prealpine arch in Italy and Switzerland. We used genome‐wide single nucleotide polymorphisms (SNPs) to reconstruct phylogenetic relationships and infer population structure among 21 cave populations. Phylogenetic tree reconstruction revealed strong divergence among Monolistra species, splitting into seven phylogenetic clades. Both species and gene trees confirmed an east–west clade divergence, yet highlighted major conflicts between morphology‐based taxonomy and genomic data. Population structure analyses further identified strong within‐clade differentiation and genetic isolation between each cave system. Our findings have important taxonomic implications. They suggest that the true level of diversity within the genus Monolistra could be much greater than currently understood, stressing the importance of genomics research to improve the general comprehension of the evolution of subterranean dwelling organisms and its implications for conservation.