On rRNA gene cluster variation, phylogeny and local ecological differentiation in the Jaera albifrons complex (Crustacea: Isopoda)

The Jaera albifrons species complex comprises several closely related species of intertidal marine isopods that exhibit limited morphological differentiation and varying degrees of hybridization. In this pilot study, we analyzed regions of the nuclear rRNA genes (D1-D2 and ITS1) from populations of J. albifrons, J. praehirsuta, and J. ischiosetosa to assess their utility as diagnostic markers for species identification and phylogenetic inference. Despite the species morphological distinctness and ecological differences, rRNA variability was remarkably shallow across the complex, with only few variable sites in D1-D2 and ITS1. This contrasted sharply with high interspecific divergence observed in other Jaera species, indicating recent divergence and nascent speciation within the complex. J. ischiosetosa showed the lowest intra-individual variation and was most distinct from the two other species. Overlap between J. albifrons and J. praehirsuta genotypes, consistent with known introgressive hybridization, was considerable and likely stems from introgressive hybridization. Local hybridization patterns identifiable morphologically varied across settlements with of the settlements demonstrating unusually high hybridization rates. Different settlements were found to demonstrate a range of abiotic factors impacting spatial separation of the different species and varying degrees of similarity between the species in rRNA genotypes. Phylogenetic analysis of the genus revealed that the J. albifrons complex originates from among the species of the Mediterranean species group and represents a recent migration from the Mediterranean rather than an early-diverging lineage as previously suggested. These findings highlight the challenges of using rRNA markers for species delimitation in recently diverged and hybridizing taxa and underscore variable hybridization and spatial segregation as key factors shaping coexistence in mixed populations.