Hidden Diversity in a Species Complex of Rockfishes from Japan ^†

The genus Sebastes comprises around 110 species of marine fish. In Japan, the Sebastes inermis complex includes three sympatric species (S. cheni, S. inermis, and S. ventricosus), and morphotypes that cannot be assigned to any of these three species. We focused on two morphotypes: (1) the ‘big red’, which is predominantly found in the Kii and Izu peninsulas and are traditionally believed to be large, older specimens of S. inermis; and (2) the ‘red white’, which is found in the Seto Inland Sea and Kagoshima and includes putative hybrids of S. cheni and S. inermis. We assessed the biological identity of both morphotypes by comparing their morphological and genetic variations with those of the three species. The meristic traits of both morphotypes overlapped with those of the three species. The ‘big red’ morphotype showed significant differences in body proportions and otolith structure, whereas the ‘red white’ morphotype differed mainly in otolith features. Phylogenetic analyses of mitochondrial and nuclear genes did not separate these morphotypes into distinct lineages. However, the ‘big red’ morphotype exhibited unique mutations at the rhodopsin gene. Analyses of microsatellite loci indicated that the divergence of both morphotypes is as large as the divergence observed between sister species within the genus. Phylogenetic analyses of genomic data placed the ‘big red’ morphotype in a basal position in relation to the three species and supported the separation of the ‘red white’ morphotype from S. cheni and S. inermis. Genomic scan analyses comparing the ‘big red’ and ‘red white’ morphotypes with S. inermis and S. cheni, respectively, indicate that genes involved in fertilization, egg hatching, immunity, and thermal resilience are under divergent selection. Overall, the results suggest that both morphotypes could represent previously undescribed cryptic species, warranting further investigation to confirm their status as independent taxa.