Integrating genetic and morphological data to assess species delimitation of two Japanese large abalones: Haliotis discus discus and H. madaka

Abstract Two large abalone species prevalent in the Japanese archipelago, Haliotis discus discus and H. madaka , are considered to have different morphological characteristics, and previous population genomics analyses have suggested that they have distinct genomic features. However, integrated analyses comparing the genetic and morphological data from these species are lacking; thus, it remains unclear whether these two species are distinct biological species. In this study, we performed integrated genetic and morphological analyses on individuals of the two species captured in Tokushima Prefecture, Japan. Genetic analysis based on 118 species-diagnostic single-nucleotide polymorphism (SNP) loci showed that H. discus discus and H. madaka were clearly assigned to distinct genetic clusters corresponding to the two species, with the exception of one H. madaka individual showing evidence of genomic introgression from H. discus discus . Multiple statistical analyses based on quantitative characteristics of shell shape and foot muscle color suggested that this H. madaka individual with genomic introgression from H. discus discus had H. discus discus -like quantitative characteristics consistently. In summary, this study suggests that H. discus discus and H. madaka are distinct biological species reproductively isolated in natural environments, but genomic introgression possibly blurs the species boundary between H. discus discus and H. madaka .