Species divergence despite minimal morphological differentiation and habitat overlap in the Patelloida saccharina (Patellogastropoda: Lottiidae) species complex

Abstract We describe the current state of speciation in the species complex of the marine gastropod Patelloida saccharina, using mitochondrial COI, 16S RNA, nuclear histone 3 gene and single-nucleotide polymorphism (SNP) markers from 165 specimens collected from 37 localities across the Japanese archipelago. In total, 28 unique COI haplotypes, 16 16S haplotypes, 11 histone 3 haplotypes and 148 734 SNPs were obtained. Genetic assignments and phylogenetic trees recovered three genetically distinct lineages: P. saccharina saccharina, P. saccharina lanx and an unknown P. sp. from Shionomisaki, Wakayama Prefecture. The divergence between P. saccharina saccharina and P. saccharina lanx was estimated to have occurred around 44 000 years ago—too recent to have accumulated the morphological differences that have confounded taxonomic identification. Continuous gene exchange after an initial split is suggested based on demographic history analyses, which allowed for introgression of the P. saccharina lanx genome and the proliferation of intermediate individuals. Speciation, despite the existence of a contact zone in the Ryukyu Islands, possibly occurred due to the eventual reproductive isolation that followed the initial split with gene flow. Patelloida saccharina saccharina and P. saccharina lanx were strongly supported by our results as two separate species, and a revision of the current taxonomic descriptions based on their phylogeny, demographic history and species distribution is proposed.