Genetic Determination of a Cryptic Species in the <i>Littoraria</i> Genus With Whole‐Genome Molecular Resolution

Recognizing cryptic species is crucial for understanding global biodiversity. The intertidal snail <i>Littoraria flammea</i> is potentially a cryptic species of <i>L. melanostoma</i> widely distributed in the Northwest Pacific. However, the evidence from traditional morphology and single genetic markers is inconsistent. Our study combined quantitative morphological and whole-genome molecular data to clarify the phylogenetic relationship of three species (<i>L. flammea</i>, <i>L.</i> aff. <i>melanostoma</i>, and <i>L. melanostoma</i>). Three-dimensional models of shells revealed significant differences in morphology between <i>L. flammea</i> and <i>L. melanostoma</i>. Neutral SNPs indicated that individuals of <i>L. flammea</i> and <i>L. melanostoma</i> were in different clusters. The ratio of interspecific <i>F</i> _ST to intraspecific <i>F</i> _ST between <i>L. flammea</i> and <i>L. melanostoma</i> (16) was much larger than the lowest ratio (2.31) in six published genera with cryptic species in gastropods. Non-neutral SNPs disclosed divergence in functional genes related to reproduction and protein binding. The morphological and phylogenetic analyses corroborated the transitional status of <i>L.</i> aff. <i>melanostoma</i>. These results confirmed that the <i>L. flammea</i> snails north of the Yangtze River Estuary is a cryptic species of <i>L. melanostoma</i>, and allopatric speciation occurs in the <i>L. melanostoma</i> complex.