Integrative genomic analyses reveal genetic structuring and cyto-nuclear incongruences within the Corbicula species complex in China

Investigating the genetic relationships within the Corbicula species complex poses significant challenges, primarily stemming from cyto-nuclear mismatches, arising from their asexual androgenesis and hybridizations between distinct genetic lineages. In this study, we examined the genetic relationships among Corbicula populations in their native range in China for the first time by integrating mitochondrial and nuclear datasets, with a specific focus on assessing cyto-nuclear incongruences. Sequencing data from 73 individuals across 17 Corbicula populations revealed marked genetic structuring, delineating three major clades: CGA (Corbicula Group A), CGB, and CGC. CGA exhibited substantial genetic differentiation from CGB and CGC, with relatively high Fst values of 0.87 and 0.83, respectively, whereas CGB and CGC showed moderate differentiation (Fst = 0.15). Phylogenetic analyses of genomic SNP and mitochondrial COI datasets uncovered significant topological conflicts within CGC. The Hap3 (invasive form B, FW1) was identified in individuals across CGB and CGC, showing high abundance and a wide distribution. CGA was inferred to be a putative estuarine species C. aff. japonica. Additionally, COI sequencing of 534 individuals from 26 populations identified three major clades, providing an updated mitochondrial phylogeny of Corbicula within its native range in China. Collectively, our findings indicate that the Corbicula species complex in its native range can be assigned into three major groups, with notable cyto-nuclear incongruences prevalent across these lineages.