Phylogenomics reveals the intricate history of the most diverse group within Atyidae (Crustacea: Decapoda)

The Atyidae is a diverse and old freshwater shrimp family distributed across all continents bar Antarctica. It is particularly speciose in the Indo-Pacific, the domain of its most diverse group, the so-called Caridella group, which includes the largest and taxonomically challenging genus, Caridina. By using a time-calibrated genomic framework, we reconstructed the biogeographic history of the Caridella group. We show that although their evolution is intimately tied to the geological history of the Tethys Ocean, a slow periodic expansion westward provided multiple invasions of Africa. The knowledge gap about African species is further covered by linking the divergence between East and West African taxa to the East African Rift. Meanwhile, sea level oscillations and landscape changes seem to be the major factors responsible for splits within the Indo-Pacific. We show that amphidromy is ancestral and that landlocked species and clades originated through multiple isolations followed by diversification, which might be related to the numerous species complexes found in this group. Constant diversification rates could reinforce this dispersal-isolation-diversification pattern. Our results also include the most robust phylogeny to date, providing the basis for an overdue re-assessment of the systematics of the Atyidae, particularly, the Caridella group.