A comparative evolutionary study reveals radically different scales of genetic structuring within two atyid shrimp species (Crustacea Decapoda: Atyidae)

Increasingly, molecular approaches are uncovering biodiversity that was previously unrecognized by traditional morphological taxonomy. Cryptic or pseudo-cryptic species are commonly documented in freshwater environments, where isolation of dispersal-limited taxa in fragmented hydrological networks often results in high intraspecific genetic divergence. The present study compares the genetic structuring of two co-distributed species of the freshwater shrimp genus Caridina, Caridina africana and Caridina typus, across their South African distributional range using the COI marker and a multilocus dataset comprising mitochondrial (COI, 16S rRNA and 12S rRNA) and nuclear (28S rRNA and H3) markers. Several species delimitation techniques were applied to both the single-locus COI dataset (automatic barcode gap discovery and generalized mixed Yule coalescent) and the multilocus dataset (BPP). Results unambiguously reveal a discordance in phylogeographical structuring between the two species, with C. typus exhibiting genetic homogeneity on this geographical scale, whereas in C. africana three DNA-delimited lineages can be recognized. These cryptic lineages exhibit strong geographical regionalization, with hydrological fragmentation during the last sea-level transgression of the Miocene/Pliocene epochs promoting lineage diversification in combination with low dispersal ability.