Deciphering demographic history and fine-scale population structure of cobia, Rachycentron canadum (Pisces: Rachycentridae) using microsatellite and mitochondrial markers

Cobia, Rachycentron canadum is a candidate species for aquaculture, distributed across the Indo-Pacific waters to the southern Atlantic Ocean. Information on genetic diversity and population structure of cobia is crucial for sustainable utilization and management of the species in natural waters. In the present study, we used 14 polymorphic microsatellite loci and mitochondrial cytochrome b gene (980 bp) to investigate the genetic diversity and population structuring of R. canadum along the Indian coast. Microsatellite analysis suggests a relatively high level of genetic diversity of cobia in the Indian region, with a mean Ho and He of 0.76 and 0.73. The PIC was also highly informative (0.841), with a mean no. of alleles of 11.304. Hierarchical AMOVA and genetic differentiation co-efficient between the populations was found to be low, but significant (FST = 0.035, P < 0.001), indicating fine scale structuring in the region. Pair-wise FST, neighbor-joining tree, principal coordinates analysis, and Bayesian analysis depict three populations of cobia in Indian waters: two in the Arabian Sea and one in the Bay of Bengal. The mitochondrial gene analyses showed discordant findings in comparison with microsatellite markers. However, both the markers yielded no inference of historical demographic bottleneck. Multi-modal mismatch distributions and ragged index, non-significant Tajima’s D and Fu’s FS, and L-shaped distribution pattern of the allele frequencies, indicated the lack of bottleneck events of the species in the recent past. Based on mitochondrial gene analysis, the population expansion was inferred to have occurred 0.046 Myrs ago, corresponding to the late Pleistocene.