Genetic evaluation of stock structure and population bottlenecks in the severely depleted cowcod

Cowcod (Sebastes levis) range from Oregon to Baja California and are currently assumed to be one continuous population.  Since 2004, it has been on the National Marine Fisheries Service “Species of Concern” list due to its dramatic decline in abundance (<3.4% - 16.3% of historical biomass).  We address the following questions: 1) Is there population subdivision within the species, specifically, between two marine biogeographic regions separated by Point Conception, and 2) Have cowcod populations experienced loss of genetic variation due to a reduction in population size?  Sixteen variable microsatellite loci were genotyped and ~500 bp of the mitochondrial control region were sequenced for 294 fish distributed throughout the species range.  We observed significant structure when fish were grouped into two regions separated by Point Conception (F_ST=0.066).  However, upon further inspection, an individual-based spatial analysis using Bayesian cluster assignment of the microsatellite genotypes localized this genetic break further south (F_ST=0.092), corresponding to separation between a Channel Islands region versus the mainland.  These results indicate a minimum of two management units in this species.  In general, cowcod shows low genetic diversity compared to other rockfishes.  However, neither cowcod stock appears to have suffered detectable loss in genetic variation, despite declines in abundance.