Remarkably low mtDNA control region diversity in an abundant demersal fish

Cape hake, Merluccius paradoxus, is a valuable commercially exploited demersal species. Using the 5' mtDNA control region we show that 96% of 1013 fishes sampled over a three-year period share one of two dominant haplotypes; 19 haplotypes were recovered in total, suggesting a genetically homogenous population of fish. Accordingly, haplotype and nucleotide diversities are low (h = 0.53, pi = 0.0014); an asymptotic haplotype accumulation curve suggests that few additional haplotypes exist. Comparing h and pi with other fish species shows that M. paradoxus and other southern African fish species have remarkably low genetic diversity values compared with other global marine fishes. Despite low genetic variability, frequency differences among M. paradoxus haplotypes suggest weakly structured populations between Namibia and South Africa. However, given the remarkably homogeneous mtDNA population genetic structure between fishes sampled along 1800 km, it is clear that faster evolving markers such a microsatellites are also needed before inferences can be made regarding stock identification and management of this species.