| Summary: | Two species of commercially exploited deep-sea fish, Pagellus bogaraveo, and Beryx splendens , were investigated in the North East Atlantic using molecular markers to detect population genetic structure. Particular emphasis was placed upon populations of these species around the Azorian Archipelago. Based upon mtDNA sequencing no members of a cryptic species related to B. splendens which have been reported in the Pacific were found in the Azores. Consequently it is likely that single species stock analysis of this species can be performed without the problem of mistaken identity caused by cryptic species. Additionally, contrary to previous evidence, there was substantial genetic differentiation between populations of B. splendens on inter-oceanic scales. Based upon mtDNA sequencing there was evidence of a genetic bottleneck and reduced genetic diversity, in Atlantic P. bogaraveo . A hypothesis of a recent (<20 000 BP) ice-age near extinction event was proposed as a mechanism causing this genetic bottleneck, and the subsequent phylogeographic structure which it may have caused. A set of 10 novel microsatellite primer pairs were developed in order to investigate the spatial and temporal genetic structure of populations of P. bogaraveo . Using microsatellite analysis there was no evidence of reduced effective population sizes of P. bogaraveo correlated with increased fishing pressure upon this species in the Azores. There was also no evidence of significant temporal fluctuation in effective population sizes between year classes in this species. There was however, substantial evidence from both mtDNA sequencing and microsatellite analysis of spatial genetic structure. Therefore it was recommended that stocks of P. bogaraveo from the Azores be treated as a separate Management Unit from those stocks found on the oceanic shelves of mainland Europe.
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