RESEARCH ARTICLE B. Stockley Æ G. Menezes Æ M. R. Pinho Æ A. D. Rogers Genetic population structure in the black-spot sea bream (Pagellus bogaraveo Bru ¨ nnich, 1768) from the NE Atlantic Received: 24 April 2004 / Accepted: 20 September 2004 / Published online: 2 December 2004 Ó Springer-Verlag 2004 Abstract The depletion of shallow-water fish stocks through overexploitation has led to increasing fishing pressure on deep-sea species. Poor knowledge of the biology of commercially valuable deep-water fish has led to the serial depletion of stocks of several species across the world. Data regarding the genetic structure of deep- sea fish populations is important in determining the impact of overfishing on the overall genetic variability of species and can be used to estimate the likelihood of recolonisation of damaged populations through immi- gration of individuals from distant localities. Here the genetic structure of the commercially fished deep-water species the blackspot sea bream, Pagellus bogaraveo is investigated in the northeastern Atlantic using partial DNA sequencing of mitochondrial cytochrome b (cyt-b) and D-loop regions and genotyping of microsatellite loci. An absence of variation in cyt-b and low genetic variation in D-loop sequences potentially indicate that P. bogaraveo may have undergone a severe bottleneck in the past. Similar bottlenecks have been detected in other Atlantic species of fish and have possibly originated from the last glaciation. P. bogaraveo may have been particularly vulnerable to the effects of low temperature and a fall in sea level because stages of its life history occur in shallow water and coastal sites. However, there are other explanations of low genetic variability in populations of P. bogaraveo, such as a low population size and the impacts of fishing on population structure. Analysis of population structure using both D-loop and microsatellite analysis indicates low to moderate, but significant, genetic differentiation between populations at a regional level. This study supports studies on other deep-sea fish species that indicate that hydrographic or topographic barriers prevent dispersal of adults and/or larvae between populations at regional and oceano- graphic scales. The implications for the management and conservation of deep-sea fish populations are dis- cussed. Introduction The depletion of fish stocks associated with the conti- nental seas of the world has led to increasing fishing efforts directed at deep-water species (e.g. Haedrich 1995; Koslow et al. 2000). These fisheries have focused on seamounts, continental slopes, and the slopes of oceanic islands. In the deep sea, it is in these habitats that concentrations of heavy-bodied, bentho-pelagic fish species, suitable for commercial exploitation, are found. Technological requirements for deep-sea fishing have meant that the majority of these fisheries have com- menced recently, since the late 1960s, starting with the exploitation of species such as slender armourhead (Pseudopentaceros wheeleri Hardy, 1983), in the Pacific, by the Soviet fishing fleet (Sasaki 1986). Since this time, fishing operations in deep waters have expanded and vessels from developed nations now target fish species such as orange roughy (Hoplostethus atlanticus Collett, 1889), oreo (Allocytus niger James, Inada, Nakamura, 1988); A. verrucosus (Gilchrist, 1906), Pseudocyttus maculates Gilchrist, 1906), and grenadiers (Coryphae- noides spp.), down to depths of up to 2,000 m all over the world (Rogers 1994; Gianni 2004). Several major problems have arisen as a result of deep-sea fisheries. The first of these is the rapid depletion of deep-sea fish populations that are subject to fishing Communicated by J.P. Thorpe, Port Erin B. Stockley School of Ocean & Earth Science, University of Southampton, Southampton Oceanography Centre, European Way, Southampton, SO14 3ZH, UK G. Menezes Æ M. R. Pinho Departamento de Oceanografia e Pescas da Universidade dos Ac¸ores, Cais de Sta Cruz, 9900 Horta, Ac¸ores, Portugal A. D. Rogers (&) British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK E-mail: ADR2@bas.ac.uk Marine Biology (2005) 146: 793–804 DOI 10.1007/s00227-004-1479-3