Molecular Ecology (2003) 12, 385–394 © 2003 Blackwell Publishing Ltd Blackwell Science, Ltd Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod H. KNUTSEN,*† P. E. JORDE,*† C. ANDRÉ ‡ and N. CHR. STENSETH *† *Flødevigen Marine Research Station, Department of Coastal Zone, Institute of Marine Research, N-4817 His, Norway, †Division of Zoology, Department of Biology, University of Oslo, Oslo, Norway, ‡Tjärnö Marine Biological Laboratory, Strömstad, Sweden Abstract Compared with many terrestrial and freshwater environments, dispersal and interbreeding is generally much less restricted in the marine environment. We studied the tendency for a marine species, the Atlantic cod, to be sub-structured into genetically differentiated popu- lations on a fine geographical scale. We selected a coastal area free of any obvious physical barriers and restricted sampling to a 300-km region, well within the dispersal ability of this species. Screening 10 polymorphic microsatellite loci in 6 samples we detected a weak, but consistent, differentiation at all 10 loci. The average F ST over loci was small (0.0023) but highly significant statistically, demonstrating that genetically differentiated populations can arise and persist in the absence of physical barriers or great distance. We found no geo- graphical pattern in the genetic differentiation and there was no apparent trend of isolation by distance along the coastline. These findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance. Keywords: Gadus morhua, gene flow, genetic differentiation, local populations, microsatellites Received 6 October 2002; revision received 7 November 2002; accepted 7 November 2002 Introduction Populations constitute interbreeding units with more or less autonomous dynamics and recruitment. In terrestrial and freshwater environments, populations are often well defined and distinct from each other, often separated physically by barriers to mixing and interbreeding (see, e.g. Avise 2000 for an extensive review). In the marine environment, in contrast, physical barriers are often absent and the continuous water instead represents a potential means for dispersal, favouring intermixing of individuals over the species range. Tides and ocean currents may further act to mix passively drifting organisms, primarily eggs and larvae, over appreciable distances (see Palumbi 2001). For these reasons, distinct populations are more difficult to detect in the marine environment and for many marine organisms it is unclear to what degree distinct populations exist at all, or whether they are organized into larger panmictic units (McQuinn 1997). The distinction is crucial, in particular for heavily exploited organisms such as many marine fish, because recruitment and sustainability are properties of the population. Failure to identify the population could lead to local over- exploitation and subsequent decline, as has become abundantly clear in recent decades (e.g. Atlantic cod in Alaska, Hutchings 2000, and along the Swedish west coast, Svedäng et al . 2001). Genetic markers are valuable tools for analysing popu- lation structure (see, e.g. Utter 1991 for a historical review of the application of genetic markers to fish populations). By characterizing the geographical distribution of allele or haplotype frequencies, population sub-structuring can be detected and local populations identified. Such applica- tions of genetic markers have been very successful in uncovering cryptic population structure in freshwater (Allendorf et al . 1976; Jorde & Ryman 1996; Carlsson et al . 1999) and marine fish (Nesbø et al . 2000; Ruzzante et al . 2000; Hutchinson et al . 2001). The use of genetic markers for population delineation requires a detectable level of genetic differentiation, however, and this has presented problems in studies of many marine organisms (Ward et al . 1994). In the marine environment many studies have failed to detect statistically significant population structuring Correspondence: H. Knutsen. Fax: +47-370-59001; E-mail: halvor@imr.no