Molecular Ecology (2004) 13, 1377–1390 doi: 10.1111/j.1365-294X.2004.02165.x © 2004 Blackwell Publishing Ltd Blackwell Publishing, Ltd. Mitochondrial DNA variation in Northeast Atlantic and Mediterranean populations of Norway lobster, Nephrops norvegicus C. STAMATIS,* A. TRIANTAFYLLIDIS,† K. A. MOUTOU * and Z. MAMURIS * *Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, 41221, Larissa, Greece, †Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece Abstract Analysis of the genetic structure of the Norway lobster (Nephrops norvegicus), a marine crustacean with high commercial value, was undertaken to gain information regarding the differentiation of Atlantic from Mediterranean populations of marine invertebrates. Restriction fragment length polymorphism analysis of two mitochondrial DNA segments, 3.6 kilobases in total, was performed. Twelve populations from the North Sea, Irish Sea, Portuguese coast and Aegean Sea were analysed. Low levels of differentiation were found among them (F ST = 0.018, P < 0.001) and there were no signs of an Atlantic–Mediterranean divide or of an isolation-by-distance scheme of differentiation. Possible reasons for these low levels of differentiation can be found in the recent expansion of N. norvegicus populations. This is supported by the mismatch distribution of pairwise haplotype differences, as well as by the high mean haplotype diversity (h = 0.93) combined with medium nucleotide diversity (π = 0.0057) (in comparison to values for marine crustaceans or teleosts) found in this study. This combination of high levels of haplotype diversity with moderate to low levels of nucleotide diversity has also been frequently attributed to a recent time of divergence for various marine species. No evidence was found for a Mediterranean refugium during glaci- ation periods, separate from the Atlantic, as has been reported for some marine species. The Irish Sea population was the most differentiated as a result of reduced levels of diversity. Results are also discussed in the light of future management of N. norvegicus stocks. Keywords: Crustacea, Europe, genetic structure, mitochondrial DNA, Nephrops, phylogeography Received 17 September 2003; revision received 15 January 2004; accepted 4 February 2004 Introduction Analyses of marine species have, generally, revealed less spatial variation in genetic structure than populations in- habiting freshwater environments. This is because of, among other reasons, their large population sizes, their high potential for dispersal and the perceived lack of barriers to dispersal (Graves 1998). In this regard, marine species with an Atlantic– Mediterranean distribution are of special interest; in addition to present day restrictions to gene flow, the Mediterranean Sea has been completely separated from the Atlantic Ocean on a number of occasions. The dispersal between the two water bodies was intermittently restricted during the Quaternary glaciations when lowered sea levels probably resulted in a narrowing or total closure of the Gibraltar Straits (Maldonado 1985). Analyses of the genetic structure of marine species with an Atlantic–Mediterranean distribution are relatively few and have mostly dealt with fish species (see Borsa et al . 1997 for a review). In the majority of the studies so far, moderately strong to strong genetic differentiation between each side of the Gibraltar strait was observed, e.g. for swordfish Xiphias gladius (Kotoulas et al . 1995), for Mytilus galloprovin- cialis (Quesada et al . 1998), for a number of sparid fishes (Bargelloni et al . 2003) and for the krill Meganyctiphanes norvegica (Zane et al . 2000). Hypotheses for the observed patterns of differentiation have included various models such as isolation by distance with limited gene flow and, Correspondence: Z. Mamuris. Fax: +30 2410579310; E-mail: zmamur@uth.gr