Molecular Ecology (2003) 12, 1497–1508 doi: 10.1046/j.1365-294X.2003.01819.x © 2003 Blackwell Publishing Ltd Blackwell Publishing Ltd. Evidence of a hybrid-zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis EINAR E. NIELSEN,* MICHAEL M. HANSEN,* DANIEL E. RUZZANTE,*† DORTE MELDRUP * and PETER GRØNKJÆR ‡ * Department of Inland Fisheries, Danish Institute for Fisheries Research, DK-8600 Silkeborg, Denmark, ‡ Department of Marine Ecology, University of Aarhus, DK-8200 Aarhus, Denmark Abstract The study of hybrid zones is central to our understanding of the genetic basis of reproduc- tive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transi- tion area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by inter- breeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy–Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transi- tion area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low- saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in rela- tion to a classical study of haemoglobin variation in cod from the Baltic Sea /Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding. Keywords: Atlantic cod, Baltic Sea, hybrid-zone, individual admixture analysis, marine fish, micro- satellite DNA Received 26 September 2002; revision received 13 January 2003; accepted 24 January 2003 Introduction Hybrid zones are defined as areas where genetically distinct groups of individuals interact and result in at least some offspring of mixed ancestry. Pure populations of the two genetically distinct groups are found outside the zone of interaction (Harrison 1990). Hybrid zones have been the focus of much attention during the last couple of decades resulting in a number of extensive reviews of hybrid zone theory and examples of their occurrence (e.g. Endler 1977; Barton & Hewitt 1985; Harrison 1990; Harrison 1993). Basically, two scenarios for hybrid zone formation have been suggested. Primary hybrid zones are formed between populations diverged in sympatry or parapatry by dif- ferential environmental selection. Secondary hybrid zones are formed between formerly allopatric populations that come into secondary contact. Similarly, there are basically two types of models explaining how stable hybrid zones are maintained. Dispersal independent models include those where hybrids are thought to be more fit than both parental types within an ecotone, ‘the Correspondence: Einar E. Nielsen. Fax: + 45 89 213150, E-mail: een@dfu.min.dk †Present address: Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada