| Summary: | The advent of novel genetic methods has made it possible to investigate population structure and connectivity in mobile marine fish species: knowledge of which is essential to ensure a sustainable fishery. Haddock ( Melanogrammus aeglefinus ) is a highly exploited marine teleost distributed along the coast and continental shelf on both sides of the North Atlantic Ocean. However, little is known about its population structure. Here, we present the first study using single nucleotide polymorphism markers to assess the genetic population structure of haddock at multiple geographic scales, from the transatlantic to the local (fjord) level. Genotyping 138 SNP loci in 1329 individuals from 19 locations across the North Atlantic revealed three main genetic clusters, consisting of a Northwest Atlantic-, a Northeast Arctic- and a Northeast Atlantic cluster. We also observed a genetically distinct fjord population and a pattern of isolation-by-distance in the Northeast Atlantic. Our results contrast with the current management regime for this species in the Northeast Atlantic, as we found structure within some management areas. The study adds to the growing recognition of population structuring in marine organisms in general, and fishes in particular, and is of clear relevance for management of haddock in the Northeast Atlantic. SNP genotype data for 1329 individuals of Atlantic haddock ( Melanogrammus aeglefinus ), genotyped at 138 loci in standard STRUCTURE file format. The first row lists the 138 SNP names. Genotypes for the 1329 individuals are listed from row 2 and onwards where genotypes for each individual is given in 2 consecutive lines. Column 1 lists the sample names and column 2 lists the sample location (given as a name, not a number), followed by the genotypes for all 138 SNPs (in the order given in the first row). 1=A, 2=C, 3=G and 4=T. Sample location names are as folows: BAR = Barents Sea, LOF_N = Lofoten north, LOF_S = Lofoten south, VAR = Varangerfjord, ALT = Altafjord, NORL = Nordland, FLOR = Florø, ...
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