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We sampled 0-group juvenile Atlantic cod Gadus morhua L. within fjords and offshore in northern Norway from 1994 to 2008 using different gears for the 3 sampling depths: shore seine (0−3 m), pelagic trawl (various depths), and bottom trawl (>80 m). Frequencies of alleles at the Pan I locus (4218 fish analysed) showed highly significant differences among samples collected in the different habitats. The Pan IA allele showed a mean frequency of ~80% in the shore seine samples, 12% in the bottom trawl samples, and between 5 and 57% in the pelagic samples. These differences are thought to reflect the co-occurrence of different populations of cod in the area with different settling regimes. Shallow-water settlers are thought to represent the stationary Norwegian coastal cod (NCC), the deep-water settlers represent the migratory Arcto-Norwegian cod (ANC), and the non-settled individuals represent a variable mixture of the 2 populations. For designated samples, we analyzed 16 microsatellites (non-neutral and neutral) that supported a genetic divergence between shallow-water and deep-water settlers. Correlations between length and Pan I genotypes within selected samples showed that the Pan IBB homozygotes (typical of ANC) were significantly longer than the Pan IAA homozygotes (typical of NCC). This could reflect differences in spawning time and growth conditions between ANC and NCC, just as well as one genotype being superior to the others in terms of growth performance. Finally, we argue that the Pan I difference between 0-group NCC and ANC is not caused by contemporary selection but reflects adaptation on an ecological post-glacial time scale

Settling-depth vs. genotype and size vs. genotype correlations at the Pan I locus in 0-group Atlantic cod Gadus morhua