Micro geographical population structure of cod Gadus morhua in the North Sea and west of Scotland: the role of sampling loci and individuals

We investigated potential microgeographical population structure among spatial and temporal samples of cod Gadus morhua L., collected in the northern North Sea and around Scotland, using microsatellite genetic markers. Results were highly dependent on the samples and microsatellite loci included. Analysis of molecular variance (AMOVA) revealed significant spatial (p = 0.04) and temporal (p = 0.02) variance when including samples of juveniles and the microsatellite Gmo 132, which is known to be subject to selection. However, neither spatial nor temporal variance components were significant (p = 0.15 and 0.23, respectively) after exclusion of juvenile samples and Gmo 132. Patterns of genetic differentiation showed a similar sensitivity to the sampling of loci. No apparent pattern was identified when only using suspected neutral microsatellites. In contrast, analysis of Gmo132 alone revealed a clear isolation of 2 samples collected at Viking and pairwise grouping of temporal adult samples from the same location. On a northeast Atlantic regional scale, inferences on local populations and patterns of population structuring were more robust to the inclusion of the microsatellite under selection. Our results demonstrate that, without cautious consideration of biased samples of individuals and loci, apparent microgeographical patterns of spatial genetic differentiation could be caused by sampling non-randomly distributed individuals of hitch-hiking selection at presumed neutral marker loci. However, while loci subject to selection may provide biased results in relation to identifying populations based on an evolutionary paradigm, they may prove valuable for separating populations on ecological time scales,