<p>Fig. C1. Testing selective neutrality of microsatellite markers based on FST-values with the BN- method (Beaumont and Nichols 1996) and FG-method (Foll and Gaggiotti 2008).</p><p>Two kinds of comparison were provided: 1) between samples from Mogilnoe Lake (Kildin cod) and Kildin Salma (marine cod); 2) between samples from marine populations of Atlantic cod (Kildin Salma, Barents Sea, White Sea).</p><p>Selection regimes obtained with the BN-method: balancing selection (yellow), neutrality (grey), positive selection (red); dots stand for locus positions. Loci Gmo-G12 and PGmo95 are likely under natural selection (with probabilities P>0.95), loci Gmo19 and Gmo35 have lower probabilities. Selection regimes obtained with the FG-method: loci on the right-hand side are considered to be under selection. Loci Gmo19, Gmo-C20, and PGmo95 are likely under natural selection (with probability P>0.95), loci Gmo8 and Gmo35 have lower probabilities.</p><p>Fig. C3. 95% confidence intervals of the imbalance index (between the open circles) and expansion (between the filled circles) indices (Kimmel et al. 1998, Zhivotovsky et al. 2000) for Kildin cod (Mogilnoe Lake) and marine populations of Atlantic cod . The indices test for historical changes in effective population size. Negative (positive) values indicate a decrease (increase) in population size. The change is considered to be insignificant for a given population if any of the two confidence intervals includes zero.</p>