Genetic divergence between sympatric Arctic charr Salvelinus alpinus morphs in Gander Lake,Newfoundland: roles of migration,mutation and unequal effective population sizes

A suite of 10 microsatellite loci was used to examine genetic divergence between two sympatric morphs of Arctic charr Salvelinus alpinus (‘dark’ and ‘pale’) inhabiting Gander Lake, Newfoundland. Results can be summarized as follows: (1) the morphs are strongly reproductively isolated – gene flow–migration estimates were consistently low in long and short‐term evolutionary timescales of analysis; (2) intermorph divergence based on allele size (R_ST) was significantly larger than those based on allele state (θ) implying a cumulative effect of stepwise‐like mutations; (3) historical (coalescent) and current (linkage disequilibrium) point estimates of effective population size (N_e) were consistently higher for dark than for pale S. alpinus. The first and second findings lend support to the hypothesis that divergence between forms may have preceded the last glacial period (ending c. 12 000 years bp ). The third finding argues for significant differences in habitat quantity and quality between morphs, which were emphasized in a previous study. Overall, these analyses underscore the importance of genetic assessment and monitoring in the conservation of fish diversity, with emphasis on ‘rare’ or under‐represented forms among temperate species pairs.