Contemporary effective population and metapopulation size (N(e) and meta-N(e)): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries

We estimated local and metapopulation effective sizes ([Image: see text] and meta-[Image: see text]) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that [Image: see text] might be inversely related to within-species population divergence as reported in an earlier study (i.e., F(ST): S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in [Image: see text] ([Image: see text]) between species, consistent with a hierarchy of adult population sizes ([Image: see text]). Using another method based on a measure of linkage disequilibrium (LDNE: [Image: see text]), we found more finite [Image: see text] values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest [Image: see text] among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in [Image: see text], suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-[Image: see text] might be significantly smaller than the sum of local [Image: see text]s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One ‘bottom-up’ or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta-[Image: see text] estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local [Image: see text]s and meta-[Image: see text]s and their relevance in ecology, evolution and conservation.