Taking stock: defining populations of American shad (Alosa sapidissima) in Canada using neutral genetic markers

Knowledge of the scale of population structure is a prerequisite for designating conservation units. American shad (Alosa sapidissima) are of increasing conservation concern, but the scale of population structure within the Canadian portion of the species range is unknown. Using 13 microsatellite loci, we examined the partitioning of genetic variation within four and among 12 Canadian drainages. We detected significant (p < 0.05) and temporally stable genetic differentiation among all drainages, supporting the hypothesis that rivers support genetically distinct populations. However, Bayesian methods identified seven clusters and provided evidence for shad metapopulation structure. We observed a significant (p < 0.01) pattern of isolation by distance (IBD) among all drainages. A strong linear IBD (r = 0.98) was observed among rivers that were outside the Bay of Fundy (BoF). A hypothesized counterclockwise migration route explained a greater proportion of genetic variation (r = 0.87) among BoF rivers than direct route based distances (r = 0.14). Although IBD patterns did not differ regionally (analysis of covariance; p > 0.05), the degree of differentiation among BoF rivers was greater than that among non-BoF rivers, regardless of the geographic scale of comparison. Our results suggest that fisheries managers need to be concerned with the loss of shad genetic diversity on both river and regional scales.