Reply to the comment by Beacham and Withler on "Gene flow increases temporal stability of Chinook salmon (Oncorhynchus tshawytscha) populations in the Upper Fraser River, British Columbia, Canada".

Beacham and Withler (2010. Can. J. Fish. Aquat. Sci. 67: 202–205) raise concerns about the experimental design and interpretation of data in the analysis of temporal genetic variation of Chinook salmon (Oncorhynchus tshawytscha) from the Upper Fraser River, Canada (Walter et al. 2009. Can. J. Fish. Aquat. Sci. 66: 167–176). They note that for the sampled populations, spatial genetic variance should far exceed temporal variance components based on previously published work and suggest that limited sample sizes biased our results by confounding sampling error with temporal variation. Here, we perform a rarefaction analysis by randomly removing up to 50% of the individuals from sample sites, yet the pattern of temporal versus spatial variation is similar to that reported in our original paper. We reiterate that caution should be applied to the interpretation of migration rates estimated from assignment tests, yet the absolute magnitude of our migration estimates was not central to the goals of the original p...