in our neighbor-joining tree, in which the bootstrap value for the Surprise Lake populations forming a clade received 96% support. Although the best information we have supports the hypothesis that the two Surprise Lake populations are genetically closer to each other than to other populations, genetic similarity is certainly not “proof” of common ancestry. Gene flow as well as common ancestry will result in close genetic relationships. This compli- cation is precisely why we want to apply the IM model to this system, as it partitions these competing homogenizing processes. As with all applications of the IM model between popula- tions, we cannot rule out that there is some level of gene flow with other populations outside of Surprise Lake. However, due to the 300 m elevation gain that may impose a substantial migratory barrier to outside populations, as well at the close proximity and the limitation of the study to the only populations sharing Sur- prise lake as the nursery lake, we believe that “the history of a sample from two populations can reasonably be described by an IM model” (Hey and Nielsen 2006). Migrate analysis We ran the program MIGRATE 3.0.3 (Beerli and Felsenstein 2001; Beerli 2006) on the same dataset to compare the output with the results from IM. This model estimates similar parameters to IM, except there is no “time since divergence” parameter. The model assumes that there has been sufficient time since divergence that migration and drift subsequent to divergence has a greater effect on current genetic relationships than shared ancestry prior to divergence. We used the same mutation rates from the method above. We used the Bayesian search strategy with slice sampling Markov chain Monte Carlo (MCMC) with four heated chains. We started with experimental runs with large priors and then performed long runs with uniform priors of 0–30 for both θ and m. We set the burn-in for 50,000 steps and collected date for 2,400,000 steps. R E C E N T D I V E R G E N C E D E S P I T E M I G R AT I O N Results ECOLOGICAL PARAMETERS Surprise Lake outlet had larger substrate than Surprise Lake beaches (Fig. 2). Surprise Lake beaches have no measurable flow in the water column, but we calculated an average current of 0.455 m/sec in the outlet. MORPHOLOGICAL TRAITS Male MOH averaged 497.9 mm (MOH; body length) and body depth averaged 186.6 mm. There was no difference in MOH be- tween the populations (P = 0.79). ANCOVA results indicated that male body depth was significantly correlated with length (P < 0.0001), and that both year (P < 0.01) and habitat (P < 0.001) were significant factors in determining body depth (Table 1, Fig. 3). Egg mass was significantly correlated with MOH of females (P < 0.01), and habitat was a significant factor as well; the eggs of outlet sockeye were larger than those of beach sockeye (Table 1, Fig. 4; P < 0.02). TIME SINCE DIVERGENCE AND MIGRATION Our WHICHLOCI simulation indicated that individuals could be assigned to the correct population most of the time (86.0%, SE 0.11% including One110; 82.3%, SE 0.12% excluding One110). Also, the program indicated no outlier loci, as the relative assign- ment ability of each locus was evenly spread (minimum score 13.4% of six loci including One110, 16.5% of five loci excluding One110). Sequential dropping of loci did not substantially change the original FST of 0.0112 reported in Pavey et al. (2007). The range of sequential dropping was FST = 0.0110–0.0135. Mutation rates calculated from the two methods were within the same order of magnitude. The geometric mean of mutation rates for all loci using the mutation rate scalar method was 7.91 × 10 −4 per generation or 1.58 × 10−4 per year (Table 2). For the Figure 2. Size distribution of substrate for the two breeding locations. EVOLUTION JUNE 2010 1 7 7 7