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Appendix A1. Polymerase Chain Reaction (PCRa) Information.

Appendix A2. Basic descriptive statistics for 10 microsatellite loci for the 8 sampling locations assessed showing the average number of alleles per locus (NA), observed (HO) and expected (HE) heterozygosities, FIS inbreeding coefficient, allelic richness (AR), and private allelic richness (PAR).

Appendix A3. Shown are typical log-likelihood plots for assignment of first generation migrants among, for example, Great Bear Lake (GBL) and Sandy Lake (A) and among two arms within GBL (B). Qualitatively, power to detect migrants appears very high when comparing between systems, but is hampered when inferring first generation migrants among arms within GBL. Quantitatively, DLR a test statistic used to assess power of assignment tests (Paetkau et al. 2004) was high between GBL and Sandy Lake (DLR ˜ 10 when comparing between systems) and very low when comparing arms within GBL (DLR < 3 between any two arms within GBL) indicating high power of assignment between systems, but not among arms within GBL. Paetkau et al. (2004) state “a value of DLR in excess of 5 was always associated with near maximum power to distinguish immigrants and residents, while a value below 3 was associated with power of less than 0.5”.

Appendix A4. Mean estimates and 95% C.I.'s for of long-term migration calculated using the program MIGRATE. Shown are estimates of migration among arms in GBL (A) and migration between Sandy Lake and GBL (B) averaged over five independent runs.

Appendix A5. Trace plots and marginal density plots of MCMC runs from BAYESASS. Shown is the trace plot and marginal density plot for estimates of contemporary gene flow among arms within GBL (A and B, respectively) and the trace plot and marginal density plot for estimates of contemporary gene flow between Sandy Lake and GBL systems (C and D, respectively). All results are averaged over 10 independent BAYESASS runs.

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