Appendix S1 Matrix of geographically adjusted genetic distance corresponding to populations shown in Fig. 1.

Appendix S2FST values for pairs of subpopulations examined within woodland caribou.

Appendix S3 Genetic clusters of individual woodland caribou samples from British Columbia and Alberta using program STRUCTURE, but showing the alternate clustering pattern that occurred in <15% of the STRUCTURE runs. Dominant runs are shown in Fig. 2. Cluster membership is shown by colour, and classification uncertainty is shown by symbols. Also shown are a priori defined ecotypes (colour-shaded polygons), and subpopulation names of woodland caribou. Sample sizes are shown in brackets.

Appendix S4 Factorial Correspondence Analysis using the program Genetix (Belkhir 1999) representing the results from program STRUCTURE at the scale of woodland caribou in British Columbia and Alberta, Canada.

Appendix S5 Expected heterozygosity and mean alleles per locus for subpopulations used in analysis of population size (Figs 3 and 4).

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