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Table S1 Pairwise population genetic divergence (FST) estimates at the MHC class I, MHC class II, and 13 microsatellite loci in five Chinook salmon populations (BQ, Big Qualicum, QR, Quinsam River, PR, Puntledge River; LS, Lower Skeena; KR, Kitsumkalum River) in British Columbia, Canada.

Fig. S1 Phylogenetic trees of bacterial 16s rDNA sequences obtained from kidney tissue of Chinook salmon (Oncorhynchus tshawytscha) from five populations in British Columbia, Canada. Trees show the sequence relationships between the bacteria isolated from each population and the sequence of the closest relative in Genbank. Neighbour-joining trees and bootstrap support values are based on 500 repetitions performed in mega v.4. The populations comprise: Quinsam River (A), Big Qualicum River (B), Puntledge River (C), Kitsumkla.

Fig. S2 MHC allele frequencies and bacterial infections in Chinook salmon (Oncorhynchus tshawytscha) from five populations in British Columbia, Canada. Bars separately denote the relative allele frequencies in uninfected (black) and infected (grey) fry for the MHC class I (A) and class II (B) loci [i.e. the overall frequency of each allele (out of a total of 1) is shown separately for infected and uninfected fish].

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