The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Fig 2
Clustering sockeye and kokanee individuals (population stratification).
This figure shows the clustering of individuals based on: A) DAPC and B) maximum likelihood analysis (phylogenetic tree). Both analyses began with the same 124,663 variants already filtered for common factors (e.g. maf 0.05) and was specifically filtered for linkage disequilibrium (LD), to reduce the effects of a single genomic location in high LD overwhelming all other signals. A) DAPC analysis clustering with the optimal group number [3] and optimal number of PCAs chosen [6]. The axes represent the first two linear discriminants (LD1 and LD2). The gray, coral (red/orange), and teal (blue) colours correspond to the different clusters. B) An unrooted maximum-likelihood phylogenetic tree, with bootstrap values (based on 1,000 bootstraps) shown as green dots with the larger dots representing greater bootstrap values (min: 0.1 max: 100). Only 7,357 variants remained after default SNPhylo filters. Colours are consistent with the DAPC analysis (DAPC group names shown for comparison). Please note in the Klukshu and Hansen groups, one individual from the other group was found in the grouping and likely represents a switched sample (see S1 Table). Also, there is one Takla kokanee in the Hansen grouping. Sockeye are represented by (S) and kokanee are represented by (K).