Computational protocol: Recurrent evolution of life history ecotypes in sockeye salmon: implications for conservation and future evolution

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Protocol publication

[…] We partitioned variation in RFLP haplotype frequencies into 3-level hierarchies (‘among groups’, ‘among populations within group’, and ‘within populations’) based on alternative groupings by geography and/or ecotype (AMOVA, ; implemented in ARLEQUIN by ). Fixation indices (FSC, FCT, and FST) based on the ratios of variance components were used to test the performance of each hierarchical structure against competing structures. Molecular differences among haplotypes were not considered in the AMOVA because most differences in haplotype frequency among populations have resulted from genetic drift rather than recent mutation (Wood et al. unpubl. data). To illustrate the grouping patterns, we used the multi-dimensional scaling (MDS) routine in based on pair-wise chord distances () computed in PHYLIP (). Chord distance is an appropriate measure of genetic distance when populations have diverged by genetic drift rather than mutation and population size has not remained constant (). In the overall MDS plot where the number of replicate populations was large, we included only samples with at least 20 individuals to improve precision and clarity; for MDS plots within regions, all relevant samples were included regardless of sample size.To compare genetic diversity among ecotypes, we examined two standardized indices of genetic diversity (). The first, gene diversity, is not directly affected by sample size, and measures both the number of haplotypes and their relative frequencies. The second index is the number of haplotypes expected in a standard sample size of 10 individuals (determined by resampling); accordingly, in these comparisons, we included only samples with at least 10 individuals. We used 2-way Kruskal-Wallis tests () to test whether median values of gene diversity were higher in the sea/river-ecotype than in the other ecotypes combined, both coast-wide, and within each region. […]

Pipeline specifications

Software tools Arlequin, PHYLIP
Application Population genetic analysis
Organisms Oncorhynchus nerka, Hemisus marmoratus, Oncorhynchus gorbuscha, Oncorhynchus keta