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Genodive sample data9/19/2023 ![]() ![]() ![]() Distinct ellipses indicate population differentiation. The DAPC analysis was run with 46 principle components (N/3) for the analysis. Site abbreviations can be found in Table 1.ĭiscriminant analysis of principle components (DAPC) of all sample sites with increasing sequencing depth (-m) in the ustacks module with m3 (a, b), m6 (c, d), m10 (e, f), m15 (g, h) and m20 (i, j) in library A (a, c, e, g, i) and B (b, d, f, h, j). Larger F ST values represent larger population differentiation. Heatmap representing the pairwise fixation indices (F ST ) estimated using GENODIVE across all sample sites with increasing sequencing depth (-m) in the ustacks module with m3 (a, b), m6 (c, d), m10 (e, f), m15 (g, h) and m20 (i, j) in library A (a, c, e, g, i) and B (b, d, f, h, j). Library A was generated using a 9mer probe, while library B was generated using a 10mer probe. The populations module was then run on each library independently using no population differentiation in the population map (NoPops), one population required to contain the locus (-p) and 30% of the individuals required to contain the locus (-r). The m parameter influences the number of loci generated per individual in the ustacks module of STACKS, which influences the total number of loci in the catalog and the matched loci in the sstacks module. Summary data from each sequencing library, A and B, with increasing sequencing depth (-m) thresholds in the ustacks module of STACKS. Library A was generated using a 9mer probe and library B was generated using a 10mer probe. Data were generated using three different population maps in the populations module, no specified populations (NoPops), Lake Huron and Dore Lake specifications (LHDL) and sample sites (Pops). Total number of polymorphic loci generated with five different levels of sequencing depth (-m) in ustacks in library A (black) and B (grey). Site abbreviations can be found in Table 1.Ĭollection data for 142 lake whitefish ( Coregonus clupeaformis) samples from Lake Huron, ON, Canada, and Dore Lake, SK, Canada.įlow chart of the bioinformatics pipeline and decisions required for analysis.Įach arrow indicates different libraries that were generated in the analysis. Fish were collected from Lake Huron sites in 2012 and Dore Lake in 2015. Map of the two lakes sampled (a) and the nine sample sites in Lake Huron (b). ![]()
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