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Genotype calls and genetic divergence from bulk segregant analysis of survivorship.

posted on 25.11.2019, 22:05 by Federico Roda, Greg Walter, Rick Nipper, Daniel Ortiz-Barrientos
We show results of the analysis of Bulk Segregant Analysis (BSA) of survivorship in reciprocal transplants between sand dune and rocky headland environments at Lennox Head (NSW, Australia) as performed with the Popoolation2 software. RADseq genotypes were mapped the a genome draft. For each SNP (defined by the position along the genomic contig where it was mapped) and genomic comparison between two pools of survivors from contrasting environments we show the identity and read counts for the major allele (maa) in the two populations (i.e. pop1 is the pool of sand dune survivors and pop2 is the pool of headland survivors). We also show the value of Fst, as calculated by Popoolation2, as well as the p-value of a fisher exact test of allelic differentiation (FET). Finally, in the last column we show if the SNPs had outlier Fst values (i.e. upper 5% tail of the distribution) and presented significantly different allelic frequencies in the FET (Bonferroni corrected p-value lower than 5%). Survivors from each environment where included in three different pools which were sequenced individually. Therefore we had three different comparisons between pools of survivors (i.e. F8-A-S-Dune_vs_F8-A-S-Headland, F8-B-S-Dune_vs_F8-B-S-Headland, and F8-C-S-Dune_vs_F8-C-S-Headland).



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