Non-synonymous Substitution Data

The aim of this analysis was to identify whether gene classes' (interacting n-mts, non-interacting n-mts, and non-n-mts) mitonuclear linkage disequilibrium metrics were mitigated by the number of non-synonymous substitutions in a gene. In other words, we wanted to know whether the relationship between gene class and mitonuclear LD differed in genes with more non-synonymous substitutions. Substitution data was provided by Molly Schumer and used to identify whether an AIM represented a non-synonymous or synonymous, species-specific variant. Of all the substitutions identified between hybridizing Xiphophorus species, substitutions included in this analysis must still be an AIM (or be able to be used for identifying species-specific ancestry in a hybrid swordtail fish). Xbirchmanni10xgenome_addmito_ancestry_informative_sites_filterF1 is the substitution data used for CALL and CHAF hybrids. xbir_xcor_10x_genomes_identify_pairwise_dxy was used for HUEX-STAC hybrids. All other files here are outputs of the analysis (either files that have AIMs' substitution identifications and relevant info or files that show statistical testing outputs). <br>'goodDat' files have information for each AIM<br>'quantDat' files have only relevant information from goodDat with the addition of mitonuclear LD values<br>'summary-stat' files have summary statistics for each grouping variable for each population'ANOVA-III' files are the type III ANOVA results for all mitonuclear LD stats for that population<br>'summary' files are the output of the summary() command in R comparing the non-n-mt class to each of the n-mt classes to identify differences in slopes for each level of the gene class variable in the model<br><br>please see the 09_dNAnalysis in the GitHub repo for scripts used to generate and make use of these files: https://github.com/sakuster/sensitivity-of-genome-wide-mtnuc/tree/main/09_dNAnalysis