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). 'goodDat' files have information for each AIM'quantDat' files have only relevant information from goodDat with the addition of mitonuclear LD values'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'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 modelplease 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