Supporting data for Robledo-Ruiz et al. (2023)

Supporting data for manuscript: Robledo-Ruiz D. A., Austin L., Amos J. N., Castrejón-Figueroa J., Magrath M. J. L., Sunnucks P. & Pavlova A. (submitted) Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex-assignment. Data usage: The two directories have the datasets and scripts for the eastern yellow robin (EYR) and yellow-tufted honeyeater (YTH), respectively. gl0.R Genlight object with the original SNP dataset. gl0_filt.R Genlight object with the SNP dataset after randomly filtering for secondaries. SCRIPT_*_standard.Rmd R script for the 'standard' filtering regime, and calculation of population genetic diversity, structure and individual He. SCRIPT_*_removing_sexlinked.Rmd R script for the 'removing sex-linked loci' filtering regime, and calculation of population genetic diversity, structure and individual He. standard_filter_diversity.csv standard_filter_het_ind.csv Output of population genetic diversity and individual He for 'before' dataset. sexlinked_filter_diversity.csv sexlinked_filter_het_ind.csv Output of population genetic diversity and individual He for 'after' dataset. colony2_standard.dat colony2_sexlinked.dat COLONY input files obtained from 'standard' and 'removing sex-linked loci' filtering regimes. seed*_without_BestConfig_Ordered.csv Output of COLONY parentage analysis for data obtained from 'standard' filtering regime. seed*_with_BestConfig_Ordered.csv Output of COLONY parentage analysis for data obtained from 'removing sex-linked loci' filtering regime. BestSocialParents.csv known_fathers.csv known_mothers.csv Data of known parents to evaluate accuracy of parentage analyses. SCRIPT_*_Results.Rmd R script comparing the population genetic diversity, individual He and parentage analysis accuracy of 'before' and 'after' datasets. SCRIPT_*_infersex_requirements.Rmd R script testing the minimum number of known-sex individuals required for function filter.sex.linked.