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