Assortative mating in the Eastern Yellow Robin

This dataset presents data, R scripts (.R) and R Markdown files (.rmd) used in the preprintAustin, L., Amos, J.N., Robledo-Ruiz, D.A., Zhou, J., Clarke, R., Pavlova, A., Sunnucks, P., 2023. <b>Random mating in a hybrid zone between two putative climate-adapted bird lineages with predicted mitonuclear incompatibilities</b>. Authorea preprintThe study aimed to determine whether female Eastern Yellow Robin mate assortatively according to mitonuclear compatibilities or local adaptations.Files include:Identification, analyses and filtering of sex-linked loci (Z-,W-loci and ZW homologs) from DArT data:· <b><i>Report_DYro21-6107_5_moreOrders_SNP_mapping_3_uniqIDs.csv</i></b> – DArT SNP genotypes before filtering· <b><i>EYR2021_cov.NONAS.csv </i></b>–<b><i> </i></b>covariate file used for colony2 input· <b><i>Lanas.version_filter.sex.linked.r </i></b>–<b><i> </i></b>R-script for identifying and filtering sex-linked loci· <b><i>PCA_ZLinkedLoci_AssortativeMating_Rmarkdown.rmd </i></b>– PCA of Z-linked loci and autosomesParentage analysis:· <b><i>bestconfig_social.parents.csv</i></b> –social breeding pairs observed in the field, in a format that is directly comparable with colony2 bestconfig output· <b><i>colony2.dat </i></b>– colony2 input file· <b><i>ExcludedMaternityandPaternityInputFiles.r </i></b>– R-script that identifies which mother-offspring and father-offspring dyads are not possible, due to either season born or, for mother-offspring, mismatched mitolineages. This script creates a dataframe that is used in the colony2.dat file· <b><i>SelectingGenotypeError.r </i></b>– R-script for selecting the most appropriate genotype error rate· <b><i>TestingColonyOutput_Nov2021.r </i></b>– Testing colony bestconfig output against observed breeding pair data· <b><i>mito_latlongs_vectorData_22.10.2023.csv</i></b><i> </i>– this csv includes the ID of all eastern yellow robins captured during this study, their mitolineage, and capture location (latitude, longitude)Simulations and modelling:· <b><i>RandomMatingModels_LinearModelsforPC1_AssortativeMating_20Oct2022.rmd</i></b> – R-markdown script for general linear models that test male.Zlinked lineage score ~ female mitolineage * female Zlinked lineage score. This rmd also tests whether the observed trend in social pairs significantly differs from the trends observed in 500 randomly simulated pairs.· <b><i>RandomMatingModels_MaleMito.by.FemaleMitoAndFemalePc1_AssortativeMating_6Feb2023.rmd</i></b> – R-markdown script for general linear models that test male mitolineage ~ female mitolineage * female Z-linked lineage score. This rmd also tests whether the observed trend in social pairs significantly differs from the trends observed in 500 randomly simulated pairs.· <b><i>GroupPointsSFwithClimateExtract_LA.csv </i></b>- mapping data (max temp of warmest month, lat longs of captured EYRs and their mitolineage)· <b><i>sites.matrix.csv </i></b><b>– </b>a manually created matrix of all breeding females on the y-axis and all breeding males on the y-axis. The data within the matrix is the sites at which both individuals were captured, to assess whether a randomly assigned breeding pair are spatially feasible.· <b><i>TravelDistances_assortativemating.r</i></b> – code used to calculate the maximum distance that individuals were observed to have travelled within any breeding season· <b><i>EYRrandom_mating_loops.r </i></b><i>–</i> 500 random simulations of breeding pairs