Assortative mating in the Eastern Yellow Robin

This dataset presents data, R scripts (.R) and R Markdown files (.rmd) used in the preprint
Austin, L., Amos, J.N., Robledo-Ruiz, D.A., Zhou, J., Clarke, R., Pavlova, A., Sunnucks, P., 2023. Random mating in a hybrid zone between two putative climate-adapted bird lineages with predicted mitonuclear incompatibilities. Authorea preprint
The 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:
· Report_DYro21-6107_5_moreOrders_SNP_mapping_3_uniqIDs.csv – DArT SNP genotypes before filtering
· EYR2021_cov.NONAS.csv – covariate file used for colony2 input
· Lanas.version_filter.sex.linked.r – R-script for identifying and filtering sex-linked loci
· PCA_ZLinkedLoci_AssortativeMating_Rmarkdown.rmd – PCA of Z-linked loci and autosomes
Parentage analysis:
· bestconfig_social.parents.csv –social breeding pairs observed in the field, in a format that is directly comparable with colony2 bestconfig output
· colony2.dat – colony2 input file
· ExcludedMaternityandPaternityInputFiles.r – 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
· SelectingGenotypeError.r – R-script for selecting the most appropriate genotype error rate
· TestingColonyOutput_Nov2021.r – Testing colony bestconfig output against observed breeding pair data
· mito_latlongs_vectorData_22.10.2023.csv – this csv includes the ID of all eastern yellow robins captured during this study, their mitolineage, and capture location (latitude, longitude)
Simulations and modelling:
· RandomMatingModels_LinearModelsforPC1_AssortativeMating_20Oct2022.rmd – 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.
· RandomMatingModels_MaleMito.by.FemaleMitoAndFemalePc1_AssortativeMating_6Feb2023.rmd – 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.· GroupPointsSFwithClimateExtract_LA.csv - mapping data (max temp of warmest month, lat longs of captured EYRs and their mitolineage)
· sites.matrix.csv – 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.
· TravelDistances_assortativemating.r – code used to calculate the maximum distance that individuals were observed to have travelled within any breeding season
· EYRrandom_mating_loops.r – 500 random simulations of breeding pairs