DOI: 10.5061/dryad.794436q
title: Data from: Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and P. eximius

description: The study of hybrid zones advances understanding of the speciation
 process, and approaches incorporating genomic data are increasingly used
 to draw significant conclusions about the impact of hybridisation. Despite
 the progress made, the complex interplay of factors that can lead to
 substantially variable hybridisation outcomes are still not well
 understood, and many systems and/or groups remain comparatively poorly
 studied. Our study aims to broaden the literature on avian hybrid zones,
 investigating a potentially geographically and temporally complex putative
 hybrid zone between two native Australian non-sister parrot species, the
 pale-headed and eastern rosellas (Platycercus adscitus and P. eximius,
 respectively). We analysed six plumage traits and &gt;1400 RADseq loci
 and detected hybrid individuals and an unexpectedly complex geographic
 structure. The hybrid zone is larger than previously described due either
 to observer bias or its movement over recent decades. It comprises
 different subregions where genetic and plumage signals of admixture vary
 markedly in their concordance. Evidence of contemporary hybridisation
 (later generation and backcrossed individuals) both within and beyond the
 previously defined zone, when coupled with a lack of F1 hybrids and
 differential patterns of introgression among potentially diagnostic loci,
 indicates a lack of post-zygotic barriers to gene flow between species.
 Despite ongoing gene flow, species boundaries are likely maintained
 largely by strong pre-mating barriers. These findings are discussed in
 detail and future avenues for research into this system are proposed which
 would be of benefit to the speciation and hybrid zone literature.
description: STRUCTURE_Data_AllIndividualsInput file used in the program STRUCTURE. This file includes data from 1945 SNPs and 81 rosellas.STRUCTURE_Data_EasternRosellasInput file used in the program STRUCTURE. This file includes data from 2149 SNPs and 22 eastern rosellas.PCA_DataPLINK file used to conduct the Principle Components Analysis (PCA) with the glPCA function in the adegenet R package. This file includes data from 1945 SNPs and 81 individuals.FST_filesThe compressed file titled 'FST_files' contains six Fst output files generated by STACKS (three generated for each of two analyses). Each file contains Fst data comparing two of the three groups described in the paper (i.e. 'eastern', 'pale-headed' and 'hybrid' rosella groups). This data was used by STACKS to calculate the mean Fst values in Table 2 of the paper.INTROGRESS_Data_77IndividualsRADseq data used for analyses in the Introgress R package. This file contains data from 77 rosellas and 152 loci shown to display interspecific alele frequency differentials greater than or equal to 0.8. The file is a modification of the 'haplotypes.tsv' file generated by STACKS.INTROGRESS_Data_46IndividualsRADseq data used for analyses in the Introgress R package. This file contains data from 46 rosellas and 128 loci shown to display interspecific alele frequency differentials greater than or equal to 0.8. The file is a modification of the 'haplotypes.tsv' file generated by STACKS.