DOI: 10.5061/dryad.v6f4d
title: Data from: Hybrid speciation by sorting of parental incompatibilities in Italian sparrows

description: Speciation by hybridization is emerging as a significant contributor to
 biological diversification. Yet, little is known about the relative
 contributions of (i) evolutionary novelty and (ii) sorting of preexisting
 parental incompatibilities to the build-up of reproductive isolation under
 this mode of speciation. Few studies have addressed empirically whether
 hybrid animal taxa are intrinsically isolated from their parents, and no
 study has so far investigated by which of the two aforementioned routes
 intrinsic barriers evolve. Here, we show that sorting of preexisting
 parental incompatibilities contributes to intrinsic isolation of a hybrid
 animal taxon. Using a genomic cline framework, we demonstrate that the
 sex-linked and mito-nuclear incompatibilities isolating the homoploid
 hybrid Italian sparrow at its two geographically separated hybrid-parent
 boundaries represent a subset of those contributing to reproductive
 isolation between its parent species, house and Spanish sparrows. Should
 such a sorting mechanism prove to be pervasive, the circumstances
 promoting homoploid hybrid speciation may be broader than currently
 thought, and indeed there may be many cryptic hybrid taxa separated from
 their parent species by sorted, inherited incompatibilities.
description: structure_input_file'structure_input.txt': input file used when running structure. numbers in second column refer to: 1: house sparrows from Oslo, Norway 2: house sparrows from Hradec Králové, Czech Republic 3: house sparrows from sympatric population near Badajoz, Spain 4: Spanish sparrows from sympatric population near Badajoz, Spain 5: Spanish sparrows from the Gargano Peninsula 6: Spanish sparrows from Sardinia 7: F1-hybrids from aviarystructure_input.txtGenotypes for house sparrow reference populationGenotypes for the individuals in the house sparrow reference population for the 77 SNP markers.genotypes_house.xlsxGenotypes for Spanish sparrow reference populationGenotypes for the individuals in the spanish sparrow reference population for the 77 SNP markersgenotypes_spanish.xlsxGenotypes for parental sympatry test populationGenotypes for the individuals in the admixed test population. 'BGC column' refers to the number given to indivudlas by the bgc output.genotypes_spain.xlsxGenotypes for the hybrid-parents test populationGenotypes for the individuals in the hybrid-parents test population. 'BGC column' refers to the number given to individuals by the bgc output.genotypes_italy.xlsxFile to link locus names with bgc outputFile showing which loci refers to which 'bgc output number' for all 77 markers, only autosomal markers and only Z-linked markersloci.xlsxFile with the code used when running bgcFile with the code used when running bgcbgc_code.txtbgc input file for house sparrow parental population (reference population), all 77 markersbgc input file for house sparrow parental population (reference population)house.txtbgc input file for Spanish sparrow parental population (reference population), all 77 markersbgc input file for Spanish sparrow parental population (reference population)spanish.txtbgc input file for hybrid-parent test population, all 77 markersbgc input file for hybrid-parent test population, all 77 markersadmixed_spain.txta.out_parental sympatryOutput from BGC run on parental sympatry test population: estimates of cline parameter alpha for the 77 loci.a.out_spain.txtb.out_parental sympatryOutput from BGC run on parental sympatry test population: estimates of cline parameter beta for the 77 loci.b.out_spain.txthi.out_parental sympatryOutput from BGC run on parental sympatry test population: estimates of hybrid index.hi.out_spain.txtqa.out_parental sympatryOutput from BGC run on parental sympatry test population: estimates of alpha parameter quantiles for the 77 loci.qa.out_spain.txtqb.out_parental sympatryoutput from BGC run on parental sympatry test population: estimates of beta parameter quantiles for the 77 lociqb.out_spain.txtbgc input file for house sparrow parental population (reference population) when analysing autosomal loci separatelyinput file for house sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatryhouse_autosomal.txtbgc input file for Spanish sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatrybgc input file for Spanish sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatryspanish_autosomal.txtbgc input file for parental sympatry test population when analysing autosomal loci separatelybgc input file for parental sympatry test population when analysing autosomal loci separatelyadmixed_spain_autosomal.txtb.out_autosomal_parental sympatryoutput from BGC run on parental sympatry test population: estimates of cline parameter beta for the 55 autosomal loci analyzed separatelyb.out_spain_autosomal.txtbgc input file for house sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatrybgc input file for house sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatryhouse_Z.txtbgc input file for Spanish sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatrybgc input file for Spanish sparrow parental population (reference population) when analysing Z-linked loci separately i parental sympatryspanish_Z.txtbgc input file for test population when analysing Z-linked loci separately in parental sympatrybgc input file for test population when analysing Z-linked loci separately in parental sympatryadmixed_spain_Z.txtb.out_Z_parental sympatryoutput from BGC: estimates of cline parameter beta for the 21 Z-linked loci analyzed separately in parental sympatryb.out_spain_Z.txtbgc input file for hybrid-parents test population (all 77 loci)bgc input file for hybrid-parents test population (all 77 loci)admixed_italy.txta.out_hybrid-parents analysisoutput from BGC: estimates of cline parameter alpha for 77 the loci used in the hybrid-parents analysisa.out_italy.txtb.out_hybrid-parents analysisoutput from BGC: estimates of cline parameter beta for 77 the loci used in the hybrid-parents analysisb.out_italy.txthi.out_hybrid-parents analysisoutput from BGC: estimates of hybrid index for the individuals in the hybrid-parents test populationhi.out_italy.txtqa.out_hybrid-parents analysisbgc output from hybrid-parents analysis: estimates of alpha parameter quantiles for the 77 lociqa.out_italy.txtqb.out_hybrid-parents analysisbgc output from hybrid-parents analysis: estimates of beta parameter quantiles for the 77 lociqb.out_italy.txt