DOI: 10.5061/dryad.9c50s
title: Data from: Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of a Choristoneura budworm

description: Populations are often exposed to multiple sources of gene flow, but
 accounts are lacking of the population genetic dynamics that result from
 these interactions or their effects on local evolution. Using a genomic
 clines framework applied to 1195 SNPs, we documented genome-wide,
 locus-specific patterns of introgression between Choristoneura
 occidentalis biennis spruce budworms and two ecologically divergent
 relatives, C. o. occidentalis and C. fumiferana, that it interacts with at
 alternate boundaries of its range. We observe contrasting hybrid indexes
 between these hybrid zones, no overlap in ‘gene flow outliers’ (clines
 showing relatively extreme extents or rates of locus-specific
 introgression), and variable linkage disequilibrium among those outliers.
 At the same time, correlated genome-wide rates of introgression between
 zones suggest the presence of processes common to both boundaries. These
 findings highlight the contrasting population genetic dynamics that can
 occur at separate frontiers of a single population, while also suggesting
 that shared patterns may frequently accompany cases of
 divergence-with-gene-flow that involve a lineage in common. Our results
 point to potentially complex evolutionary outcomes for populations
 experiencing multiple sources of gene flow.
description: all_samplesGenotypes for all samples in the study Blackburn et al 2017.pcadapt_inPCADAPT input file.hiest_bie&occ&fum_parent_inHIEST parent input file.hiest_bie-occ-fum_hybridzone_inHIEST hybrid zone input file.bgc_bie_parent_inBGC bie parent input file.bgc_occ_parent_inBGC occ parent input file.bgc_fum_parent_inBGC fum parent input file.bgc_bie-occ_hybridzone_inBGC bie-occ hybrid zone input file.bgc_bie-fum_hybridzone_inBGC bie-fum hybrid zone input file.bayescan_bie&occ_inBAYESCAN bie & occ parent input file.bayescan_bie&fum_inBAYESCAN bie & fum parent input file.blast_bayescan&bgcoutlier_outlier&10kbflanks_inBLAST and BLAST2GO input file.parent_samplelist_bie_pcadaptSample list of bie parent population, determined using PCADAPT.parent_samplelist_occ_pcadaptSample list of occ parent population, determined using PCADAPT.parent_samplelist_fum_pcadaptSample list of fum parent population, determined using PCADAPT.hybridzone_samplelist_bie-occ-fum_pcadaptSample list of bie-occ-fum hybrid populations, determined using PCADAPT.hybridzone_samplelist_bie-occ_pcadapt&hiestSample list of bie-occ hybrid zone, determined using PCADAPT and HIEST.hybridzone_samplelist_bie-fum_pcadapt&hiestSample list of bie-fum hybrid zone, determined using PCADAPT and HIEST.bayescan_bie&occ_locuslistBAYESCAN bie and occ parent locus list.bayescan_bie&fum_locuslistBAYESCAN bie and fum parent locus list.blast_bayescan&bgcoutlier_outlierstatusBLAST: Outlier status of loci employed in gene function analyses.blast_bayescan&bgcoutlier_seqinfoBLAST: Sequence information of flanking regions surrounding loci employed in gene function analyses.h_allsnp_genindSNP data in genind format for heterozygosity analysis in R package ADEGENET.h_pooled_bie&fumparents_inADEGENET pooled bie and fum parent SNP data for heterozygosity analysis.h_pooled_bie&occ&fumparents_inADEGENET pooled bie, occ, and fum parent SNP data for heterozygosity analysis.h_pooled_bie&occparents_inADEGENET pooled bie and occ parent SNP data for heterozygosity analysis.h_separate_populations_inADEGENET separate population SNP data for heterozygosity analysis.ld_bfoutliers_bfadvhybrids_inLD analysis bie-fum advanced hybrids genotypes for bie-fum gene flow outliers.ld_bfoutliers_boadvhybrids_inLD analysis bie-occ advanced hybrids genotypes for bie-fum gene flow outliers.ld_bfoutliers_bparents_inLD analysis bie parents genotypes for bie-fum gene flow outliers.ld_bfoutliers_fparents_inLD analysis fum parents genotypes for bie-fum gene flow outliers.ld_bfoutliers_oparents_inLD analysis occ parents genotypes for bie-fum gene flow outliers.ld_booutliers_bfadvhybrids_inLD analysis bie-fum advanced hybrids genotypes for bie-occ gene flow outliers.ld_booutliers_boadvhybrids_inLD analysis bie-occ advanced hybrids genotypes for bie-occ gene flow outliers.ld_booutliers_bparents_inLD analysis bie parents genotypes for bie-occ gene flow outliers.ld_booutliers_fparents_inLD analysis fum parents genotypes for bie-occ gene flow outliers.ld_booutliers_oparents_inLD analysis occ parents genotypes for bie-occ gene flow outliers.advancedhybrid_samplelist_boLD analysis list of bie-occ advanced hybrid samples.advancedhybrid_samplelist_bfLD analysis list of bie-fum advanced hybrid samples.READMEAnalysis notes for Blackburn et al 2017.