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.
all_samples
Genotypes for all samples in the study Blackburn et al 2017.
pcadapt_in
PCADAPT input file.
hiest_bie&occ&fum_parent_in
HIEST parent input file.
hiest_bie-occ-fum_hybridzone_in
HIEST hybrid zone input file.
bgc_bie_parent_in
BGC bie parent input file.
bgc_occ_parent_in
BGC occ parent input file.
bgc_fum_parent_in
BGC fum parent input file.
bgc_bie-occ_hybridzone_in
BGC bie-occ hybrid zone input file.
bgc_bie-fum_hybridzone_in
BGC bie-fum hybrid zone input file.
bayescan_bie&occ_in
BAYESCAN bie & occ parent input file.
bayescan_bie&fum_in
BAYESCAN bie & fum parent input file.
blast_bayescan&bgcoutlier_outlier&10kbflanks_in
BLAST and BLAST2GO input file.
parent_samplelist_bie_pcadapt
Sample list of bie parent population, determined using PCADAPT.
parent_samplelist_occ_pcadapt
Sample list of occ parent population, determined using PCADAPT.
parent_samplelist_fum_pcadapt
Sample list of fum parent population, determined using PCADAPT.
hybridzone_samplelist_bie-occ-fum_pcadapt
Sample list of bie-occ-fum hybrid populations, determined using PCADAPT.
hybridzone_samplelist_bie-occ_pcadapt&hiest
Sample list of bie-occ hybrid zone, determined using PCADAPT and HIEST.
hybridzone_samplelist_bie-fum_pcadapt&hiest
Sample list of bie-fum hybrid zone, determined using PCADAPT and HIEST.
bayescan_bie&occ_locuslist
BAYESCAN bie and occ parent locus list.
bayescan_bie&fum_locuslist
BAYESCAN bie and fum parent locus list.
blast_bayescan&bgcoutlier_outlierstatus
BLAST: Outlier status of loci employed in gene function analyses.
blast_bayescan&bgcoutlier_seqinfo
BLAST: Sequence information of flanking regions surrounding loci employed in gene function analyses.
h_allsnp_genind
SNP data in genind format for heterozygosity analysis in R package ADEGENET.
h_pooled_bie&fumparents_in
ADEGENET pooled bie and fum parent SNP data for heterozygosity analysis.
h_pooled_bie&occ&fumparents_in
ADEGENET pooled bie, occ, and fum parent SNP data for heterozygosity analysis.
h_pooled_bie&occparents_in
ADEGENET pooled bie and occ parent SNP data for heterozygosity analysis.
h_separate_populations_in
ADEGENET separate population SNP data for heterozygosity analysis.
ld_bfoutliers_bfadvhybrids_in
LD analysis bie-fum advanced hybrids genotypes for bie-fum gene flow outliers.
ld_bfoutliers_boadvhybrids_in
LD analysis bie-occ advanced hybrids genotypes for bie-fum gene flow outliers.
ld_bfoutliers_bparents_in
LD analysis bie parents genotypes for bie-fum gene flow outliers.
ld_bfoutliers_fparents_in
LD analysis fum parents genotypes for bie-fum gene flow outliers.
ld_bfoutliers_oparents_in
LD analysis occ parents genotypes for bie-fum gene flow outliers.
ld_booutliers_bfadvhybrids_in
LD analysis bie-fum advanced hybrids genotypes for bie-occ gene flow outliers.
ld_booutliers_boadvhybrids_in
LD analysis bie-occ advanced hybrids genotypes for bie-occ gene flow outliers.
ld_booutliers_bparents_in
LD analysis bie parents genotypes for bie-occ gene flow outliers.
ld_booutliers_fparents_in
LD analysis fum parents genotypes for bie-occ gene flow outliers.
ld_booutliers_oparents_in
LD analysis occ parents genotypes for bie-occ gene flow outliers.
advancedhybrid_samplelist_bo
LD analysis list of bie-occ advanced hybrid samples.
advancedhybrid_samplelist_bf
LD analysis list of bie-fum advanced hybrid samples.
README
Analysis notes for Blackburn et al 2017.