DOI: 10.5061/dryad.918m0n2
title: Data from: Differential introgression across newt hybrid zones – evidence from replicated transects

description: Genomic heterogeneity of divergence between hybridizing species may
 reflect heterogeneity of introgression, but also processes unrelated to
 hybridization. Heterogeneous introgression and its repeatability can be
 directly tested in natural hybrid zones by examining multiple transects.
 Here, we studied hybrid zones between the European newts: Lissotriton
 montandoni and two lineages of L. vulgaris, with replicate transects
 within each zone. Over 1000 nuclear genes located on a linkage map and
 mtDNA were investigated using geographic and genomic clines. Overall, the
 five transects were all similar, showing hallmarks of strong reproductive
 isolation: bimodal distribution of genotypes in central populations and
 narrow allele frequency clines. However, the extent of introgression
 differed between the zones, likely as a consequence of their different
 ages, indicated by the analysis of heterozygosity runs in diagnostic
 markers. In three transects genomic signatures of small-scale (ca. 2 km)
 zone movements were detected. We found a limited overlap of cline outliers
 between transects, and no evidence of stronger differentiation between
 zones than between transects within zones. Introgression was heterogeneous
 across linkage groups, with patterns of heterogeneity similar between
 transects and zones. Predefined candidates for increased or reduced
 introgression exhibited only a subtle tendency in the expected direction,
 suggesting that interspecific differentiation is not a reliable indicator
 for the strength of introgression. These hierarchically sampled hybrid
 zones of different ages show how introgression unfolds with time and offer
 an excellent opportunity to dissect the dynamics of hybridization and
 architecture of reproductive isolation at advanced stages of speciation.
description: VCF file with nuclear
 genotypes File contains nuclear,
 biallelic variants and genotypes. Nuclear_genotypes.vcf Admixture data and results File contains nuclear genotypes used for Admixture analysis (.ped and .map) and estimated per individual ancestry proportions (excel). File with ancestry proportions contains also assignment of individuals to populations (populations names and order correspond to this in Table S1). Admixture_data_and_results.zip Geographic cline data and results Zip file which contains 7 .csv files (one per transect) with average population allele frequency data per locus. This files were used to fit geographic clines in HZAR. Geographic_clines_results.txt file contains estimated cline parameters. Geographic_clines_data_and_results.zip   Genomic cline data and results Zip file which contains one subfolder per transect with data used to fit genomic clines in bgc. Translation_table.xlsx allows to translate loci names from input files to this present in Genomic_clines_results.txt containing estimated cline parameters. Genomic_clines_data_and_results.zip   Assignment individuals to populations This excel file allows to assign individuals to populations. Population names correspond to Table S1. Individual_assignment_to_populations.xlsx