DOI: 10.5061/dryad.f0b2f083
title: Data from: Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species

description: Speciation is the process by which reproductively isolated lineages arise,
 and is one of the fundamental means by which the diversity of life
 increases. Whereas numerous studies have documented an association between
 ecological divergence and reproductive isolation, relatively little is
 known about the role of natural selection in genome divergence during the
 process of speciation. Here we use genome-wide DNA sequences and Bayesian
 models to test the hypothesis that loci under divergent selection between
 two butterfly species (Lycaeides idas and L. melissa) also affect fitness
 in an admixed population. Locus-specific measures of genetic
 differentiation between L. idas and L. melissa and genomic introgression
 in hybrids varied across the genome. The most differentiated genetic
 regions were characterized by elevated L. idas ancestry in the admixed
 population, which occurs in L. idas-like habitat, consistent with the
 hypothesis that local adaptation contributes to speciation. Moreover,
 locus-specific measures of genetic differentiation (a metric of divergent
 selection) were positively associated with extreme genomic introgression
 (a metric of hybrid fitness). Interestingly, concordance of
 differentiation and introgression was only partial. We discuss multiple,
 complementary explanations for this partial concordance.
description: Sequence allele
 countsAllele counts form
 indiviudal-based Illumina sequence data for Lycaeides butterflies. This
 file contains counts of the number of times each allele was observed for
 each locus and individual. Each locus begins with a line with the contig
 number and location (in bp) in the reference genome. This is followed by a
 single line per individual with the individuals name, the number of times
 the reference allele was observed (i.e., how many reads included the
 reference allele), and the number of times the alternative allele (i.e.,
 nucleotide) was observed. This file contains 119,677
 loci.sequence_allele_counts.txtReference sequenceThis is the fasta formatted reference sequence used for the reference-based assembly. This reference was generated by concatenating short (~92 bp) contigs from a de novo assembly and separating these sequences with 30 'N' characters.referenceseq.fastaSource code for allele frequency estimation with genotype uncertaintyThis compressed directory contains the source code for the allele frequency model described in the publication. Please contact the Zach Gompert (zgompert@uwyo.edu) to inquire about updates to the software, usage, and whether a manual or example files exist.allelefreqSource.tar.gzSource code for Bayesian F-modelThis compressed directory contains the source code for the Bayesian F-model described in the publication. Please contact the Zach Gompert (zgompert@uwyo.edu) to inquire about updates to the software, usage, and whether a manual or example files exist.f-modSource.tar.gzSource code for composite disequilibriumThis compressed directory contains the source code for estimating Burrow's composite linkage and Hardy-Weinberg disequilibrium, as described in the publication. Please contact the Zach Gompert (zgompert@uwyo.edu) to inquire about updates to the software, usage, and whether a manual or example files exist.ldSource.tar.gz