DOI: 10.5061/dryad.j4b543t
title: Data from: The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks

description: Theory predicts that structural genomic variants such as inversions can
 promote adaptive diversification and speciation. Despite increasing
 empirical evidence that adaptive divergence can be triggered by one or a
 few large inversions, the degree to which widespread genomic regions under
 divergent selection are associated with structural variants remains
 unclear. Here we test for an association between structural variants and
 genomic regions that underlie parallel host-plant associated ecotype
 formation in Timema cristinae stick insects. Using mate-pair re-sequencing
 of 20 new whole genomes we find that modest-sized structural variants such
 as inversions, deletions, and duplications are widespread across the
 genome, being retained as standing variation within and among populations.
 Using 160 previously published, standard-orientation whole genome
 sequences we find little to no evidence that the DNA sequences within
 inversions exhibit accentuated differentiation between ecotypes. In
 contrast, a formerly described large region of reduced recombination that
 harbors genes controlling color-pattern exhibits evidence for accentuated
 differentiation between ecotypes, which is consistent with differences in
 the frequency of color-pattern morphs between host-associated ecotypes.
 Our results suggest that some types of structural variants (e.g., large
 inversions) are more likely to underlie adaptive divergence than others,
 and that structural variants are not required for subtle yet genome-wide
 genetic differentiation with gene flow.
description: Deletion variants VCF file with the 194
 deletion structural variants found that were identified using Lumpy and
 Delly. Data for all 20 Timema cristinae individuals are
 included. mod_del_genotyped.vcf.gz
 Duplication variants VCF file with the 223
 duplication structural variants found that were identified using Lumpy and
 Delly. Data for all 20 Timema cristinae individuals are
 included. mod_dup_genotyped.vcf.gz
 Inversion variants VCF file with the 492
 inversion structural variants found that were identified using Lumpy and
 Delly. Data for all 20 Timema cristinae individuals are
 included.
 mod_lumpy_inversions_genotyped.vcf.gz SV
 population genetics script R script for population
 genetic analyses and plots of the structural variant data. This includes
 calculations for Fst. svSummary.R
 SV allele frequencies This compressed
 directory includes maximum l likelihood allele frequency estimates for the
 SVs. There is one file per SV type (inv = inversion, del = deletion, dup =
 duplication) and population. Files without population IDs are for all
 individuals together. In each file, there is one row per SV, the first
 column gives the locus ID, and the third column gives the non-reference SV
 allele frequency. svAlleleFreqs.tar.gz
 MeasureOrientationFreqs One of two
 complementary perl scripts used to identify the inversions from the whole
 genome comparative alignment.
 ExtractOrientInversions One of two
 complementary perl scripts used to identify the inversions from the whole
 genome comparative alignment. SNP variant
 file VCF file with SNPs from the 160 Timema cristinae
 genomes. filtered1X_tcr_wgs_variants_x.vcf.gz
 SNP allele frequencies This compressed
 directory includes maximum l likelihood allele frequency estimates for the
 SNPs from the 160 genomes. There is one file per population. In each file,
 there is one row per SNP, the first column gives the locus ID, and the
 third column gives the non-reference allele frequency.
 snpAlleleFreqs.tar.gz R population genomics
 script This R script contains the core analyses of
 genetic variation within inversions sequences based on SNPs from the 160
 Timema cristinae genomes. popgen.R