DOI: 10.5061/dryad.jt644
title: Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

description: How polymorphisms are maintained within populations over long periods of
 time remains debated, because genetic drift and various forms of selection
 are expected to reduce variation. Here, we study the genetic architecture
 and maintenance of phenotypic morphs that confer crypsis in Timema
 cristinae stick insects, combining phenotypic information and
 genotyping-by-sequencing data from 1360 samples across 21 populations. We
 find two highly divergent chromosomal variants that span megabases of
 sequence and are associated with color polymorphism. We show that these
 variants exhibit strongly reduced effective recombination, are
 geographically widespread, and probably diverged millions of generations
 ago. We detect heterokaryotype excess and signs of balancing selection
 acting on these variants through the species’ history. A third chromosomal
 variant in the same genomic region likely evolved more recently from one
 of the two color variants and is associated with dorsal pattern
 polymorphism. Our results suggest that large-scale genetic variation
 associated with crypsis has been maintained for long periods of time by
 potentially complex processes of balancing selection.
description: N1_sampleCoordinates.csvCoordinates for Timema cristinae sampled in population N1N1_variants.tar.gzGenetic variants called for population N1 of Timema cristinae using Samtools and Bcftools. Uncompressed file sizes: 2.5G and 0.5GFHA_variants.tar.gzGenetic variants called for population FHA of Timema cristinae using Samtools and Bcftools. Uncompressed file sizes: 4.4G and 2.0GCombined21pop_variants.tar.gzGenetic variants called for the combined set of 21 Timema cristinae populations using Samtools and Bcftools. Uncompressed file sizes: 4.3G and 0.7GTimema5species_variants.gzGenetic variants called for five related Timema species using Samtools and Bcftools. Uncompressed file size: 258MTimema5species_variants.flt_s085p001.vcf.gzInput_N1.tar.gzInput files for various analyses for population N1 of Timema cristinaeInput_FHA.tar.gzInput files for various analyses for population FHA of Timema cristinaeInput_Combined21pop.tar.gzInput files for various analyses for the combined set of 21 Timema cristinae populationsGemma.tar.gzInput files for running GEMMA software for population FHA of Timema cristinaebeast_div_times.tar.gzFiles and scripts for conducting BEAST 2 phylogenetic analyses for estimating divergence times between chromosomal variantsABC.tar.gzFiles and scripts for conducting ABC for estimating divergence time between color morphs of Timema cristinaeselectionmodels.tar.gzFiles and scripts for testing different models of selection and mating preferences for generating observed karyotype frequencies in Timema cristinae populationsN1_samplePhenotypes.csvInformation on phenotype for samples from population N1FHA_samplePhenotypes.csvInformation on phenotype for samples from population FHACombined21pop_samplePhenotypes.csvInformation on phenotype for samples from the combined set of 21 Timema cristinae populationsN1_assignments.csvPCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population N1FHA_assignments.csvPCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population FHACombined21pop_assignments.csvSTRUCTURE karyotype assignments for combined set of 21 Timema cristinae populationsN1_gprob_s090p001.txt.bz2Posterior genotype probabilities that were determined by MCMC from N1_variants.flt_s090p001.bcf. Uncompressed file size: 4.3GN1_inVar_snpIDs_bins_s090p001.txt.bz2Positions of all sites (variants and invariant nucleotides) and their 20-kb bins for population N1, discarding variants where less than 90% of individuals were coveredFHA_gprob_s090p001.txt.bz2Posterior genotype probabilities that were determined by MCMC from FHA_variants.flt_s090p001.bcf. Uncompressed file size: 7.5GFHA_inVar_snpIDs_bins_s090p001.txt.bz2Positions of all sites (variants and invariant nucleotides) and their 20-kb bins for population FHA, discarding variants where less than 90% of individuals were covered