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.
N1_sampleCoordinates.csv
Coordinates for Timema cristinae sampled in population N1
N1_variants.tar.gz
Genetic variants called for population N1 of Timema cristinae using Samtools and Bcftools. Uncompressed file sizes: 2.5G and 0.5G
FHA_variants.tar.gz
Genetic variants called for population FHA of Timema cristinae using Samtools and Bcftools. Uncompressed file sizes: 4.4G and 2.0G
Combined21pop_variants.tar.gz
Genetic variants called for the combined set of 21 Timema cristinae populations using Samtools and Bcftools. Uncompressed file sizes: 4.3G and 0.7G
Timema5species_variants.gz
Genetic variants called for five related Timema species using Samtools and Bcftools. Uncompressed file size: 258M
Timema5species_variants.flt_s085p001.vcf.gz
Input_N1.tar.gz
Input files for various analyses for population N1 of Timema cristinae
Input_FHA.tar.gz
Input files for various analyses for population FHA of Timema cristinae
Input_Combined21pop.tar.gz
Input files for various analyses for the combined set of 21 Timema cristinae populations
Gemma.tar.gz
Input files for running GEMMA software for population FHA of Timema cristinae
beast_div_times.tar.gz
Files and scripts for conducting BEAST 2 phylogenetic analyses for estimating divergence times between chromosomal variants
ABC.tar.gz
Files and scripts for conducting ABC for estimating divergence time between color morphs of Timema cristinae
selectionmodels.tar.gz
Files and scripts for testing different models of selection and mating preferences for generating observed karyotype frequencies in Timema cristinae populations
N1_samplePhenotypes.csv
Information on phenotype for samples from population N1
FHA_samplePhenotypes.csv
Information on phenotype for samples from population FHA
Combined21pop_samplePhenotypes.csv
Information on phenotype for samples from the combined set of 21 Timema cristinae populations
N1_assignments.csv
PCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population N1
FHA_assignments.csv
PCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population FHA
Combined21pop_assignments.csv
STRUCTURE karyotype assignments for combined set of 21 Timema cristinae populations
N1_gprob_s090p001.txt.bz2
Posterior genotype probabilities that were determined by MCMC from N1_variants.flt_s090p001.bcf.
Uncompressed file size: 4.3G
N1_inVar_snpIDs_bins_s090p001.txt.bz2
Positions of all sites (variants and invariant nucleotides) and their 20-kb bins for population N1, discarding variants where less than 90% of individuals were covered
FHA_gprob_s090p001.txt.bz2
Posterior genotype probabilities that were determined by MCMC from FHA_variants.flt_s090p001.bcf.
Uncompressed file size: 7.5G
FHA_inVar_snpIDs_bins_s090p001.txt.bz2
Positions 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