Tests for effects of colour-pattern and CHCs on sexual isolation and genome wide FST ------------------------------------------------------------------------------- These files and directories contain the SNVs, colour pattern population frequencies, CHC measurements, IPSI estimates, FST estimates, and geographic distances used for testing the effect of colour pattern and CHCs on sexual isolation and differentiation. For more information, see sections titled 'Colour-pattern loci are not associated with genome-wide differentiation', 'CHCs and mate choice', 'CHCs are associated with genome-wide differentiation', 'Quantifying dorsal colour-pattern (% body area striped)', 'Cuticular hydrocarbon (CHC) variation', 'Tests for effects of colour-pattern and CHCs on sexual isolation and genome wide FST' and Fig. 3 in the main text, and 'Quantifying colour-pattern and CHCs' and 'Differences between ecotypes in CHCs', and Supplementary Tables 6 and 7 in the OSM. Sequence data was deposited in NCBI under BioProject accessions PRJNA356885 and PRJNA284835 (the last one being FHA data previously published in Comeault et al. 2015 doi:10.1016/j.cub.2015.05.05). The files included here are: chc_data.dsv Contains measurements of CHCs and PCs from PCA. Sequences ids are also included, but be aware that sequences for FHA (marked with an asterisk) come from a previous study (Comeault et al. 2013 doi...) and not from the actual individuals used to extract CHCs. fst_summary.dsv Contains Hudson's FST estimates for all pairs of populations carried out with the Perl program fst.pl (code also included in this Dryad submission) variants.flt_s09_p001.bcf BCF file containing variants called after aligning GBS data of 342 individuals to the Timema cristinae draft. A Perl script using bcftools 0.1.19 was used to call the variants (fst.pl -pr 0 -sep 0 -fm 0 -ms 0.5 -mf 0.05). chc_females_subset_matrix.dsv Matrix of female CHC distances for the subset of 21 population pairs used to analyse how CHCs affect sexual isolation and divergence (CHC vs IPSI, CHC vs FST). chc_males_subset_matrix.csv Matrix of male CHC distances for the subset of 21 population pairs used to analyse how CHCs affects sexual isolation and differentiation (CHC vs IPSI, CHC vs FST). fst_subset_matrix.dsv Matrix of FST values for the subset of 21 population pairs used to analyse the how CHCs and colour pattern affect differentiation (CHC vs FST, colpat vs FST). colpattern_subset_matrix.dsv Matrix of colour pattern distances for the subset of 21 populations pairs used to analyse how colour pattern affects sexual isolation and differentiation (colpat vs IPSI, colpat vs FST) geodist_subset_matrix.dsv Matrix of geographic distances for the subset of 21 population pairs used in the mixed model to analyse how colour pattern and CHCs affect sexual isolation and differentiation ipsi_subset_matrix.dsv Matrix of sexual isolation (IPSI) distances for the subset of 21 population pairs used to analyse correlation between CHC, IPSI and FST. isolationByDistanceAndCHC.R R script to run a Bayesian linear mixed model (BLMM) to analyse how colour pattern and CHCs affect sexual isolation and differentiation taking into account population-specific random effects and geographic distance. Some lines need to be commented/uncommented to run the model for the effect of the different traits.