Tests for effects of colour-pattern and CHCs on sexual isolation and genome wide FST
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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.