Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.GWAS of CHCs and colour patterngwas_chc_colour_pattern.tar.bz2Whole-genome analyses of published T. cristinae genomeswgs_cristinae_reanalysis.tar.bz2Whole-genome transplant-and-sequence experimentwgs_transplant_experiment.tar.bz2Perfuming trials with no-choice copulation experimentsperfuming_experiment.tar.bz2Tests for effects of colour-pattern and CHCs on sexual isolation and genome wide FSTchc_ipsi_colour_pattern_fst.tar.bz2Genomic differentiation between sympatric Timema populations and species (part 00 of 09)This is the first part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part00Genomic differentiation between sympatric Timema populations and species (part 01 of 09)This is the second part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part01Genomic differentiation between sympatric Timema populations and species (part 02 of 09)This is the third part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part02Genomic differentiation between sympatric Timema populations and species (part 03 of 09)This is the fourth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part03Genomic differentiation between sympatric Timema populations and species (part 04 of 09)This is the fifth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part04Genomic differentiation between sympatric Timema populations and species (part 05 of 09)This is the sixth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part05Genomic differentiation between sympatric Timema populations and species (part 06 of 09)This is the seventh part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part06Genomic differentiation between sympatric Timema populations and species (part 07 of 09)This is the eighth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part07Genomic differentiation between sympatric Timema populations and species (part 08 of 09)This is the ninth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part08Genomic differentiation between sympatric Timema populations and species (part 09 of 09)This is the tenth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.wgs_speciation_continuum.tar.bz2.part09Genotyping-by-sequencing (GBS) and stages of speciationfst_gsi_admixture_stages_speciation.tar.bz2Phylogenetic inference and molecular datingphylogenetics.tar.bz2Evolution of reproductive isolation and phenotypic differentiation through timeipsi_morphology_ri_through_time.tar.bz2Programs and scripts for processing and analysing dat