BEAST 2 phylogenetic analyses for estimating divergence times between chromosomal variants ------------------------------------------------------------------------------------------ The dataset used comprises 140 individuals: 60 T. cristinae individuals from population N1 (20 per homokaryotypic cluster) along with 20 individuals from a single population per species (T. californicum LICK, T. knulli HB, T. landelsensis BCBOG, and T. poppensis TBARN). Sequencing data for T. cristinae N1 has been deposited in NCBI BioProject PRJNA386212. Sequencing data for the other species was published on Riesch et al. 2017 Nature Ecology & Evolution doi:10.1038/s41559-017-0082 and was previously archived as BioProject PRJNA356405. variants.flt_s085p001.vcf.gz => total variants called for the 140 samples dataset variants.flt_s085p001.set_i.vcf.gz => variants called for scaffolds 931, 318, and 1440 variants.flt_s085p001.set_ii.vcf.gz => variants called for high-differentiation scaffolds common to all three pairwise combinations of homokaryotypic clusters effpriors => Empty data run to evaluate joint calibration distributions variants.flt_s085p001.set_i.ebsp.monoph.ucldmeangamma.effpriors.winv.xml => BEAST 2 XML input file set_i_concat.effpriors.log.bz2 => log of run without data set i => 202 variant sites + 1326 constant sites from scaffolds 931, 318, and 1440 variants.flt_s085p001.set_i.ebsp.monoph.ucldmeangamma.winv.xml => BEAST 2 XML input file set_i_concat.6runs85burn.log.bz2 => Combined log of 6 runs after burnin 85% samples set_i_concat.6runs85burn.trees.bz2 => Combined posterior trees of 6 runs after burnin 85% samples set_i_concat.6runs85burn.extended.log => Extended log including divergence times taken from the posterior distribution of tree set_i_concat.6runs85burn.extended.loganalyser.dsv => Summary of extended log set_i_concat.6runs85burn.sumca.tree => Summary tree obtained with TreeAnnotator using the common ancestor (CA) tree approach set_i_concat.6runs85burn.sumca.figtree.tree => Summary tree edited with Figtree to improve readability set_i_concat.6runs85burn.sumca.figtree.tree.mod.tree => Summary tree modified for publication set_i_concat.6runs85burn.logcombine.sh => R script used to produce extended log including divergence times taken from the posterior distribution of trees, and also to obtain the summary CA tree set_i_concat.6runs85burn.loganalyser.R => R script used to summarize extended log set_i_concat.6runs85burn.renameTree.sh => bash script to slightly modify figtree edited summary tree for publication set ii => 834 variant sites + 6317 constant sites from high-differentiation scaffolds common to all three pairwise combinations of homokaryotypic clusters variants.flt_s085p001.set_ii.ebsp.monoph.ucldmeangamma.winv.xml => BEAST 2 XML input file set_ii_concat.6runs85burn.log.bz2 => Combined log of 6 runs after burnin 85% samples set_ii_concat.6runs85burn.trees.bz2 => Combined posterior trees of 6 runs after burnin 85% samples set_ii_concat.6runs85burn.extended.log => Extended log including divergence times taken from the posterior distribution of tree set_ii_concat.6runs85burn.extended.loganalyser.dsv => Summary of extended log set_ii_concat.6runs85burn.sumca.tree => Summary tree obtained with TreeAnnotator using the common ancestor (CA) tree approach set_ii_concat.6runs85burn.sumca.figtree.tree => Summary tree edited with Figtree to improve readability set_ii_concat.6runs85burn.sumca.figtree.tree.mod.tree => Summary tree modified for publication set_ii_concat.6runs85burn.logcombine.sh => R script used to produce extended log including divergence times taken from the posterior distribution of trees, and also to obtain the summary CA tree set_ii_concat.6runs85burn.loganalyser.R => R script used to summarize extended log set_ii_concat.6runs85burn.renameTree.sh => bash script to slightly modify figtree edited summary tree for publication