Phylogeny_of_Typhlocharis_BEAST_dated_tree_(Rates_ULN_bd)_Complete

Dated phylogenetic tree obtained with BEAST 1.8.1 (Drummond et al. 2012). For the analyses the original concatenated dataset was collapsed to haplotypes and the outgroups were excluded, resulting in a dataset of 330 terminals. We used as calibration prior for each gene an uniform function on the mean substitution rate encompassing the 95% confident interval values obtained for the same DNA fragments (cox1-a, cox1-b, rrnL, LSU and SSU genes) in the confamilial genus Carabus (Andújar et al., 2014, 2012) and the tribe Anillini (Andújar et al., 2016) (Table 1 in original paper). We additionally applied a gamma prior on the root age for the most recent common ancestor (crown group) of Typhlocharina. We used TreeStat 1.6.1 (Rambaut & Drummond 2010) to recover the node age of the ancestor of Typhlocharina from the sample of the MCMC search of the BEAST analysis favoured in Andújar et al. (2016), and we used the “fitdistr” option of the R package MASS to obtain the values of a gamma function adjusting the distribution of sampled ages, thus accounting for the uncertainty associated to the age estimations (Table 1 on the original paper).
Analyses were conducted under the model of substitution best fitting to each gene and codon partition as above, and were run for 50 million generations sampling one tree in every 5,000 generations. In the molecular clock settings gene partitions were uncorrelated, and two independent analyses were conducted applying an uncorrelated lognormal (ULN) to all genes. Analyses were conducted under a Birth-Death model (BD) and with the inclusion of the constraint on the age for the ancestor of Typhlocharina (Table 1 on the original paper)