PHOT_BI_chronogram_BEAST

The chronogram of plant phototropin and neochroem, inferred from "PHOT_alignment.fas", using BEAST. A total of 15 tmrca priors were employed as the calibration points (see SI Appendix), and a birth-death speciation prior was used as the tree prior. We used the uncorrelated relaxed-clock model with rates drawn from a lognormal distribution. A starting tree was first estimated by r8s and provided to BEAST to initiate the run. Two independent MCMC runs were carried out and the output was inspected in Tracer to ensure convergence and mixing (effective sample sizes all > 200). The trees from the two runs were combined in LogCombiner with a 25% burn-in and summarized in TreeAnnotator. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.