Figure 2

Galileo phylogenetic analyses. A) Unrooted tree inferred using 238 TIR sequences of Galileo. Phylogenetic reconstructions were carried out by means of maximum likelihood (ML, PhyML) and Bayesian inference (BI, BEAST) methods using a HKY+G evolutionary model. Numbers on nodes indicate the support of each group as bootstrap and Bayesian posterior probability, respectively. The five groups show strong support. B) BEAST ultrametric summary tree inferred using 148 TIR sequences of Galileo (only one TIR of each Galileo copy was used and chimeric copies were excluded). The yellow bars correspond to the 95% highest posterior density intervals for node ages. The best-fit model of diversification was a yule-2-rate in which a constant duplication rate changes to another constant rate at a certain time, and the discontinuous vertical line indicates the shift in the duplication rate (0.048 substitutions/position, about 4.36 myr) and the grey area represents the 95% confidence interval obtained using 10,000 trees sampled from the Bayesian analysis. C) Lineages through time (LTT) plot representing the accumulation of cladogenesis events. Red lines represent the LTT plot for each of the 10,000 trees sampled from the Bayesian analysis. Black and green lines show the median and the mean, respectively. Blue lines represent the 95% credible interval.” This would be followed by the figure abbreviations.