Fig. 1: Divergence time estimate using the mitochondria-based strategy.

The evolutionary timeline of the Alphaproteobacteria estimated using the best-practiced dating scheme for the mito-encoded (the top) and nuclear-encoded (the bottom) data sets with Magnetococcales as the outgroup. Node bars denote the 95% HPD interval of estimated dates. Nodes with red circles denote calibration points. The organism images above the timeline indicate the origin times of eukaryotic lineages that Rickettsiales and Holosporales are mostly associated with, inferred simultaneously with Alphaproteobacteria using the same data set. The potential time range of mitochondrial endosymbiosis is also indicated. The panels in the upper and lower left corners are the infinite-sites plots, where the uncertainty in the divergence time (measured as the 95% HPD width) is plotted against the posterior mean of estimated times for each node. A lower value of the slope indicates less changes in the 95% HPD width, hence higher precision in dating. The image of mitochondria is credited to artist Kevin Song under CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/) with slight modifications. All other organism images are distributed under CC0. The mito- and nuclear-encoded data sets have 5250 and 4936 sites, respectively. Calibrations for the mito-encoded data set: crown group angiosperms 250–125 Ma, crown group land plants 509–450 Ma, total group Florideophyceae 1891–550 Ma, total group red algae 1891–1033 Ma, root 3000–1000 Ma. Calibrations for the nuclear-encoded data set: crown group angiosperms 250–125 Ma, crown group land plants 509–450 Ma, total group Florideophyceae 1891–550 Ma, total group red algae 1891–1033 Ma, crown group Foraminifera 1891–525 Ma, crown group Amniota 332–318 Ma, crown group Chordata 636–520 Ma, crown group Metazoa 833–550 Ma, total group fungi 1891–890 Ma, crown group Dikarya 1891–400 Ma, root 3000–1000 Ma. A uniform distribution ranging from the minimum to maximum bound is applied for each calibration point. Both maximum and minimum bounds are soft, meaning that there is a small probability (2.5% by default) that the age is beyond the bound (see also Supplementary Note 2.1).