Fig. 2: Agreement between transfer-based relative ages and molecular clocks.

a, Relative ages derived from 12 fossil calibrations from a phylogeny of 36 extant mammals were compared with node ages sampled from four different relaxed molecular clock models implemented in Phylobayes and with node ages derived from random chronograms, keeping the species phylogeny fixed. b–d, Relative ages derived from gene transfers in Cyanobacteria (b), Archaea (c) and Fungi (d) using the MaxTiC algorithm were compared with estimates from the same five models as in a. For each model and each sampled chronogram, we calculated the fraction of relative age constraints that are satisfied. Each violin plot shows the distribution of the fraction of relative age constraints satisfied by 5,000 sampled chronograms. Inside the violins, boxes correspond to the first and third quartiles of the distribution, while a thick horizontal line corresponds to the median, and the whiskers extend to extrema no farther than 1.5 times the interquartile range. The blue distribution corresponds to random chronograms drawn from the prior with the 95% confidence interval denoted by broken lines. The orange distribution corresponds to the strict molecular clock model, purple to the autocorrelated lognormal model, green to the uncorrelated gamma model and grey to the white-noise model.