Fig. 1: Gene transfers, like fossils, carry information on the timing of species divergence.

a, The geological record provides the only source of information concerning absolute time. That is, the age of the oldest fossil representative of a clade provides direct evidence of its minimum age (for example, the broken line for the blue clade), but inferring maximum age constraints (for example, the broken line for the red clade), and by extension the relative age of speciation nodes, must rely on indirect evidence of the absence of fossils in the geological record^5,31,42,43. b, Gene transfers, in contrast, do not carry information on absolute time, but they do define relative node age constraints by providing direct evidence of the relative age of speciation events. For example, the gene transfer depicted by the black arrow implies that the diversification of the blue donor clade predates the diversification of the red clade (that is, node D is necessarily older than node R). Note, however, that the depicted transfer is not informative about the relative age of nodes D′ and R. c, Sequence divergence (here measured in units of expected number of nucleotide substitutions along a strict molecular clock time tree, see Supplementary Information) for 36 mammals² is correlated (Pearson’s R² = 0.664, P < 0.003) with age estimates based on the fossil record (ages corresponding to the time of divergence in million years (Myr)). d, A similar relationship can be seen for gene transfer-based relative ages by plotting the sequence divergence (measured similar to c) against the relative age of ancestral nodes for 40 cyanobacterial genomes (Spearman’s rank correlation ρ = 0.741, P < 10⁻⁶) inferred by the MaxTiC algorithm²⁵.