Fig. 3. Gene content reconstruction of the ancestral embryophyte.

a, Ancestral gene content was inferred for the internal branches of the embryophyte tree. A maximum likelihood tree was inferred from an alignment of 30 species of plants and algae, comprising 185 single-copy orthologues and 71,855 sites, under the LG + C60 + G4 + F model in IQ-TREE⁶⁹, and rooted in accordance with our previous phylogenetic analysis. A timescale for the tree was then calculated using a subset of 18 applicable fossil calibrations in MCMCtree. We reconciled 20,822 gene family clusters, inferred using Markov clustering⁸⁷, against the rooted dated species tree using the ALEml algorithm⁸⁸. The summed copy number of each gene family (under each branch) was determined using custom Python code (branchwise_number_of_events.py). Branches with reduced copies from the ancestral node are coloured in red. The numbers of DTL events are represented by purple, blue and red circles, respectively. The sizes of the circles are proportional to the summed number of events (the scale is indicated by the grey circle). b, The number of DTL events scaled by time for four clade-defining branches in the embryophyte tree. c, The number of shared gene families between the ancestral embryophyte, liverwort and angiosperm. The ancestral embryophyte shares more gene families with the ancestral angiosperm than with the ancestral liverwort.