Fig. 3: Quantified mechanisms of proteome evolution.

The quantitative and qualitative predictions of the proteome changes were estimated across the thaumarchaeotal history and reported on the thaumarchaeotal cladogram possessing the topology of the ML tree presented in Fig. 1. In addition to the changes in proteome size (panel a), four mechanisms of proteome changes were quantified: duplication (panel b; copying of a gene within a genome), loss (panel c; loss of a gene within a genome), intra-LGT (panel d; defined as the acquisition of a gene from other member(s) of the phylum) and origination (panel e; defined as the acquisition of a gene from members of phyla outside the sampled genome set (Inter-LGT) or by de novo gene formation). For each cladogram, scale numbers indicate the range of the predicted number of events for a given mechanism. The number of events occurring on each branch is represented by the colour of the associated boxes using the colour legend at the bottom of the cladogram and box sizes increase relatively to the number of events. The order-level classification of the genomes is indicated by the coloured bar on the right. Duplication and loss hotspots within the Nitrososphaerales were highlighted by vertical bars in panels (b) and (c) and letters A, B, C (which corresponds to NS-2 LCA) and D indicate branches with extensive duplication. Originations occurring in the last common ancestors of all Thaumarchaeota, all ammonia-oxidising archaea, all Nitrososphaerales and a multifamily sub-group within Nitrososphaerales are labelled Thaum LCA, AOA LCA, NS LCA and NS-2 LCA, respectively.