Fig. 3: Inferred gene originations, duplications, intra-phylum transfers and losses during the evolution of Thermoplasmatota.
a The quantitative and qualitative predictions of the genome content changes were estimated across the Thermoplasmatota history and reported on the circular cladograms possessing the topology of the Thermoplasmatota tree (see Supplementary Fig. 6). The mechanisms of gene content changes quantified were duplication (copying of a gene within a genome), loss (loss of a gene within a genome), intra-phylum transfers (defined as the acquisition of a gene from another member of the same phylum) (Intra-LGT) and origination (defined as the acquisition of a gene from members of phyla outside the sampled genome set or by de novo gene formation). Scale numbers indicate the range of the predicted number of events for each given mechanism. The order-level classification of the genomes is indicated by the coloured bar surrounding the circle. b The boxplots represent normalised events per branch ((events per branch - µ)/σ) for each mechanism. Numbered circles mark branches of the tree with the highest numbers of events, and the position of these branches is also indicated with numbered circles on the trees (in a). Horizontal lines within boxes indicate the medians, box boundaries indicate the 1st and 3rd quartiles, whiskers indicate the minima and maxima, and points beyond these whiskers are outliers. A punctuation score is measured for each given mechanism. It represents the sum of events in the 10% of branches with the highest event numbers divided by 10% of the sum of events into all branches (Σevents in top10%/(Σevents in all branches* 0.1).
