Fig. 6

Evolutionary analysis of Thaumarchaeota. A Dynamic evolution of orthogroup gene families in Thaumarchaeota. Ancestral genome content reconstruction applied using COUNT. A number of genes are present and gene gain and loss events in the predicted ancestral genomes are marked at each lineage of the tree. Numbers at the right of the nodes represent the predicted present genes. “ + ” represents gene gain events, and “–” represents gene loss events. The topology tree was constructed based on the concatenated alignment of 122 archaeal marker genes from 81 high-quality genomes (completeness > 80%). Nitrosocaldales, Nitrosophaerales, and Nitrosopumilales in ammonia-oxidizing archaea (AOA) and Aigarchaeota all collapsed. B Timing estimation analysis between key nodes of Thaumarchaeota and the geological time scales throughout the Earth’s history. The tree added 21 Euryarchaeota, 16 Crenarchaeota, one Korarchaeota, two Bathyarchaeota, and two DPANN archaea (as outgroup). The added genomes of Thaumarchaeota are the same as in Fig. 6A. Complete tree is shown in Fig. S8. Nodes with bootstrap and data coverages (defined as the proportion of sites where there is at least one taxon in each descendent lineage that has available data to perform timing estimation) in the ranges of (70-100) and (50-80) are shown as gray dots; bootstrap and data coverage in the ranges of (70-100) and (80-100) are shown as black dots. The time unit at the bottom is millions of years (Ma), which corresponds to the geological time periods in the top panel