English: Phylogenomic analyses based on 57 concatenated non-ribosomal proteins support the emergence of eukaryotes as a sister to Hodarchaeales. a, BI based on 278 archaeal taxa, using Euryarchaea and TACK archaea as the outgroup (not shown) (NM57-A175-nDK_sr4 alignment, 15,733 amino acid positions). The concatenation was SR4-recoded and analysed using the CAT+GTR model (4 chains, approximately 25,000 generations). b, Schematic representation of the shift in the position of eukaryotes (grey branches) in ML and BI analyses of this dataset under different treatments. Untreated, unprocessed dataset; Recoding, SR4-recoded dataset; Recoding+FSR, Fast-site removal combined with SR4-recoding (the topology most often recovered after removing 10–50% fastest-evolving sites, in steps of 10%, is shown). The indices 175 and 64 refer to phylogenomic datasets containing 175 and 64 Asgard archaea, respectively. Note that BI was not performed for the 175 untreated dataset owing to computational limitations. Scale bar denotes the average expected number of substitutions per site.