Extended Data Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface

Extended Data Fig. 4 | Ribosomal protein- and 16S rRNA gene-based phylogeny of MK-D1. a, Phylogenomic tree of MK-D1 and select cultured archaea,eukaryotes and bacteria based on 31 ribosomal proteins conserved across the three domains (Supplementary Table 7). Ribosomal protein sequences of MK-D1,the organisms shown in the tree and MAGs of uncultured archaeal lineages (Supplementary Table 8) were aligned individually using MAFFT.MAG-derived sequences (except for Ca. Korarchaeum) were then removed for tree construction.After removing all-gap positions and concatenation,the maximum-likelihood tree was constructed using RAxML- NG.Bootstrap values around critical branching points are also shown.In total, 14,875 sites of the alignment were used for tree construction. b, A ribosomal protein-based phylogenomic tree constructed using MrBayes.Bayesian inference phylogenies were calculated using MrBayes 3.2.7a and a ribosomal protein concatenated alignment used for Fig.4a. c, Phylogenetic tree of MK-D1 and related archaea based on 16S rRNA genes.The 16S rRNA gene sequences were aligned using SINA against the Silva v.132 alignment and the maximumlikelihood tree was calculated using RAxML.