Fig. 4

Phylogenetic analysis of ancient and modern Methanobrevibacter diversity. The colours in the trees corresponds to the age of the samples: Paleolithic: >12,000 BCE, Neolithic: 6000–3500 BCE, Copper Age: 3500–2200 BCE, Bronze Age: 2200–1000 BCE, Early Middle Age: 400–1000 CE, High Middle Age: 1000–1300 CE, Modern time: 1492 CE–present. A Phylogenetic tree showing the Methanobrevibacter MAGs with modern Methanobrevibacter genomes. B Geographical location of ancient calculus samples placed in the phylogenetic context in (C–E). C Phylogenetic tree of ancient calculus samples aligned to the highest quality TS-1 MAG (>50% covered at least 3 folds). D Phylogenetic tree of ancient calculus samples aligned to the highest quality TS-2 MAG (>50% covered at least 3 folds). E Phylogenetic tree of samples aligned to M. oralis (50% covered at least 3-folds)