Fig. 3: Composition and function of oral microbiomes and smallpox phylogeny.
From: An ancient DNA perspective on the Russian conquest of Yakutia
a, PCoA of 74 oral samples carried out on Aitchison distances calculated on high-quality counts for 719 unique taxonomic species (abundance greater than 1%) from the MetaPhlAn4 database29. b, PCA of 65 oral samples performed on the abundance of 303 functional pathways after a centred log-ratio transformation. c, Relative abundance of the pathways underlying carbohydrate metabolism (for details on pathways, see Supplementary Fig. 2_18). d, Relative species abundance of five bacterial complexes and five oral pathogens (for details on each species from these complexes, see Supplementary Fig. 2_12). Similar analyses are provided in Extended Data Fig. 4c for three other pathogens. Box plots represent the 25%, 50% and 75% quantiles, with upper and lower whiskers showing values within the 1.5 interquartile range. The horizontal black segment indicates the mean value for each species at each stage. e, Maximum likelihood phylogenetic tree of the two Yakut smallpox strains (red labels). Node supports are on the basis of 1,000 ultrafast bootstraps. Scale bar, 0.01.
