Extended Data Fig. 4: Authentication and analysis of oral microbiome sequence data.
From: An ancient DNA perspective on the Russian conquest of Yakutia
a) Authentication with Sourcetracker293. The analysis included our data plus five published samples of known to be of high quality, and three others of low quality, that we used as controls (names in pink). Different microbiome sources were used (Supplementary Table 1k): bones as environmental controls (N = 10), modern dental calculus (N = 18), subgingival plaque (N = 20), skin (N = 10), and gut samples (N = 20). Most of the calculus samples and approximately half the tooth samples demonstrated a genuine oral profile (with the sum of Modern Calculus and Plaque source contribution above 25%). b) Diversity indexes for taxonomic diversity across the four archaeological stages. Left: Boxplot of both Shannon (top) and Simpson (bottom) diversity indexes for each Stage. Right: Per-individual diversity indexes. c) Relative species abundance of three oral pathogens. Boxplots represent the 25%, 50% and 75% quantiles, with upper and lower whiskers showing values within the 1.5 interquartile range. Horizontal black segments indicate the mean value for each species at each stage.
