Fig. 6: Concordance of phylogenomic analyses and ecological distributions of hot spring populations.

a Phylogenetic distances of metagenome-assembled-genomes (MAGs) to the phylogenetic root. Distances to the phylogenetic root (i.e. the archaeal-bacterial bifurcation) were calculated for each MAG as the distance of the placement of that MAG to the root in a maximum likelihood (ML) phylogenomic tree (see materials and methods for details). The ML tree contained representatives of OTUs for all bacterial and archaeal MAGs analyzed in this study (n = 372) along with 622 other isolate genomes and MAGs from major archaeal and bacterial orders used in a previous phylogenetic analysis of major archaeal and bacterial lineages¹⁰⁵. The distances calculated for each mOTU (defined at >95% genome homology) were used for all MAGs within that mOTU. Root-to-tip distance distributions are shown for the collection of MAGs from each hot spring community, arranged in order of ascending pH of the spring extending from the top to the bottom of the plot. The hot spring community identifier is shown on the Y-axis. Additional details for each hot spring are provided in Supplementary Dataset 1. Black lines within boxplots show median values for that hot spring community distribution, the edges of the boxes show the 25th and 75th quartile ranges, whiskers show the range of data. Outliers are not shown to facilitate visualization. b Root-to-tip distances for all 1466 MAGs of this study, arranged by the pH of the spring they derive from on the X-axis. c) Statistical analysis of the distributions of root-to-tip distances for MAGs within acidic (AS; pH < 5, n = 298), mixed (MS; pH 5–7, n = 840), and circumneutral/alkaline (CS; pH > 7, n = 314) spring types. Boxplots are shown and defined the same as in (a), except that outliers are shown as black circles. Differences in overall distributions were statistically assessed by pairwise Wilcoxon rank sum tests with Benjamini & Hochberg multiple comparison correction. The resulting pairwise p-values (two-sided) are shown for each comparison. The distance values for each MAG in association with metagenome origin and taxonomic classification are provided in Supplementary Dataset 2. The phylogenies used to evaluate distances are shown in Supplementary Figs. 21–24 and Supplementary Dataset 11.