Figure 4
From: Cage and maternal effects on the bacterial communities of the murine gut
Abundant, low-level taxa distinguish cage microbiomes but not age or niche. The phylogenetic scale of each clade was measured as the number of nodes in the phylogenetic tree between the clade and root (small values associated with large-scale taxa such as phyla). Phylogenetic scale was compared against the ‘mean decrease in accuracy’ (MDA) value when running a random forest that distinguished the niche (a), age (b), cage (c) and mother (d). Clade abundance was measured as the number of sequences (tips) descending from each clade. Each clade’s abundance was compared against its MDA value, when running a forest that distinguished the niche (d), age (e), cage (f) and mother (g). The smoothed mean for the ‘real’ random forest model is illustrated in blue and for a null (negative control) random forest model in red. The grey areas refer to confidence intervals. Each small vertical ‘rug’ line above the horizontal axis indicates the location of a single taxon. Note the logarithmic scales on all axes. Similar plots using a different measure of phylogenetic scale (distance of clades from the root of the tree) are in Supplementary Figure S5. Figure produced in R 3.6.0 for Windows.
