Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Fig 2
Examples of hits from standard linear (blue highlights) and phylogenetic (orange highlights) models.
In each panel, the tree on the left is colored by species prevalence (black to orange), while the tree on the right is colored by gene presence-absence (blue to black). Selected species are displayed in the middle; lines link species with the leaves to which they refer. The color of the line matches the color of the leaf. A-B) The standard model recovered hits that matched large clades but without recapitulating fine structure. C-D) The phylogenetic model recovered associations for which more of the fine structure was mirrored between the left-hand and right-hand trees, as exemplified by the species labeled in the middle. E) Violin plots of Ives-Garland α, a summary of the rate of gain and loss of a binary trait across a tree, for genes significantly associated with prevalence in the standard (left, blue) and phylogenetic (right, orange) linear models. Horizontal lines mark the median of the distributions. The phylogenetic (orange) and standard linear (blue) models were significantly different for each phylum (Wilcox test for Bacteroidetes: 8.2 × 10−41; Firmicutes: 7.6 × 10−279; Proteobacteria: 1.8 × 10−235; Actinobacteria: 9.0 × 10−133).