Fig. 1

Phylogenetic signal of 16S gene copy numbers (SILVA-derived tree). a Pearson autocorrelation function of 16S GCNs depending on phylogenetic distance between tip pairs, estimated based on ∼ 6,800 sequenced genomes. b Distances of tips in the SILVA-derived tree to the nearest sequenced genome. Each bar spans an NSTD interval of 2%. c Cross-validated coefficients of determination (\(R^{2}_{\text {cv}}\)) for 16S GCNs predicted on the SILVA-derived tree and depending on the minimum NSTD of the tips tested, for various ancestral state reconstruction algorithms (PIC: phylogenetic independent contrasts, WSCP: weighted squared-change parsimony, SA: subtree averaging, MPR: maximum parsimony reconstruction, Mk: continuous-time Markov chain model with equal-rates transition matrix). MPR transition costs either increased exponentially with transition size (“exp”), proportionally to transition size (“pr”), or were equal for all transitions (“ae”). For analogous results using the original SILVA tree, see Additional file 1: Figure S1