A unified framework reveals how evolutionary scale and abundance weighting shape phylogenetic community structure

Metrics describing phylogenetic community structure are widely used to infer assembly processes in biological communities, but existing metrics capture only fixed phylogenetic scales and provide limited control over how rare and abundant taxa influence ecological patterns. Here we introduce q-weighted interpolated mean phylogenetic distance (qiMPD), a framework that continuously interpolates between broad evolutionary divergence and nearest-taxon distance while incorporating tunable abundance weighting. Applied to 3661 wastewater microbiomes, qiMPD revealed that abundance weighting had little effect on broad-scale phylogenetic dispersion but strongly altered local phylogenetic structure. Null-model analyses showed that within-community signals of phylogenetic overdispersion and clustering, and between-community signals of phylogenetic divergence and convergence, emerged at different combinations of phylogenetic locality and abundance weighting. Thus, the qiMPD framework enables phylogenetic scale- and abundance-resolved inference of community assembly. It is implemented in the Python package qdiv version 4.2.0.