‘PNC': a trait‐based workflow for evaluating phylogeny as a proxy for ecological similarity across communities

Phylogenetic relatedness is often used as a proxy for ecological similarity in community and macroecological analyses. Yet whether phylogeny is informative about similarity in measured traits can vary among traits and species pools, while incomplete trait data may further affect the resulting inference. We developed ‘PNC', an R package that links trait data preparation and coverage assessment with phylogenetic signal analysis within focal species pools and across multiple communities. The package includes curated quantitative trait datasets for plants, birds, mammals, reptiles, amphibians, and fishes, and uses paired simulations to assess how observed missing data patterns influence Pagel's λ estimates and significance classifications for individual traits. Applications to the Barro Colorado Island (BCI) plant species pool and Himalayan bird communities showed that phylogenetic signal varied among traits, taxonomic levels, and local species pools. In both applications, significance classifications for the individual traits were generally stable under the observed missing data patterns. ‘PNC' therefore provides an integrated workflow for evaluating whether phylogeny is an informative proxy for measured trait similarity in the assemblage under study and how sensitive that inference is to incomplete trait data.