RCVT: a diagnostic to quantify compositional biases among taxa for large phylogenomic studies

Abstract

Phylogenomics aims to reconstruct the history of genes and genomes. However, noise or error during inference can stem from diverse sources, such as compositional biases. Here, we introduce RCVT (Relative Composition Variability among Taxa), a metric to quantify compositional biases among taxa. We demonstrate the utility of RCVT using example data and quantify compositional biases in 16 empirical phylogenomic datasets, revealing variation in bias among taxa within phylogenomic data matrices. Systematic removal of taxa with high RCVT scores substantially reduces compositional heterogeneity compared to randomly pruning taxa among large phylogenomic data matrices. RCVT may help researchers diagnose and potentially ameliorate phylogenomic noise associated with compositional biases.