Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families

Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications of gene trees require that the gene trees be correctly rooted. As a result, several computational methods have been developed for inferring the root of unrooted gene trees. However, the accuracy of such methods has never been systematically evaluated on prokaryotic gene families, where horizontal gene transfer is often one of the dominant evolutionary events driving gene family evolution. In this work, we address this gap by conducting a thorough comparative evaluation of five different rooting methods using large collections of both simulated and empirical prokaryotic gene trees. Our simulation study is based on 6000 true and reconstructed gene trees on 100 species and characterizes the rooting accuracy of the four methods under 36 different evolutionary conditions and 3 levels of gene tree reconstruction error. The empirical study is based on a large, carefully designed data set of 3098 gene trees from 504 bacterial species (406 Alphaproteobacteria and 98 Cyanobacteria) and reveals insights that supplement those gleaned from the simulation study. Overall, this work provides several valuable insights into the accuracy of the considered methods that will help inform the choice of rooting methods to use when studying microbial gene family evolution. Among other findings, this study identifies parsimonious Duplication-Transfer-Loss (DTL) rooting and Minimal Ancestor Deviation (MAD) rooting as two of the most accurate gene tree rooting methods for prokaryotes and specifies the evolutionary conditions under which these methods are most accurate, demonstrates that DTL rooting is highly sensitive to high evolutionary rates and gene tree error, and that rooting methods based on branch-lengths are generally robust to gene tree reconstruction error.