Error in Phylogenetic Estimation for Bushes in the Tree of Life

Many rapid radiations, or bushes, throughout the Tree of Life remain unresolved. Here, we investigated how the shape of a bush interacts with two key processes - coalescence and mutation - that can lead to errors in phylogenetic inference under specific conditions. For this study, we focused on the tradeoff between sampling more individuals per species and sampling more loci as well as the utility of a species tree method based upon gene tree reconciliation and the concatenation of multiple loci for resolving bushes. We examined different bush shapes, varying both the speciation rate during the radiation and the depth of the radiation, to encompass a broad range of situations. Using simulations based upon parameters derived from empirical studies, we investigated the performance of phylogenetic analyses under different conditions to identify approaches with the greatest potential to resolve difficult phylogenies. Sampling a single individual for more loci outperformed sampling multiple individuals for one locus in all cases except the most recent radiations. We found that error due to homoplastic mutations increased with depth, while error due to the coalescent process remained unchanged. These simulations also revealed that, for certain ancient bushes, analyses of concatenated data matrices surprisingly resulted in more accurate phylogenies than gene tree reconciliation. The poor performance of gene tree reconciliation in this study appeared to reflect the poor estimation of gene trees, not the superiority of concatenation per se. Our results suggest concatenation remains a useful approximate method for species tree estimation, even for rapid evolutionary radiations. However, improved estimation of gene trees combined with use of gene tree reconciliation has the greatest potential for resolving the remaining bushes of the Tree of Life.