“Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high

The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix, in the case where incomplete lineage sorting is high. We found that gene tree error correction only increases the level of error in gene tree topologies by “correcting” them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Gene tree correction must be considered a multi-locus task where the gene tree distribution is taken into account, rather than treating gene trees independently. Significance statement Gene tree information is essential for studying elucidating gene, genome, species, and phenotypic evolution, and a wide array of phylogenetic methods have been developed for gene tree estimation. Given that gene tree estimates are often inaccurate, several methods for “correcting” gene tree estimates have been devised. Here we show that correction methods that neglect the distribution of gene trees that is induced by the species phylogeny could produce poor results, calling for the development of species phylogeny-aware gene tree correction.