Updated site concordance factors minimize effects of homoplasy and taxon sampling

MotivationSite concordance factors (sCFs) have become a widely used way to summarize discordance in phylogenomic datasets. However, the original version of sCFs were calculated by sampling a quartet of tip taxa and then applying parsimony-based criteria for discordance. This approach has the potential to be strongly affected by multiple hits at a site (homoplasy), especially when substitution rates are high or taxa are not closely related. ResultsHere, we introduce a new method for calculating site concordance factors. The updated version uses likelihood to generate probability distributions of ancestral states at internal nodes of the phylogeny. By sampling from the states at internal nodes adjacent to a given branch, this approach substantially reduces--but does not completely abolish--the effects of homoplasy and taxon sampling. Availability and implementationUpdated sCFs are implemented in IQ-TREE 2.2.2. The software is freely available at https://github.com/iqtree/iqtree2/releases. Contactmoyu@iu.edu