Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees

Abstract

Phylogenetic trees inferred from different genomic regions, or from organellar and nuclear genomes, frequently disagree owing to incomplete lineage sorting, hybridization, introgression or horizontal gene transfer. Such discordance is informative, yet the standard tool for comparing trees visually, the tanglegram, is restricted to two trees and is known to misrepresent their similarity. Here we introduce phylogenetic parallelograms, drawings in which any number of rooted trees are embedded into a common scaffold, a rooted phylogenetic network that displays all of them, and are drawn in parallel so that shared branches align while conflicting branches visibly diverge. On synthetic tree pairs, the complexity of a parallelogram tracks the topological distance between the trees, whereas the complexity of an optimized tanglegram does not. We apply the approach to genome-wide introgression in the Anopheles gambiae species complex and to organellar discordance in cats, grasses and Fagaceae. PhyloParallelograms is an open-source interactive application.