Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees
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…
Phylogenetic trees derived from distinct genomic regions, such as organellar and nuclear genomes, often contradict each other due to factors like incomplete lineage sorting, hybridization, introgression, or horizontal gene transfer. While this discordance is valuable, the traditional method for visually comparing trees, the tanglegram, only allows for the simultaneous comparison of two trees and has been shown to inaccurately portray their similarities.
In this study, researchers present an alternative approach called phylogenetic parallelograms. These diagrams feature multiple rooted trees embedded within a single scaffold, a rooted phylogenetic network that includes all the trees, and are drawn in parallel to highlight shared branches while clearly showing diverging branches.
The researchers demonstrate that the complexity of a parallelogram is directly proportional to the topological distance between the trees, unlike the complexity of an optimized tanglegram which does not reflect this relationship. To validate the effectiveness of their method, they apply phylogenetic parallelograms to real-world examples, including genome-wide introgression in the Anopheles gambiae species complex and organellar discordance in cats, grasses, and Fagaceae.
PhyloParallelograms is an open-source interactive application designed to facilitate the use of this new visualization technique.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
