Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees
Huson, D. H.; Cetinkaya, B.; Zhang, L.
Show 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.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data 95%
- SODA: Multi-locus species delimitation using quartet frequencies 94%
- AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer and loss. 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.