Visualizing Geophylogenies -- Internal and External Labeling with Phylogenetic Tree Constraints

TL;DR

This paper explores methods for effectively visualizing geophylogenies by optimizing internal and external labeling techniques, introducing algorithms and heuristics to improve clarity and reduce crossings.

Contribution

It presents new quality measures, efficient algorithms, and heuristics for internal and external labeling of geophylogenies, addressing NP-hard problems and providing practical solutions.

Findings

Polynomial-time algorithms for crossing-free instances

Fixed-parameter tractable algorithm for external labeling

Heuristics near optimal on real-world data

Abstract

A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing next to a map. The correspondence between the taxa and the sites is either shown with matching labels on the map (internal labeling) or with leaders that connect each site to the corresponding leaf of the tree (external labeling). In both cases, a good order of the leaves is paramount for understanding the association between sites and taxa. We define several quality measures for internal labeling and give an efficient algorithm for optimizing them. In contrast, minimizing the number of leader crossings in an external labeling is NP-hard. On the positive side, we show that crossing-free instances can be solved in polynomial time and give a fixed-parameter tractable (FPT) algorithm. Furthermore, optimal solutions can be found in a matter of seconds on realistic instances using integer linear programming. Finally, we provide several efficient heuristic algorithms and experimentally show them to be near optimal on real-world and synthetic instances.