Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

TL;DR

This paper introduces formal algorithms to reconcile taxonomy with phylogenetic trees, including methods for identifying discord and inferring taxonomic roots, improving computational efficiency and providing practical tools.

Contribution

It formalizes the problem of reconciling taxonomy and phylogeny and develops new algorithms for discord detection and tree rooting, with improved complexity and real-data performance.

Findings

New efficient algorithm for subcoloring problem

Branch-and-bound method significantly reduces computation time

Algorithms implemented in freely available software

Abstract

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.