Most Compact Parsimonious Trees

TL;DR

This paper introduces new algorithms for constructing the most parsimonious live phylogenetic trees with polytomies, addressing computational challenges in applications like viral evolution, paleontology, and linguistics.

Contribution

It proves unique properties of these trees and develops novel algorithms that avoid exhaustive enumeration of all topologies.

Findings

Proves properties of most parsimonious live phylogenetic trees with polytomies.

Develops algorithms to efficiently find such trees.

Addresses computational complexity in phylogeny inference.

Abstract

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and describe novel algorithms to find the such trees without resorting to exhaustive enumeration of all possible tree topologies.