Combinatorial views on persistent characters in phylogenetics

TL;DR

This paper explores the properties and counting of persistent characters in phylogenetics, linking them to maximum parsimony, tree balance, and the uniqueness of tree reconstruction.

Contribution

It introduces a formula for counting persistent characters based on tree balance and analyzes the minimal number of characters needed to uniquely identify a phylogenetic tree.

Findings

Persistent characters relate to Fitch algorithm's first phase.

Number of persistent characters depends on tree balance, quantified by Sackin index.

Upper bound established for characters needed to uniquely determine a phylogenetic tree.

Abstract

The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary) persistent characters, i.e. characters that can be realized on a phylogenetic tree by at most one $0 \rightarrow 1$ transition followed by at most one $1 \rightarrow 0$ transition in the tree, and analyze these characters under different aspects. First, we illustrate the connection between persistent characters and Maximum Parsimony, where we characterize persistent characters in terms of the first phase of the famous Fitch algorithm. Afterwards we focus on the number of persistent characters for a given phylogenetic tree. We show that this number solely depends on the balance of the tree. To be precise, we develop a formula for counting the number of persistent characters for a given phylogenetic tree based on an index of tree balance, namely the Sackin index. Lastly, we consider the question of how many (carefully chosen) binary characters together with their persistence status are needed to uniquely determine a phylogenetic tree and provide an upper bound for the number of characters needed.