Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony

Abstract

In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex v of an evolutionary tree T from the states that are observed at the leaves of the tree. A simple and fast estimation method -maximum parsimony -takes the ancestral state at v to be any state that minimises the number of state changes in T required to explain its evolution on T . In this paper, we investigate the reconstruction accuracy of this estimation method further, under a simple symmetric model of state change, and obtain a number of new results, both for 2-state characters, and r-state characters (r > 2). Our results rely on establishing new identities and inequalities, based on a coupling argument that involves a simpler 'coin toss' approach to ancestral state reconstruction.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

“…Other PCMs permit reconstructing ancestral states of characters (Finarelli & Flynn, 2006;Puttick, 2016;Sallan et al, 2018;Herbst, Li, & Steel, 2019;Ponti, Arcones, & Vieites, 2020), correlating evolution of separate traits (Soul & Wright, 2021), identifying regime shifts (Lamsdell & Selden, 2017;Soul & Wright, 2021), and assessing stratigraphic congruence (Bell & Lloyd, 2015). A pertinent example is that of shifts between marine and non-marine habitats (and coincident changes in morphology and disparity; Lamsdell, 2016).…”