The Identifiability of Covarion Models in Phylogenetics

TL;DR

This paper proves that covarion models in phylogenetics are identifiable for generic parameters when the number of classes does not exceed the observable states, ensuring reliable inference of evolutionary histories.

Contribution

It establishes the identifiability of covarion models with generic parameters on known trees, extending previous results to models with multiple classes.

Findings

Identifiability holds for models with classes not exceeding observable states.

Tree and parameters are identifiable for models with fewer classes than observable states.

Results apply to generic parameters, excluding measure-zero sets.

Abstract

Covarion models of character evolution describe inhomogeneities in substitution processes through time. In phylogenetics, such models are used to describe changing functional constraints or selection regimes during the evolution of biological sequences. In this work the identifiability of such models for generic parameters on a known phylogenetic tree is established, provided the number of covarion classes does not exceed the size of the observable state space. `Generic parameters' as used here means all parameters except possibly those in a set of measure zero within the parameter space. Combined with earlier results, this implies both the tree and generic numerical parameters are identifiable if the number of classes is strictly smaller than the number of observable states.