The Identifiability of Covarion Models in Phylogenetics

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 that 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 that both the tree and generic numerical parameters are identifiable if the number of classes is strictly smaller than the number of observable states.