 
Summary: 1
The Identifiability of Covarion Models in
Phylogenetics
Elizabeth S. Allman, John A. Rhodes
Abstract Covarion models of character evolution describe
inhomogeneities in substitution processes through time. In phy
logenetics, 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.
Index Terms phylogenetics, Markov processes on trees, co
varion models, statistical consistency
I. INTRODUCTION
