Dimensions of Level-1 Group-Based Phylogenetic Networks

Abstract: Phylogenetic networks represent evolutionary histories of sets of taxa where horizontal evolution or hybridization has occurred. Placing a Markov model of evolution on a phylogenetic network gives a model that is particularly amenable to algebraic study by representing it as an algebraic variety. In this paper, we give a formula for the dimension of the variety corresponding to a triangle-free level-1 phylogenetic network under a group-based evolutionary model. On our way to this, we give a dimension formula for codimension zero toric fiber products. We conclude by illustrating applications to identifiability.