Dimensions of Group-Based Phylogenetic Mixtures.

Mixtures of group-based Markov models of evolution correspond to joins of toric varieties. In this paper, we establish a large number of cases for which these phylogenetic join varieties realize their expected dimension, meaning that they are nondefective. Nondefectiveness is not only interesting from a geometric point-of-view, but has been used to establish combinatorial identifiability for several classes of phylogenetic mixture models. Our focus is on group-based models where the equivalence classes of identified parameters are orbits of a subgroup of the automorphism group of the abelian group defining the model. In particular, we show that for these group-based models, the variety corresponding to the mixture of r trees with n leaves is nondefective when $$n \ge 2r+5$$ . We also give improved bounds for claw trees and give computational evidence that 2-tree and 3-tree mixtures are nondefective for small n.