Phylogenomic Models from Tree Symmetries

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting. Chifman and Kubatko initiated the study of such models, leading to the development of the SVDquartets methods of species tree inference. A key observation was that symmetries in an ultrametric species tree led to symmetries in the joint distribution of bases at the taxa. In this work, we explore the implications of such symmetry more fully, defining new models incorporating only the symmetries of this distribution, regardless of the mechanism that might have produced them. The models are thus supermodels of many standard ones with mechanistic parameterizations. We study phylogenetic invariants for the models, and establish identifiability of species tree topologies using them.