Computing algebraic degrees of phylogenetic varieties

Abstract

A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with applications in phylogeny reconstruction. In the broader area of algebra statistics, there have been important theoretical advances in computing certain invariants associated to algebraic varieties arising in applications. Beyond the dimension and degree of a variety, one is interested in computing other algebraic degrees, such as the maximum likelihood degree and the Euclidean distance degree. Despite these efforts, the current literature lacks explicit computations of these invariants for the particular case of phylogenetic varieties. In our work, we fill this gap by computing these invariants for phylogenetic varieties arising from the simplest group-based models of nucleotide substitution Cavender-Farris-Neyman model, Jukes-Cantor model, Kimura 2-parameter model, and the Kimura 3-parameter model on small phylogenetic trees with at most 5 leaves.