On geometry of binary symmetric models of phylogenetic trees (Q2466996)

The basic object studied in the present paper is a trivalent tree, i.e.\ an unoriented graph \(\mathcal T\) without cycles whose vertices have either valency one (the ``leaves'') or three (the inner ``nodes''). It gives rise to a certain lattice polytope \(\Delta(\mathcal T)\) with vertices corresponding to networks of mutually non-intersecting paths connecting leaves along edges of \(\mathcal T\). In the easiest case of three leaves being connected to a unique node, \(\Delta(\mathcal T)\) is the three-dimensional standard tetrahedron. In general, if \(\ell\) denotes the number of leaves, \(\Delta(\mathcal T)\) has exactly \(2^{\ell-1}\) vertices. The first result in the present paper is that the 4th scalar multiple of \(\Delta(\mathcal T)\) is a reflexive polytope, i.e.\ the associated toric variety \(X(\mathcal T)\) is Fano of index \(4\) having at most Gorenstein terminal singularities. Moreover, the authors show (by providing an explicit polyhedral subdivision of \(\partial\Delta(\mathcal T)\)) that \(X(\mathcal T)\) admits a small, crepant resolution. While the authors give the example that different trees (with the same number of leaves) might lead to mutually non-isomorphic polytopes, it was their striking observation that the Ehrhart polynomial of \(\Delta(\mathcal T)\) (i.e.\ the Hilbert polynomial of \(X(\mathcal T)\)) does depend only on \(\ell\). The second result of the paper is an explanation (and proof) of this fact by presenting a flat family that contains all varieties \(X(\mathcal T)\) with a fixed number \(\ell\) as special fibers. In particular, the freedom of choosing the easiest tree for a given \(\ell\) leads to a formula for the Ehrhart polynomial of \(\Delta(\mathcal T)\).