We resolve a conjecture about a class of binomial initial ideals of $I_{2,n}$, the ideal of the Grassmannian, Gr$(2,\mathbb{C}^n$), which are associated to phylogenetic trees. For a weight vector $��$ in the tropical Grassmannian, $in_��(I_{2,n}) = J_\mathcal{T}$ is the ideal associated to the tree $\mathcal{T}$. The ideal generated by the $2r \times 2r$ subpfaffians of a generic $n \times n$ skew-symmetric matrix is precisely $I_{2,n}^{\{r-1\}}$, the $(r-1)$-secant of $I_{2,n}$. We prove necessary and sufficient conditions on the topology of $\mathcal{T}$ in order for $in_��(I_{2,n})^{\{2\}} = J_\mathcal{T}^{\{2\}}$. We also give a new classof prime initial ideals of the Pfaffian ideals.

14 pages