Initial ideals of Pfaffian ideals

Gröbner bases; other bases for ideals and modules (e.g., Janet and border bases) (13P10) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25) Toric varieties, Newton polyhedra, Okounkov bodies (14M25)

Abstract: We resolve a conjecture about a class of binomial initial ideals of

I_{2, n}

, the ideal of the Grassmannian, Gr

(2, m a t h b b C^{n}

), which are associated to phylogenetic trees. For a weight vector

o m e g a

in the tropical Grassmannian,

i n_{o} m e g a (I_{2, n}) = J_{m} a t h c a l T

is the ideal associated to the tree

m a t h c a l T

. The ideal generated by the

2 r i m e s 2 r

subpfaffians of a generic

n i m e s 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

m a t h c a l T

in order for

i n_{o} m e g a (I_{2, n})^{2} = J_{m} a t h c a l T^{2}

. We also give a new classof prime initial ideals of the Pfaffian ideals.

Review text

The aim of the paper is to establish the relationship between secant ideals and initial ideals of the ideal \(I_{2,n}\) generated by the Plücker equations, i.e. the ideal of the Grassmann variety \(\operatorname{Gr}(2,\mathbb{C}^n)\). It is a known fact that the \((r-1)\)-secant ideal of \(I_{2,n}\) is generated by the \(2r \times 2r\) subpfaffians of a generic skew-symmetric matrix. Given a phylogenetic tree \(\mathcal{T}\), one can define the \textit{Plücker tree ideal} of \(\mathcal{T}\) as the initial ideal \(J_{\mathcal{T}}\) of \(I_{2,n}\) determined by a suitable weight vector associated to the tree. The main result is to show that a conjecture on the equality between the initial ideal of the \(r\)-secant ideal of \(I_{2,n}\) and the \(r\)-secant ideal of \(J_{\mathcal{T}}\) fails for a class of phylogenetic trees. On the other hand the author establishes a necessary and sufficient condition to make the conjecture true in terms of \textit{cherries} of the tree. In order to achieve this result, it is shown that the initial ideal of the \(r\)-secant ideal of \(I_{2,n}\) is always prime. Eventually the author proves that the dimensions of the initial ideal of the \(2\)-secant ideal of \(I_{2,n}\) and the \(2\)-secant ideal of \(J_{\mathcal{T}}\) are equal computing them via tropical techniques.

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