Related papers: On phylogenetic trees - a geometer's view

In this paper we study group-based Markov models of evolution and their mixtures. In the algebreo-geometric setting, group-based phylogenetic tree models correspond to toric varieties, while their mixtures correspond to secant and join…

In this paper, we study holomorphic foliations of degree four on complex projective space $\mathbb{P}^n$, where $n\geq 3$, with a special focus on obtaining a structural theorem for these foliations. Furthermore, for a foliation…

We prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different…

We continue study of some algebraic varieties (called resultantal varieties) started in a paper of A. Grishkov, D. Logachev "Resultantal varieties related to zeroes of L-functions of Carlitz modules". These varieties are related with the…

We study degenerations of complex projective spaces $\mathbb P^n$ into normal projective klt varieties $X$. If the tangent sheaf of $X$ is semi-stable, we show that $X$ itself is a projective space. If $X$ is a threefold with canonical…

The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…

Toric geometry provides a bridge between algebraic geometry and combinatorics of fans and polytopes. For each polarized toric variety (X,L) we have associated a polytope P. In this thesis we use this correspondence to study birational…

In this paper, extending some ideas of Fano, we study the birational geometry of the Hilbert scheme of 0-dimensional subschemes of length 2 of a rational normal scroll. This fourfold has three elementary contractions associated to the three…

Hilbert curves of special varieties like Fano manifolds of low coindex as well as fibrations having such a manifold as general fiber, endowed with appropriate polarizations, are investigated. In particular, all most relevant varieties…

In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…

A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…

In this paper we connect degenerations of Fano threefolds by projections. Using Mirror Symmetry we transfer these connections to the side of Landau--Ginzburg models. Based on that we suggest a generalization of Kawamata's categorical…

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…

The aim of this paper is to prove Golyshev's conjecture in the cases of Fano threefolds $V_{10}$ and $V_{14}$. This conjecture states modularity of D3 equations for smooth Fano threefolds with Picard group Z. More precisely, we find…

The \textit{slope} of a fibered $3$-folds $f:X \to B$ is a relative numerical invariant defined by $\lambda(f) := K_{f}^{3}/\mathrm{deg}(f_{\ast}\omega_{f})$, where $K_{f}$ is the relative canonical divisor and $\omega_{f}$ is the relative…

We prove that smooth projective varieties with equivalent derived categories have isogenous (and sometimes isomorphic) Picard varieties. In particular their irregularity and number of independent vector fields are the same. This is turn…

We examine connections between the gonality, treewidth, and orientable genus of a graph. Especially, we find that hyperelliptic graphs in the sense of Baker and Norine are planar. We give a notion of a bielliptic graph and show that each of…

In a previous paper we defined the concept of an affinized projective variety and its associated Hilbert series. We computed the Hilbert series for varieties associated to quadratic monomial ideals. In this paper we show how to apply these…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

We classify three-dimensional Fano varieties with canonical Gorenstein singularities of degree bigger than 64.