Related papers: Classification of normal phylogenetic varieties fo…

We define phylogenetic projective toric model of a trivalent graph as a generalization of a binary symmetric model of a trivalent phylogenetic tree. Generators of the pro- jective coordinate ring of the models of graphs with one cycle are…

We coin the term \emph{$T$-trivial varieties} to denote smooth proper schemes over ground fields $k$ whose tangent sheaf is free. Over the complex numbers, this are precisely the abelian varieties. However, Igusa observed that in…

We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…

On an abelian variety $A$, sheaf convolution gives a Tannakian formalism for perverse sheaves. Let $X$ be an irreducible algebraic variety with generic point $\eta$. Let $K$ be a family of perverse sheaves (more precisely, a relative…

A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…

We study phylogenetic invariants of models of evolution whose group of symmetries is the cyclic group with 3 elements. We prove that projective schemes corresponding to the ideal I of phylogenetic invariants of such a model and to its…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…

In this paper, we consider the problem of determining when two tensor networks are equivalent under a heterogeneous change of basis. In particular, to a string diagram in a certain monoidal category (which we call tensor diagrams), we…

Let $X$ be a smooth affine algebraic variety over the field of complex numbers which is contractible. Then every algebraic $G$-torsor on $X$ is algebraically trivial if $G$ is a semi-simple algebraic group. We also show that if $X$ is a…

While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…

We classify all normal Schubert varieties in the affine Grassmannian of a semisimple group over an arbitrary field with special attention to small positive characteristic. The proof is elementary and relies on tangent space calculations for…

Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…

We determine positive-dimensional G-periodic proper subvarieties of an n-dimensional normal projective variety X under the action of an abelian group G of maximal rank n-1 and of positive entropy. The motivation of the paper is to…

A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…

Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…

We prove that any smooth complex projective variety $X$ with plurigenera $P_1(X)=P_2(X)=1$ and irregularity $q(X)=dim (X)$ is birational to an abelian variety.

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

We study generic objects in triangulated categories and characterize the finite dimensional algebras $A$ such that the derived categories $D(\Mod A)$ are generically trivial. This is an analogue of a result of Crawley-Boevey for module…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

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…