Related papers: Classification of normal phylogenetic varieties fo…

We prove that if $f:X \rightarrow A$ is a morphism from a smooth projective variety $X$ to an abelian variety $A$ over a number field $K$, and $G$ is a subgroup of automorphisms of $X$ satisfying certain properties, and if a prime $p$…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

We study derived categories of coherent sheaves on abelian varieties. We give a criterion for the equivalence of the derived categories on two abelian varieties. We describe the autoequivalence group for the derived category of coherent…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…

We prove that Grothendieck's Hodge standard conjecture holds for abelian varieties in arbitrary characteristic if the Hodge conjecture holds for complex abelian varieties of CM-type. For abelian varieties with no exotic algebraic classes,…

For an ordinary abelian variety $X$, $F^e_*\mathcal{O}_X$ is decomposed into line bundles for every positive integer $e$. Conversely, if a smooth projective variety $X$ satisfies this property and its Kodaira dimension is non-negative, then…

Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…

In this note, we prove that for any finite dimensional vector space $V$ over an algebraically closed field $k$, and for any finite subgroup $G$ of $GL(V)$ which is either solvable or is generated by pseudo reflections such that the $|G|$ is…

Trinomial varieties are affine varieties given by a system of equations consisting of polynomials with three terms. Such varieties are total coordinate spaces of normal varieties with torus action of complexity one. For an affine variety…

Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…

We explicitly describe the tropicalization of a cluster variety of finite type C, realizing it as the space of axially symmetric phylogenetic trees. We also find all occurring sign patterns of coordinates, for both the cluster variety and…

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…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…

Let $(X,B)$ be a complex projective klt pair, and let $f\colon X\to Z$ be a surjective morphism onto a normal projective variety with maximal albanese dimension such that $K_X+B$ is relatively big over $Z$. We show that such pairs have good…

A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…

Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover…

We call a triangulated category \emph{hereditary} provided that it is equivalent to the bounded derived category of a hereditary abelian category, where the equivalence is required to commute with the translation functors. If the…

We explicitly describe the tropicalization of a type C cluster variety by identifying it with the space of axially symmetric phylogenetic trees. We also study the signed tropicalizations of this cluster variety, realizing them as subfans of…