Related papers: Classification of normal phylogenetic varieties fo…

Less rigid than phylogenetic trees, phylogenetic networks allow the description of a wider range of evolutionary events. In this note, we explain how to extend the rank invariants from phylogenetic trees to phylogenetic networks evolving…

Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…

Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…

Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…

The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…

We extend to characteristic $2$ and $3$ the classification of projective homogeneous varieties of Picard group isomorphic to $\mathbf{Z}$, corresponding to parabolic subgroup schemes with maximal reduced subgroup. The latter are all…

We study notions such as finite presentability and coherence, for partially ordered abelian groups and vector spaces. Typical results are the following: (i) A partially ordered abelian group G is finitely presented if and only…

We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…

We estimate the fraction of isogeny classes of abelian varieties over a finite field which have a given characteristic polynomial P(T) modulo l. As an application we find the proportion of isogeny classes of abelian varieties with a…

Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…

Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…

For a nondegenerate projective variety $X$, the Eisenbud-Goto conjecture asserts that $\operatorname{reg}X\leq\operatorname{deg}X-\operatorname{codim}X+1$. Despite the existence of counterexamples, identifying the classes of varieties for…

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…

A differential analogue of the conjecture of Reichstein, Rogalski, and Zhang in algebraic dynamics is here established: if $X$ is a projective variety over an algebraically closed field of characteristic zero which admits a global algebraic…

A projective log variety (X, D) is called "a log Fano manifold" if X is smooth and if D is a reduced simple normal crossing divisor on X with -(K_X+D) ample. The n-dimensional log Fano manifolds (X, D) with nonzero D are classified in this…

We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.

Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…

This paper gives sharp linear bounds on the genus of a normal surface in a triangulated compact, orientable 3--manifold in terms of the quadrilaterals in its cell decomposition---different bounds arise from varying hypotheses on the surface…