Related papers: Dimensions of Group-based Phylogenetic Mixtures

Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…

Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…

Common experience suggests that many networks might possess community structure - division of vertices into groups, with a higher density of edges within groups than between them. Here we describe a new computer algorithm that detects…

Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…

We address a natural question in noncommutative geometry, namely the rigidity observed in many examples, whereby noncommutative spaces (or equivalently their coordinate algebras) have very few automorphisms by comparison with their…

Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…

Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…

The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…

In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…

The tree metric theorem provides a combinatorial four point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A similar (but weaker) four point condition characterizes dissimilarity maps derived…

Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable the investigator to pinpoint the sites…

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…

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…

The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…

This paper introduces a new family of models of intensional Martin-L\"of type theory. We use constructive ordered algebra in toposes. Identity types in the models are given by a notion of Moore path. By considering a particular gros topos,…

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 this paper, we present and study a new…