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Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not accurately reflect the true underlying ancestral history of…

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…

Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…

We introduce regenerative tree growth processes as consistent families of random trees with n labelled leaves, n>=1, with a regenerative property at branch points. This framework includes growth processes for exchangeably labelled Markov…

Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…

This paper demonstrates that every ultrametric space is homeomorphic to a clade space of a pruned tree, i.e., a subspace of a tree's canopy. Furthermore, it characterizes several topological properties of ultrametrizable spaces through the…

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…

The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…

We show that the homology of ordered configuration spaces of finite trees with loops is torsion free. We introduce configuration spaces with sinks, which allow for taking quotients of the base space. Furthermore, we give a concrete…

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…

Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…

Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…

The relative importance of the intrinsic and extrinsic factors determining the variety of geometric shapes exhibited by dendritic trees remains unclear. This question was addressed by developing a model of the growth of dendritic trees…

We define and give explicit construction of the universal tree-graded space with a given collection of pieces. We apply that to proving uniqueness of asymptotic cones of relatively hyperbolic groups whose peripheral subgroups have unique…

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…

Given a finite group G and a natural number n, we study the structure of the complex of nested sets of the associated Dowling lattice Q(G) and of its subposet of the G-symmetric partitions Q_G which was recently introduced by Hultman…

Using the wedge sum of metric spaces, for all compact metrizable spaces, we construct a topological embedding of the compact metrizable space into the set of all metric trees in the Gromov--Hausdorff space with finite prescribed values. As…

It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…

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…

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…