Distinguishing Phylogenetic Networks

Distinguishing Phylogenetic Networks

Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic networks and their associated geometry. We restrict our attention to large-cycle networks, networks with a single undirected cycle of length at least four. Using t...

Distinguishing Convergence on Phylogenetic Networks

In phylogenetics, the evolutionary history of a group of taxa, for example, groups of species, genera or subspecies, can be modelled using a phylogenetic tree. Alternatively, we can model evolutionary history with a phylogenetic network. On phylogenetic networks, edges that have previously evolved independently from a common ancestor may subsequently converge for a period of time. Examples of p...

Phylogenetic Networks

Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and e...

Phylogenetic Dependency Networks

Since its identification as the pathogenic cause of Acquired Immunodeficiency Syndrome (AIDS) in the early 1980s, Human Immunodeficiency Virus Type 1 (HIV) has emerged as a major global pandemic with an estimated 33 million infected individuals worldwide at the end of 2007 [1]. Specifically targeting the so-called “helper T cells” that help coordinate the adaptive immune response, HIV causes a ...