Related papers: Which Phylogenetic Networks are Level-k Networks w…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
Recently, there has been a growing interest in the relationships between unrooted and rooted phylogenetic networks. In this context, a natural question to ask is if an unrooted phylogenetic network U can be oriented as a rooted phylogenetic…
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and Regraft). Recently, these moves were generalized to rooted…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…
A normal (phylogenetic) network with $k$ reticulations displays $2^k$ phylogenetic trees. In this paper, we establish an analogous result for tree-child (phylogenetic) networks with no underlying $3$-cycles. In particular, we show that a…
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…
In previous work, we gave asymptotic counting results for the number of tree-child and normal networks with $k$ reticulation vertices and explicit exponential generating functions of the counting sequences for $k=1,2,3$. The purpose of this…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
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 consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
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…