相关论文: Phylogenetic networks form partial trees

Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…

We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…

Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…

The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…

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…

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…

While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…

Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…

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 mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…

We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…

Throughout the last decade, we have seen much progress towards characterising and computing the minimum hybridisation number for a set P of rooted phylogenetic trees. Roughly speaking, this minimum quantifies the number of hybridisation…

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 a recent series of papers devoted to the…

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…

Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…

The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

We give the first data structure for the problem of maintaining a dynamic set of n elements drawn from a partially ordered universe described by a tree. We define the Line-Leaf Tree, a linear-sized data structure that supports the…