Related papers: Weighted Food Webs Make Computing Phylogenetic Div…
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…
The structure of ecological networks, in particular food webs, determines their ability to evolve further, i.e. evolvability. The knowledge about how food web evolvability is determined by the structures of diverse ecological networks can…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
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…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
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…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
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…
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…
Real food web data available in the literature presents us with the relations between various species, sizes of these species, metabolic types of the species and other useful information, which allows us to define parameters for the…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
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…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…