Related papers: Reconstruction of time-consistent species trees
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
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…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…
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 analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene…
Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
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 are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
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…