Related papers: Forbidden Time Travel: Characterization of Time-Co…
The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
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…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
An arborescence, which is a directed analogue of a spanning tree in an undirected graph, is one of the most fundamental combinatorial objects in a digraph. In this paper, we study arborescences in digraphs from the viewpoint of…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
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…
An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In…
A temporal graph is a graph whose edges appear at certain points in time. These graphs are temporally connected (in class TC) if all vertices can reach each other by temporal paths (traversing the edges in chronological order). Reachability…
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…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…