Related papers: Bounding the softwired parsimony score of a phylog…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of species), it is possible to determine in polynomial time whether there exists a level-1…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…
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…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
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 investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k).poly(n) whether there exists a level-<= k network (i.e. a network where each biconnected component has reticulation…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…