Related papers: Counting and optimising maximum phylogenetic diver…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Optimal control problems driven by evolutionary partial differential equations arise in many industrial applications and their numerical solution is known to be a challenging problem. One approach to obtain an optimal feedback control is…
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…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
The reconstruction of phylogenetic trees from discrete character data typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate $\lambda$. When $\lambda$ is too high…
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…
Time evolution of number of species (genera, families, and others), population of them, and size distribution of present ones and life times are studied in terms of a new model, where population of each genetic taxon increases by a (random)…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, where each taxon is associated…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were…
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…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…