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Ecologists are interested in modeling the population growth of species in various ecosystems. Studying population dynamics can assist environmental managers in making better decisions for the environment. Traditionally, the sampling of…
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.…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
The Maximum Entropy Theory of Ecology (METE) is a unified theory of biodiversity that predicts a large number of macroecological patterns using only information on the species richness, total abundance, and total metabolic rate of the…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
There has been considerable recent interest in computing a diverse collection of solutions to a given optimization problem, both in the AI and theory communities. Given a classical optimization problem $\Pi$ (e.g., spanning tree, minimum…
Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens in a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
Dynamic programming is a powerful technique that is, unfortunately, often inherently sequential. That is, there exists no unified method to parallelize algorithms that use dynamic programming. In this paper, we attempt to address this issue…
Most biological data are multidimensional, posing a major challenge to human comprehension and computational analysis. Principal component analysis is the most popular approach to rendering two- or three-dimensional representations of the…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
Nowadays hybrid evolutionary algorithms, i.e, heuristic search algorithms combining several mutation operators some of which are meant to implement stochastically a well known technique designed for the specific problem in question while…
Reconstructing the evolutionary history of a set of species is a central task in computational biology. In real data, it is often the case that some information is missing: the Incomplete Directed Perfect Phylogeny (IDPP) problem asks,…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Innovation and its complement exnovation describe the progression of realized possibilities from the past to the future, and the process depends on the structure of the underlying graph. For example, the phylogenetic tree represents the…
Modern ecology has re-emphasized the need for a quantitative understanding of the original 'survival of the fittest theme' based on analyzis of the intricate trade-offs between competing evolutionary strategies that characterize the…
Hundreds of Evolutionary Computation approaches have been reported. From an evolutionary perspective they focus on two fundamental mechanisms: cultural inheritance in Swarm Intelligence and genetic inheritance in Evolutionary Algorithms.…