Related papers: Registering the evolutionary history in individual…
During the last decades macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full…
In this working paper, we present a simple theoretical framework based on network theory to study how speciation, the process by which new species appear, shapes spatial patterns of diversity. We show that this framework can be expanded to…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food…
We present an explicit unified stochastic model of fluctuations in population size due to random birth, death, density-dependent competition and environmental fluctuations. Stochastic dynamics provide insight into small populations,…
Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a…
Diffusion Models generate data by reversing a stochastic diffusion process, progressively transforming noise into structured samples drawn from a target distribution. Recent theoretical work has shown that this backward dynamics can undergo…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
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.…
Parapatric speciation is studied using an individual--based model with sexual reproduction. We combine the theory of mutation accumulation for biological ageing with an environmental selection pressure that varies according to the…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness", i.e. their relative…
Ecosystems are governed by dynamic processes such as competition for resources, reproduction and dispersal. These shape their biodiversity and how the system responds to change. Current approaches to modelling ecosystems, especially plants,…
The main topic of this thesis is the analysis of evolution equations reflecting issues in ecology and population dynamics. In mathematical modelling, the impact of environmental elements and the interaction between species is read into the…
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires prior knowledge of change-point locations on the phylogeny or…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Convergence of discrete-time Markov chains with two timescales is a powerful tool to study stochastic evolutionary games in subdivided populations. Focusing on linear games within demes, convergence to a diffusion process for the strategy…