Biology subjects

Doekes, H. M.

Publications and source records attributed to Doekes, H. M..

3 recordsLinked to original sources

bioRxiv2025

Microdiversity is higher in temperate than in virulent bacteriophages from soil environments

Bacteriophages are not only the most ubiquitous biological entity on earth, they also display remarkable genetic diversity across and within populations. While macrodiversity has been extensively studied, the drivers of microdiversity (intra-species genetic diversity) remain poorly understood, particularly in relation to phage lifestyle. The distinguishing ability of temperate phages to integrate themselves into the host genome has an unknown influence on the microdiversity present. This difference in microdiversity could impact the adaptability of phages to (a)biotic factors. To identify a possible association between microdiversity and lifestyle, we analysed 12 existing viromics datasets focusing on soil bacteriophages, including 43 171 viral genomes in total. We found that phages predicted to be temperate consistently exhibit higher microdiversity than their virulent counterparts in eight of 12 datasets. Of the remaining four datasets, one showed the opposite trend and three datasets did not show a significant trend at all. The detected pattern holds across multiple quality thresholds and lifestyle prediction methods. These findings suggest that lifestyle has a significant impact on genetic variation within phage populations, with potential implications for phage-host coevolution and environmental adaptability.

genomics↗

bioRxiv2021

Multiscale selection in spatially structured populations

The spatial structure of natural populations is key to many of their evolutionary processes. Formal theories analysing the interplay between natural selection and spatial structure have mostly focused on populations divided into distinct, non-overlapping groups. Most populations, however, are not structured in this way, but rather (self-)organise into dynamic patterns unfolding at various spatial scales. Here, we present a mathematical framework that quantifies how patterns and processes at different spatial scales contribute to natural selection in such populations. To that end, we define the Local Selection Differential (LSD): a measure of the selection acting on a trait within a given local environment. Based on the LSD, natural selection in a population can be decomposed into two parts: the contribution of local selection, acting within local environments, and the contribution of interlocal selection, acting among them. Varying the size of the local environments subsequently allows one to measure the contribution of each length scale. To illustrate the use of this new multiscale selection framework, we apply it to two simulation models of the evolution of traits known to be affected by spatial population structure: altruism and pathogen transmissibility. In both models, the spatial decomposition of selection reveals that local and interlocal selection can have opposite signs, thus providing a mathematically rigorous underpinning to intuitive explanations of how processes at different spatial scales may compete. It furthermore identifies which length scales--and hence which patterns--are relevant for natural selection. The multiscale selection framework can thus be used to address complex questions on evolution in spatially structured populations.

evolutionary biology↗

bioRxiv2020

How repeated outbreaks drive the evolution of bacteriophage communication: Insights from a mathematical model

Communication based on small signalling molecules is widespread among bacteria. Recently, such communication was also described in bacteriophages. Upon infection of a host cell, temperate phages of the Bacillus subtilis-infecting SPbeta group induce the secretion of a phage-encoded signalling peptide, which is used to inform the lysis-lysogeny decision in subsequent infections: the phages produce new virions and lyse their host cell when the signal concentration is low, but favour a latent infection strategy, lysogenising the host cell, when the signal concentration is high. Here, we present a mathematical model to study the ecological and evolutionary dynamics of such viral communication. We show that a communication strategy in which phages use the lytic cycle early in an outbreak (when susceptible host cells are abundant) but switch to the lysogenic cycle later (when susceptible cells become scarce) is favoured over a bet-hedging strategy in which cells are lysogenised with constant probability. However, such phage communication can evolve only if phage-bacteria populations are regularly perturbed away from their equilibrium state, so that acute outbreaks of phage infections in pools of susceptible cells continue to occur. Our model then predicts the selection of phages that switch infection strategy when half of the available susceptible cells have been infected.

evolutionary biology↗