Biology subjects

Alexandre, A.

Publications and source records attributed to Alexandre, A..

4 recordsLinked to original sources

bioRxiv2026

Hydrodynamic flow in the gut hinders the fixation of beneficial mutants but accelerates their invasion

Gut bacteria experience a spatially structured environment with hydrodynamic flow. Using a branching-process approach, we show that beneficial mutants arising randomly upon division have a reduced fixation probability compared to the well-mixed case. The suppression factor is set by the spatial heterogeneity of mutant fate across the gut. In contrast, the invasion of mutant lineages that avoid early stochastic extinction is accelerated in the gut compared to a matched well-mixed case. Stronger advective flow decreases fixation probabilities while accelerating mutant invasion.

biophysics↗

bioRxiv2025

Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations

Complex spatial structure, with partially isolated subpopulations, and environment heterogeneity, such as gradients in nutrients, oxygen, and drugs, both shape the evolution of natural populations. We investigate the impact of environment heterogeneity on mutant fixation in spatially structured populations with demes on the nodes of a graph. When migrations between demes are frequent, we find that environment heterogeneity can amplify natural selection and simultaneously accelerate mutant fixation and extinction, thereby fostering the quick fixation of beneficial mutants. We demonstrate this effect in the star graph, and more strongly in the line graph. We show that amplification requires mutants to have a stronger fitness advantage in demes with stronger migration outflow, and that this condition allows amplification in more general graphs. As a baseline, we consider circulation graphs, where migration inflow and outflow are equal in each deme. In this case, environment heterogeneity has no impact to first order, but increases the fixation probability of beneficial mutants to second order. Finally, when migrations between demes are rare, we show that environment heterogeneity can also foster amplification of selection, by allowing demes with sufficient mutant advantage to become refugia for mutants.

evolutionary biology↗

bioRxiv2024

Impact of spatial structure on early and long-term adaptation in rugged fitness landscapes

We study how rugged fitness landscapes are explored by spatially structured populations with demes on the nodes of a graph, connected by migrations. In the weak mutation and rare migration regime, we find that, in most landscapes, migration asymmetries associated with some suppression of natural selection allow the population to reach higher fitness peaks first. In this sense, suppression of selection can make early adaptation more efficient. However, the time it takes to reach the first fitness peak is then increased. We also find that suppression of selection tends to enhance finite-size effects. Finite structures can adapt more efficiently than very large ones, especially in high-dimensional fitness landscapes. We extend our study to frequent migrations, suggesting that our conclusions hold in this regime. We then investigate the impact of spatial structure with rare migrations on long-term evolution by studying the steady state of the population with weak mutation, and introducing an associated steady-state effective population size. We find that suppression of selection is associated to small steady-state effective population sizes, and thus to small average steady-state fitnesses.

evolutionary biology↗

bioRxiv2018

The Ocean Gene Atlas: exploring the biogeography of plankton genes online

The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for homology and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences, and ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes, both produced by the Tara Oceans sequencing effort. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.

bioinformatics↗