Spéciation | EPFL Graph Search

La est, en biologie, le processus évolutif par lequel de nouvelles espèces vivantes se forment à partir d'ancêtres communs. Les espèces s'individualisent à partir de populations appartenant à une espèce d'origine (sauf exception pour certains végétaux). Une espèce, au sens du concept biologique d'espèce, est définie comme ayant une communauté d'ascendance au sein de laquelle tout individu est interfécond avec les autres et donnera une descendance fertile. Il y a donc spéciation lorsque deux groupes partageant les mêmes ancêtres ne sont plus interféconds, et prennent ainsi le statut d'espèces biologiques vraies. La « zone grise » dans laquelle deux populations commencent à diverger et au-delà de laquelle on considère que ces deux groupes sont désormais deux espèces distinctes s'étend de 0,5 % jusqu'à 2 % de divergences moléculaires. La spéciation résulte principalement des modifications des chromosomes quand elle vient à empêcher la plupart des appariements. L

Insights into the microbial reduction of pentavalent and hexavalent uranium species by Shewanella oneidensis MR-1

Margaux Camille Andréa Molinas

Decades of uranium-related activities such as ore mining, nuclear power generation, weapon manufacture, storage of nuclear wastes, have contributed to the release of U in the environment. U occurrence is concerning, since in surface environments, U is typically found in the U(VI) oxidation state, as uranyl, complexed with various ligands, and is highly soluble. Therefore, this toxic metal is likely to leech into soils and contaminate surface waters and groundwaters. In addition, owing to the long half-lives of the predominant isotopes 238U and 235U, U is considered as a persistent contaminant over geological timescales. For several decades, efforts have focused on the development of in situ remediation solutions to tackle U pollution in the subsurface, and limit its mobility.With this aim, interest in the metabolic potential for U(VI)-respiration by dissimilatory metal-reducing bacteria (DMRB), such as Shewanella oneidensis MR-1, has seen a significant increase. This metabolically-versatile bacterium has been reported to reduce mobile U(VI) to typically insoluble crystalline and amorphous U(IV). The reduction of U(VI) in S. oneidensis MR-1 is coupled to the oxidation of an electron donor, which feeds electrons into an electron transport chain, extending from the cytoplasm to the outer-membrane of the cells. The microbially mediated reduction of U(VI) to U(IV) is the result of a two-step process. It is assumed that one electron is first transferred to U(VI) to form a pentavalent U(V) intermediate, followed by the abiotic disproportionation of two U(V) atoms into U(IV) and U(VI). However, evidence for this mechanism is limited to experimental systems rich in carbonate, which permits the rapid disproportionation of U(V). Thus, it remains unclear whether a second, biologically-mediated, electron transfer to U(V) is possible under conditions in which disproportionation is limited. To explore this, a novel U(V)-dpaea complex, that is stable in water at pH 7, was utilized to investigate the second step of the reduction mechanism. Here, we observed that U(V) can be biologically reduced by an additional one-electron transfer, resulting in the accumulation of U(IV) without the need for disproportionation. To improve our understanding of the molecular mechanism of U-dpaea reduction, we incubated mutant strains of S. oneidensis MR-1, lacking (i) only outer-membrane c-type cytochromes or (ii) all c-type cytochromes, with solid phase U(VI)-dpaea and aqueous U(V)-dpaea. We determined that U(VI)-dpaea reduction proceeds via the initial dissolution of the solid phase and that U(V)-dpaea reduction is mediated by outer-membrane c-type cytochromes. In particular, in vitro reactions between the purified outer-membrane c-type cytochrome MtrC and U(V)-dpaea demonstrated that MtrC can directly transfer electrons to U(V)-dpaea.Finally, we sought to determine the factors that influence electron transfer kinetics between DMRB and U. To this end, we reacted U(VI) coordinated by various aminocarboxylate ligands with purified MtrC. Here, U speciation significantly impacted reduction rates and appeared to be related to the binding strength of the U-MtrC interaction, i.e., hydrogen bonding versus electrostatic.All together, these findings provide further insights in the reduction mechanism of U by DMRB, and underline the importance of U speciation in controlling the pathway and rate of electron transfer.

EPFL2021

Linking micro and macroevolution in the presence of migration

Sophie Myriam Hautphenne, Laurent Lehmann, Nicolas Salamin

Understanding macroevolutionary patterns is central to evolutionary biology. This involves the process of divergence within a species, which starts at the microevolutionary level, for instance, when two sub populations evolve towards different phenotypic optima. The speed at which these optima are reached is controlled by the degree of stabilising selection, which pushes the mean trait towards different optima in the different subpopulations, and ongoing migration that pulls the mean phenotype away from that optimum. Traditionally, macro phenotypic evolution is modelled by directional selection processes, but these models usually ignore the role of migration within species. Here, our goal is to reconcile the processes of micro and macroevolution by modelling migration as part of the speciation process. More precisely, we introduce an Ornstein-Uhlenbeck (OU) model where migration happens between two subpopulations within a branch of a phylogeny and this migration decreases over time as it happens during speciation. We then use this model to study the evolution of trait means along a phylogeny, as well as the way phenotypic disparity between species changes with successive epochs. We show that ignoring the effect of migration in sampled time-series data biases significantly the estimation of the selective forces acting upon it. We also show that migration decreases the expected phenotypic disparity between species and we analyse the effect of migration in the particular case of niche filling. We further introduce a method to jointly estimate selection and migration from time-series data. Our model extends traditional quantitative genetics results of selection and migration from a microevolutionary time frame to multiple speciation events at a macroevolutionary scale. Our results further support that not accounting for gene flow has important consequences in inferences at both the micro and macroevolutionary scale. (C) 2019 The Authors. Published by Elsevier Ltd.

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD2020

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

Doris Herrmann, Pierre Taberlet

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.