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1. Power and limits of selection genome scans on temporal data from a selfing population

Author

de Navascués, Miguel, Becheler, Arnaud, Gay, Laurène, Ronfort, Joëlle, Loridon, Karine, and Vitalis, Renaud

Subjects
Archaeology, CC1-960, Science
Abstract

Tracking genetic changes of populations through time allows a more direct study of the evolutionary processes acting on the population than a single contemporary sample. Several statistical methods have been developed to characterize the demography and selection from temporal population genetic data. However, these methods are usually developed under the assumption of outcrossing reproduction and might not be applicable when there is substantial selfing in the population. Here, we focus on a method to detect loci under selection based on a genome scan of temporal differentiation, adapting it to the particularities of selfing populations. Selfing reduces the effective recombination rate and can extend hitch-hiking effects to the whole genome, erasing any local signal of selection on a genome scan. Therefore, selfing is expected to reduce the power of the test. By means of simulations, we evaluate the performance of the method under scenarios of adaptation from new mutations or standing variation at different rates of selfing. We find that the detection of loci under selection in predominantly selfing populations remains challenging even with the adapted method. Still, selective sweeps from standing variation on predominantly selfing populations can leave some signal of selection around the selected site thanks to historical recombination before the sweep. Under this scenario, ancestral advantageous alleles at low frequency leave the strongest local signal, while new advantageous mutations leave no local footprint of the sweep.

Published
2021
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5. Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa

Author

Gilabert, Aude, Rieux, Adrien, Robert, Stéphanie, Vitalis, Renaud, Zapater, Marie-Françoise, Abadie, Catherine, Carlier, Jean, Ravigné, Virginie, Gilabert, Aude, Rieux, Adrien, Robert, Stéphanie, Vitalis, Renaud, Zapater, Marie-Françoise, Abadie, Catherine, Carlier, Jean, and Ravigné, Virginie

Abstract

The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step toward improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana Pseudocercospora fijiensis, by testing the historical hypothesis against other plausible hypotheses. We analyzed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.

Published
2023

11. Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus

Author

Gallet, Romain, Di Mattia, Jeremy, Ravel, Sébastien, Zeddam, Jean-Louis, Vitalis, Renaud, Michalakis, Yannis, Blanc, Stéphane, Gallet, Romain, Di Mattia, Jeremy, Ravel, Sébastien, Zeddam, Jean-Louis, Vitalis, Renaud, Michalakis, Yannis, and Blanc, Stéphane

Abstract

Multipartite viruses have a segmented genome, with each segment encapsidated separately. In all multipartite virus species for which the question has been addressed, the distinct segments reproducibly accumulate at a specific and host-dependent relative frequency, defined as the 'genome formula'. Here, we test the hypothesis that the multipartite genome organization facilitates the regulation of gene expression via changes of the genome formula, and thus via gene copy number variations. In a first experiment, the faba bean necrotic stunt virus (FBNSV), whose genome is composed of eight DNA segments each encoding a single gene, was inoculated into faba bean or alfalfa host plants, and the relative concentrations of the DNA segments and their corresponding mRNAs were monitored. In each of the two host species, our analysis consistently showed that the genome formula variations modulate gene expression, the concentration of each genome segment linearly and positively correlating to that of its cognate mRNA but not of the others. In a second experiment, twenty parallel FBNSV lines were transferred from faba bean to alfalfa plants. Upon host switching, the transcription rate of some genome segments changes but the genome formula is modified in a way that compensates for these changes and maintains a similar ratio between the various viral mRNAs. Interestingly, a deep-sequencing analysis of these twenty FBNSV lineages demonstrated that the host-related genome formula shift operates independently of DNA-segment sequence mutation. Together, our results indicate that nanoviruses are plastic genetic systems, able to transiently adjust gene expression at the population level in changing environment, by modulating the copy number but not the sequence of each of their genes.

Published
2022

21. f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat.

Author

Gautier, Mathieu, Vitalis, Renaud, Flori, Laurence, and Estoup, Arnaud

Subjects
*HAPLOTYPES, *ALLELES, *DROSOPHILA suzukii, *GENETIC variation, *GENE frequency, *ERROR rates
Abstract

By capturing various patterns of the structuring of genetic variation across populations, f‐statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariances of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly relevant for the analysis of pooled sequencing (Pool‐Seq) data. We here propose a reinterpretation of the F (and D) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool‐Seq data and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three‐population test of admixture; (ii) four‐population test of treeness; (iii) F4‐ratio estimation of admixture rates; and (iv) fitting, visualization and (semi‐automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool‐Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost‐effective Pool‐Seq design involving relatively low sequencing coverages. We further analysed a real Pool‐Seq data made of 14 populations of the invasive species Drosophila suzukii, which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user‐friendly and efficient all‐in‐one tool to unravel complex population genetic histories from large‐size Pool‐Seq or allele count SNP data. [ABSTRACT FROM AUTHOR]

Published
2022
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31. Gene copy number variation impacts on gene expression in a multipartite virus

Author

Gallet, Romain, Di Mattia, Jeremy, Ravel, Sébastien, Vitalis, Renaud, Michalakis, Yannis, Blanc, Stéphane, Gallet, Romain, Di Mattia, Jeremy, Ravel, Sébastien, Vitalis, Renaud, Michalakis, Yannis, and Blanc, Stéphane

Abstract

Multipartite viruses have a segmented genome and each segment is encapsidated independently. Earlier studies reported that the distinct genome segments reproducibly accumulate at a specific and host-dependent relative frequency, defined as the 'genome formula'. It has been hypothesized that variations of the genome formula could affect gene expression via changes of the viral gene copy number. The multipartite virus model used in this work is a nanovirus, the faba bean necrotic stunt virus (FBNSV), composed of eight DNA genome segments each encoding a single gene. We initiated twenty parallel FBNSV lineages in faba bean plants, transferred them to medicago plants, and monitored both the relative amounts of the DNA segments and those of the corresponding mRNAs in all lineages. Our analyses showed that the genome formula variations directly impact on gene expression. Moreover, when passaging FBNSV from one host species to the other, we observed that the variation of the genome formula allowed the maintenance of similar proportions of the eight viral mRNAs, suggesting that the genome formula adjusts gene expression to a changing environment. Deep-sequencing analysis of FBNSV lineages similarly alternating from faba bean to medicago host plants demonstrated that the genome formula changes result from the flexibility of this viral system. By this we mean that no DNA sequence mutations could be associated to the genome formula host-dependent switch, which can thus be viewed as a plastic phenomenon. Together, our results indicate that the genome formula adapts gene expression of this multipartite virus in a changing environment in a DNA-sequence mutation-independent way.

Published
2019

33. Temporal FST genome scans: the case of partially selfing populations

Author

Navascues, Miguel, Becheler, Arnaud, Gay, Laurène, Ronfort, Joëlle, Vitalis, Renaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and European Society of Evolutionnary Biology (ESEB). INT.

Subjects
Animal biology, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDE]Environmental Sciences, Biologie animale, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

In an isolated population, allele frequencies change through time because of selection (acting on specific loci) and genetic drift (acting on the whole genome). Theeffective size of a population (which characterizes the strength of genetic drift) can be estimated from temporal changes in allele frequencies at presumably neutral markers. Furthermore, generating the expected distribution of differentiation statistics conditionally on the inferred effective size, allows to test for the homogeneity of locus-specific estimates of temporal differentiation. Outlier loci, for which the extent of temporal differentiation is unlikely to be explained by the inferred rate of genetic drift, can therefore be characterized. However, self-fertilization may pose a problem for the detection of loci under selection. Selfing indeed reduces the effective size of populations and the effective recombination rate between loci, thereby promoting hitch-hiking. Here, we first propose a new test for the homogeneity of temporal differentiation at many loci, based on temporal measures of FST. We then investigate the effect of partial selfing on the power to detect selected loci and the false discovery rate , using simulated populations. In addition, we characterize the footprints of selection along a chromosome containing a selected site for a range of selfing rates.

Published
2018

34. Measuring genetic differentiation from pooled population samples

Author

Hivert, Valentin, Leblois, Raphaël, Petit, Eric, Gautier, Mathieu, Vitalis, Renaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, European Society of Evolutionnary Biology (ESEB). INT., and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

35. How to characterize local adaptation from genome-wide polymorphisms?

Author

Vitalis, Renaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Groupement de Recherche Génomique Environnementale (GDR3692). FRA. Approche Interdisciplinaire de l'Evolution Moléculaire (AIEM), FRA.

Subjects
[SDV.BA]Life Sciences [q-bio]/Animal biology
Abstract

National audience; L'avènement des technologies de séquençage et de génotypage à haut débit permet de comparer des patrons de polymorphisme pour un très grand nombre de marqueurs. Distinguer les effets de l'histoire démographique (au sens large) des effets de la sélection, permet de caractériser les régions génomiques impliquées dans l'adaptation des organismes à leur environnement local. Dans cet exposé, je présenterai différentes méthodes, développées dans notre groupe, visant à identifier des régions génomiques sous sélection. Je parlerai également de certains développements récents, permettant notamment de mieux prendre en compte l'information apportée par le déséquilibre de liaison entre marqueurs.

Published
2018

36. Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden : XXXX

Author

UCL - SST/ELI/ELIC - Earth & Climate, Rohfritsch, Audrey, Galan, Maxime, Gautier, Mathieu, Gharbi, Karim, Olsson, Gert, Gschloessl, Bernhard, Zeimes, Caroline, Vanwambeke, Sophie, Vitalis, Renaud, Charbonnel, Nathalie, UCL - SST/ELI/ELIC - Earth & Climate, Rohfritsch, Audrey, Galan, Maxime, Gautier, Mathieu, Gharbi, Karim, Olsson, Gert, Gschloessl, Bernhard, Zeimes, Caroline, Vanwambeke, Sophie, Vitalis, Renaud, and Charbonnel, Nathalie

Abstract

Natural reservoirs of zoonotic pathogens generally seem to be capable of tolerating infections. Tolerance and its underlying mechanisms remain difficult to assess using experiments or wildlife surveys. High‐throughput sequencing technologies give the opportunity to investigate the genetic bases of tolerance, and the variability of its mechanisms in natural populations. In particular, population genomics may provide preliminary insights into the genes shaping tolerance and potentially influencing epidemiological dynamics. Here, we addressed these questions in the bank vole Myodes glareolus, the specific asymptomatic reservoir host of Puumala hantavirus (PUUV), which causes nephropathia epidemica (NE) in humans. Despite the continuous spatial distribution of M. glareolus in Sweden, NE is endemic to the northern part of the country. Northern bank vole populations in Sweden might exhibit tolerance strategies as a result of coadaptation with PUUV. This may favor the circulation and maintenance of PUUV and lead to high spatial risk of NE in northern Sweden. We performed a genome‐scan study to detect signatures of selection potentially correlated with spatial variations in tolerance to PUUV. We analyzed six bank vole populations from Sweden, sampled from northern NE‐endemic to southern NE‐free areas. We combined candidate gene analyses (Tlr4, Tlr7, and Mx2 genes) and high‐throughput sequencing of restriction site‐associated DNA (RAD) markers. Outlier loci showed high levels of genetic differentiation and significant associations with environmental data including variations in the regional number of NE human cases. Among the 108 outliers that matched to mouse protein‐coding genes, 14 corresponded to immunerelated genes. The main biological pathways found to be significantly enriched corresponded to immune processes and responses to hantavirus, including the regulation of cytokine productions, TLR cascades, and IL‐7, VEGF, and JAK–STAT signaling. In the future, genome‐scan r

Published
2018

38. Estimation of the sex-ratio in population trees from allele frequency data

Author

Clemente, Florian, Gautier, Mathieu, Vitalis, Renaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV.BA]Life Sciences [q-bio]/Animal biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

40. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Author

Nouhaud, Pierre, primary, Gautier, Mathieu, additional, Gouin, Anaïs, additional, Jaquiéry, Julie, additional, Peccoud, Jean, additional, Legeai, Fabrice, additional, Mieuzet, Lucie, additional, Smadja, Carole M., additional, Lemaitre, Claire, additional, Vitalis, Renaud, additional, and Simon, Jean‐Christophe, additional

Published
2018
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43. Author Correction: Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time

Author

Frachon, Léa, primary, Libourel, Cyril, additional, Villoutreix, Romain, additional, Carrère, Sébastien, additional, Glorieux, Cédric, additional, Huard-Chauveau, Carine, additional, Navascués, Miguel, additional, Gay, Laurène, additional, Vitalis, Renaud, additional, Baron, Etienne, additional, Amsellem, Laurent, additional, Bouchez, Olivier, additional, Vidal, Marie, additional, Le Corre, Valérie, additional, Roby, Dominique, additional, Bergelson, Joy, additional, and Roux, Fabrice, additional

Published
2017
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44. REHH 2.0: a reimplementation of the R package REHH to detect positive selection from haplotype structure

Author

Gautier, Mathieu, Klassmann, Alexander, Vitalis, Renaud, Gautier, Mathieu, Klassmann, Alexander, and Vitalis, Renaud

Abstract

Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g. EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. The REHH package for R was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance was not sufficient to cope with the growing size of available data sets. Here, we propose a major upgrade of the REHH package, which includes an improved processing of the input files, a faster algorithm to enumerate haplotypes, as well as multithreading. As illustrated with the analysis of large human haplotype data sets, these improvements decrease the computation time by more than one order of magnitude. This new version of REHH will thus allow performing iHS-, Rsb-or XP-EHH-based scans on large data sets. The package REHH 2.0 is available from the CRAN repository (http://cran.r-project.org/web/packages/rehh/index.html) together with help files and a detailed manual.

Published
2017

45. Inferring sex-specific population histories using genome-wide gene frequency data

Author

Clemente, Florian, Gautier, Mathieu, Vitalis, Renaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV.BA]Life Sciences [q-bio]/Animal biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

46. A new method to detect and measure selection from genome-wide SNP data

Author

Vitalis, Renaud, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

47. Subspecific taxonomy of the desert locust, Schistocerca gregaria (Orthoptera: Acrididae), based on molecular and morphological characters

Author

Chapuis, Marie-Pierre, Bazelet, Corinna S., Blondin, Laurence, Foucart, Antoine, Vitalis, Renaud, Samways, Michael J., Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Dept Conservat Ecol & Entomol, Stellenbosch University, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
Identification, [SDV]Life Sciences [q-bio], Flux de gènes, Espèce, Génétique des populations, Marqueur génétique, Schistocerca gregaria, Biologie moléculaire, Microsatellite, Taxonomie, Anatomie animale, H10 - Ravageurs des plantes, [SDE]Environmental Sciences, Mutation, Conformation animale, ADN mitochondrial
Abstract

International audience; We evaluated the validity of the subspecific designation for Schistocerca gregaria gregaria (Forskal) and Schistocerca gregaria flaviventris (Burmeister), isolated in distinct regions along the north-south axis of Africa. Towards this goal, we assessed the variation of multiple morphological and molecular traits within species. We first used elliptic Fourier and landmark-based relative warps analyses to compare the size and shape of two internal and two external structures of male genitalia. We provide a discriminant function which classified the specimens with 100% accuracy and selected shape elements of the external structures only (cercus and epiproct). We also tested eight molecular markers, and because of either absence of variation or contamination by mitochondrial DNA (mtDNA)-like sequences, we used a clone-and-sequence analysis of the standard cytochrome c oxidase subunit I mitochondrial DNA barcode only. We differentiated 185 true mitochondrial sequences from 66 mitochondrial DNA-like sequences, most of which were from S. g. gregaria specimens. On the dataset of mitochondrial origin, we identified three characteristic point mutations that diagnosed the two allopatric subspecies with 94% accuracy. Minimum spanning network and parsimony tree analyses identified S. g. flaviventris as a monophyletic lineage distinct from the nominate subspecies. Accordingly, microsatellite data indicate rarely occurring admixture events only, showing that independent evolutionary history is the norm.

Published
2016

48. Tracking adaptation in selfing plant populations

Author

Navascues, Miguel, Becheler, Arnaud, Jullien, Margaux, Frachon, Lea, Libourel, Cyril, Villoutreix, Romain, Ronfort, Joelle, Roux, Fabrice, Vitalis, Renaud, Gay, Laurène, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod. Paris, FRA., and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, food and beverages, ComputingMilieux_MISCELLANEOUS
Abstract

Plants exhibit a large diversity of reproductive systems but only a small proportion of them reproduce mainly by selfing. Despite the two-fold transmission advantage of self-fertilization, selfing is considered as an “evolutionary dead end”. Theoretical predictions suggest that selfing reduces the effective population size, which in turn may reduce the adaptive potential of populations and the efficiency of selection. In addition, due to recombination events between identical haplotypes, the effective recombination is also reduced, thereby favoring the accumulation of slightly deleterious mutations. Whether highly selfing populations can rapidly track environmental changes is an open question. In our work, we characterized the contemporary evolution of two populations of highly selfing species, i.e. Arabidopsis thaliana and Medicago truncatula. The A. thaliana population is located in Burgundy and seeds were sampled in 2002 and 2010, whereas the M. truncatula population is located in Corsica and seeds were sampled in 1987 and 2009. In both species, heritable changes between the two sampling years were evidenced for some phenotypic traits when grown in common garden conditions. Genomic regions under selection were identified by a temporal-FST genome-scan approach, which was adapted to the case of self-fertilization. The power of the method was assessed through simulations which identified a maximum selfing rate from which neutral and selected loci are indistinguishable. When applied to the A. thaliana population, several biological processes related to either plant development or response to abiotic and biotic stresses were identified as enriched in single nucleotide polymorphisms (SNPs) with significant FST values. In contrast, no significant SNPs were identified in M. truncatula. In agreement with our predictions based on simulations, this result confirms that the outlier test is not applicable to a population with such a high selfing rate and the persistence of multi-locus genotypes through time. Other approaches will be necessary to identify the action of selection in such highly selfing populations.

Published
2016
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49. Génétique et évolution des populations et des métapopulations

Author

Olivieri, I., Vitalis, Renaud, Gouyon, P.H., Université de Montpellier (UM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Muséum national d'Histoire naturelle (MNHN), T. Lefèvre, M. Raymond, and F. Thomas

Subjects
[SDV.BA]Life Sciences [q-bio]/Animal biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

50. The evolution of dispersal in a Levins' type metapopulation mode

Author

Jansen, Vincent A.A. and Vitalis, Renaud

Subjects
Hamiltonian function -- Analysis, Fitness (Genetics) -- Analysis, Biological sciences
Abstract

The evolution of the dispersal rate in a metapopulation model with different dynamics similar to that described by Levins is studied. Results of the analysis show that an increase in the dispersal rate leads to a reduction in the competitive ability of any organism.

Published
2007

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