Tempo et mode de l'évolution des populations cavernicoles de l'espèce Astyanax mexicanus

The fish Astyanax mexicanus is a particularly suitable model for evolutionary biology studies. Indeed, in this species there are several subterranean populations which live in the total and permanent darkness of cave. These cavefish are well adapted to the life in this inhospitable environment and they show several differences with their surface conspecific such as depigmentation, eye loss and behavioral changes. A major unresolved issue is about the relative role of surface fish standing genetic variation and de novo mutations appeared in cavefish populations after their settlement in caves in their phenotypic evolution. In order to examine this issue, accurate estimations of population ages are very important because many new mutations cannot appear and fix in a recent population. In this thesis we aimed to estimate the age of the Pachón cave population which is considered as one of the oldest and most isolated populations. We developed a new method which is based on measures of the distribution of single nucleotide polymorphism within each population and between populations. Our results, as well as reanalyses of published data about mitochondrial haplotypes and microsatellite loci polymorphism suggest that cavefish populations are much more recent than previously thought (several thousand years and not several hundred thousand years). The consequences of a fast tempo of evolution on the mode of evolution of cavefish are also discussed.Le poisson Astyanax mexicanus est un modèle particulièrement intéressant pour l'étude de l'évolution. En effet, dans cette espèce de poissons d'eau douce, il existe des populations vivant de façon pérenne dans des grottes. Dans cet environnement, l'obscurité est totale et permanente et les ressources en nourriture souvent faibles. Les poissons cavernicoles se sont adaptés à la vie souterraine et ils présentent de nombreuses modifications phénotypiques comme la dépigmentation, la perte des yeux, l’augmentation du nombre et de la taille d’organes sensoriels non-visuels et plusieurs changements du comportement. Un des problèmes majeurs est de savoir si ces modifications phénotypiques sont dues à des mutations préexistantes à la colonisation de l'environnement cavernicole ou si elles sont apparues après. Pour répondre à cette question, connaître l'âge des populations est un facteur important car dans une population récente, il n'y aura probablement pas eu suffisamment de temps pour l'apparition de beaucoup de mutations et leur fixation. L'objet de cette thèse est donc l'estimation de l'âge d'une population, celle de la grotte Pachón qui est souvent considérée comme étant une des plus anciennes et une des plus isolées. Au cours de ces travaux de thèse, nous avons développé une nouvelle méthode de datation qui repose d’une part sur la caractérisation du polymorphisme nucléotidique à l’intérieur de chaque population et entre populations, et d’autre part la comparaison de ces données avec des simulations de l’évolution du polymorphisme. Les résultats obtenus, ainsi que la réanalyse de données sur le polymorphisme d’haplotypes mitochondriaux et de loci microsatellites précédemment publiées, suggèrent que les populations cavernicoles seraient bien plus récentes qu’habituellement indiqué dans la littérature (quelques milliers d’années, et non plusieurs centaines de milliers d’années). Les conséquences d’un tempo rapide d’évolution sur le mode d’évolution de ces poissons cavernicoles ont aussi été présentées

Tempo and mode of the Astyanax mexicanus cavefish evolution

Le poisson Astyanax mexicanus est un modèle particulièrement intéressant pour l'étude de l'évolution. En effet, dans cette espèce de poissons d'eau douce, il existe des populations vivant de façon pérenne dans des grottes. Dans cet environnement, l'obscurité est totale et permanente et les ressources en nourriture souvent faibles. Les poissons cavernicoles se sont adaptés à la vie souterraine et ils présentent de nombreuses modifications phénotypiques comme la dépigmentation, la perte des yeux, l’augmentation du nombre et de la taille d’organes sensoriels non-visuels et plusieurs changements du comportement. Un des problèmes majeurs est de savoir si ces modifications phénotypiques sont dues à des mutations préexistantes à la colonisation de l'environnement cavernicole ou si elles sont apparues après. Pour répondre à cette question, connaître l'âge des populations est un facteur important car dans une population récente, il n'y aura probablement pas eu suffisamment de temps pour l'apparition de beaucoup de mutations et leur fixation. L'objet de cette thèse est donc l'estimation de l'âge d'une population, celle de la grotte Pachón qui est souvent considérée comme étant une des plus anciennes et une des plus isolées. Au cours de ces travaux de thèse, nous avons développé une nouvelle méthode de datation qui repose d’une part sur la caractérisation du polymorphisme nucléotidique à l’intérieur de chaque population et entre populations, et d’autre part la comparaison de ces données avec des simulations de l’évolution du polymorphisme. Les résultats obtenus, ainsi que la réanalyse de données sur le polymorphisme d’haplotypes mitochondriaux et de loci microsatellites précédemment publiées, suggèrent que les populations cavernicoles seraient bien plus récentes qu’habituellement indiqué dans la littérature (quelques milliers d’années, et non plusieurs centaines de milliers d’années). Les conséquences d’un tempo rapide d’évolution sur le mode d’évolution de ces poissons cavernicoles ont aussi été présentées.The fish Astyanax mexicanus is a particularly suitable model for evolutionary biology studies. Indeed, in this species there are several subterranean populations which live in the total and permanent darkness of cave. These cavefish are well adapted to the life in this inhospitable environment and they show several differences with their surface conspecific such as depigmentation, eye loss and behavioral changes. A major unresolved issue is about the relative role of surface fish standing genetic variation and de novo mutations appeared in cavefish populations after their settlement in caves in their phenotypic evolution. In order to examine this issue, accurate estimations of population ages are very important because many new mutations cannot appear and fix in a recent population. In this thesis we aimed to estimate the age of the Pachón cave population which is considered as one of the oldest and most isolated populations. We developed a new method which is based on measures of the distribution of single nucleotide polymorphism within each population and between populations. Our results, as well as reanalyses of published data about mitochondrial haplotypes and microsatellite loci polymorphism suggest that cavefish populations are much more recent than previously thought (several thousand years and not several hundred thousand years). The consequences of a fast tempo of evolution on the mode of evolution of cavefish are also discussed

Prise en charge chirurgicale du cancer de prostate chez le transplanté rénal (particularités clinique, anatomique et immunologique, efficacité et tolérance néphrologique)

CAEN-BU Médecine pharmacie (141182102) / SudocSudocFranceF

L’apophénie d’ENCODE ou Pangloss examine le génome humain

En septembre 2012, les principaux résultats du projet ENCODE (Encyclopedia of DNA Elements) furent publiés sous la forme de 30 articles, dont une grande partie dans les deux plus prestigieuses revues scientifiques généralistes Nature et Science. Ce projet, qui avait mobilisé des centaines de chercheurs et des centaines de millions de dollars, avait permis de renverser un des paradigmes les mieux établis portant sur l’évolution des génomes : notre génome ne compterait pas 80 % d’ADN « poubelle » mais il serait au contraire à 80 % utile. Il ne restait plus qu’à savoir à quoi ! Dans le microcosme de la biologie évolutive, il y eut quelques réactions amusées, voire agacées, face à cette revitalisation d’un adaptationnisme naïf. Des réfutations argumentées furent publiées, mais qui ne pouvaient rivaliser avec la publicité faite à ENCODE. En 2014, une nouvelle série d’articles présentaient les avancées récentes du projet. Étonnamment, on n’y trouvait plus aucune trace de l’extraordinaire découverte de 2012, sans que cette « disparition » d’un résultat majeur ne soit commentée. Une forme de rétractation par omission sans doute. Mais le mal était fait, l’affirmation « 80 % d’ADN utile » d’ENCODE est désormais intégrée par de nombreux biologistes comme le nouveau cadre d’étude des génomes, ou pour le moins comme une hypothèse alternative valable. Il nous semble donc indispensable de rappeler quelques concepts généraux qui expliquent l’architecture et le fonctionnement des génomes, concepts qui, à ce jour, n’ont pas été réfutés et qui permettent d’éviter l’écueil que représente l’approche panglossienne d’ENCODE

Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called “old” and “new” lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations.We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (\u3c 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years.Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populat

Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called “old” and “new” lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations.We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (\u3c 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years.Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populat

A new cave locality for Astyanax cavefish in Sierra de El Abra, Mexico

International audienceThe characiform fish Astyanax mexicanus comes in two forms, a surface-dwelling morph which lives in the rivers of North and Central America and a blind, depigmented cave-dwelling morph which inhabits caves in Mexico. In recent years, this species has arguably become among the most influential model system for the study of evolutionary development and genomics in cave biology. While recent articles have analysed in great detail Astyanax genetics, development, physiology, phylogeny and behaviour, there have been comparatively few recent studies concerning its ecology and in particular its biogeography. Mitchell et al. (1977) reported the species inhabiting 29 caves in the Sierra de El Abra region. Despite the elapsing of over 40 years and the latest surge of interest in the model, not a single new cave locality had been described for the species. We describe here a new and 30 th cave locality, Chiquitita Cave, inhabited by troglomorphic A. mexicanus. Their morphology, eye histology, 16S rRNA DNA sequence, and smelling capabilities are analysed. This cave represents the southernmost extension for the cave morph's habitat within the Sierra de El Abra. Its name, Chiquitita Cave (Tiny Cave), was chosen in reference to a potential hydrologic connection to "Chica Cave" (small cave), which is among the most studied populations of Astyanax

Diversity of olfactory responses and skills in Astyanax mexicanus cavefish populations inhabiting different caves

International audienceAnimals in many phyla are adapted to and thrive in the constant darkness of subterranean environments. To do so, cave animals have presumably evolved mechano- and chemosensory compensations to the loss of vision, as is the case for the blind characiform cavefish, Astyanax mexicanus. Here, we systematically assessed the olfactory capacities of cavefish and surface fish of this species in the lab as well as in the wild, in five different caves in northeastern Mexico, using an olfactory setup specially developed to test and record olfactory responses during fieldwork. Overall cavefish showed lower (i.e., better) olfactory detection thresholds than surface fish. However, wild adult cavefish from the Pachón, Sabinos, Tinaja, Chica and Subterráneo caves showed highly variable responses to the three different odorant molecules they were exposed to. Pachón and Subterráneo cavefish showed the highest olfactory capacities, and Chica cavefish showed no response to the odors presented. We discuss these data with regard to the environmental conditions in which these different cavefish populations live. Our experiments in natural settings document the diversity of cave environments inhabited by a single species of cavefish, A. mexicanus, and highlight the complexity of the plastic and genetic mechanisms that underlie cave adaptation

Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions

International audienceIn 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SAU : Pleasenotetha ARS-CoV-2) pandemic that drastically altered people's lives. Since then, many countries have been forced to suspend public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels. The same year, as a committee, we were in charge of organizing the major French annual conference that covers all computational biology areas: The "Journé es Ouvertes en Biologie, Informatique et Mathé matiques" (JOBIM). Despite the health crisis, we succeeded in changing the conference format from face to face to remote in a very short amount of time. Here, we propose 10 simple rules based on this experience to modify a conference format in an optimized and cost-effective way. In addition to the suggested rules, we decided to emphasize an unexpected benefit of this situation: a significant reduction in greenhouse gas (GHG) emissions related to travel for scientific conference attendance. We believe that even once the SARS-CoV-2 crisis is over, we collectively will have an opportunity to think about the way we approach such scientific events over the longer term

La fable de l'échalote

International audienceDes forêts et océans saccagés, des matières premières de plus en plus rares, une énergie de plus en plus onéreuse : notre modèle de consommation est à bout de souffle. Il est urgent de réfléchir à la façon dont nous allons être obligés de le refonder pour faire face aux contraintes environnementales et à la nécessité de répartir plus équitablement les ressources. Nous sommes tous conscients qu’il va nous falloir faire des choix radicaux pour changer notre modèle de consommation, et donc notre mode de vie. C’est une condition non négociable pour construire des relations plus apaisées, plus harmonieuses et plus signifiantes avec les autres et avec nous-mêmes. Mais sommes-nous pour autant prêts à le faire