Éditeur(s) : INRA : Institut National de la Recherche Agronomique Université des Antilles. Service commun de la documentation
Extrait de : 52e congrès annuel de la Société caribéenne des plantes alimentaires / 52nd annual meeting of the Caribbean food crops society (CFCS), du 10 au 16 juillet 2016. INRA, CFCS
Description : Loss of agrodiversity mediated by varietal legacy is an important concern, translating as crop species being at risk for genetic erosion, while loss of genetic resources may deplete material available for future breeding strategies. We explored varietal dynamics in the Guadeloupean agricultural yam system. Interviewing farmers about the varieties cultivated in the past compared to their current varieties demonstrated that no dramatic loss of varieties occurred in the two to three latest decades, and changes in variety frequency mostly affected former widespread varieties while frequency of uncommon varieties demonstrated some stability in cultivation frequency. Varietal dynamics nevertheless reflected strong sub-regional trends, and socio-economic impacts such as age of producers or in farm crop diversity. Recurrent epidemics of anthracnose since its historical start in the 70s did not change varietal turnover too strongly, but resulted into transition from Dioscorea alata to less susceptible species or into a decrease of yam cultivation especially for farmers with financial dissatisfaction. La perte d'agrodiversité négociée par le legs variétal est un souci important, traduisant comme espèces de culture étant en danger pour l'érosion génétique, alors que la disparition des ressources génétiques peut épuiser le matériel disponible pour de futures stratégies d'élevage. Nous avons exploré la dynamique variétale dans le système agricole d'igname en Guadeloupe. Les agriculteurs enquêtés au sujet des variétés cultivées dans le passé comparé à leurs variétés actuelles ont démontré qu'aucune perte dramatique de variétés ne s'est produite pendant les deux à trois dernières décennies, et les changements de la fréquence de variété ont en grande partie affecté d'anciennes variétés répandues tandis que la fréquence des variétés rares démontrait une certaine stabilité dans la fréquence de culture. La dynamique variétale a néanmoins reflété des tendances sous-régionales fortes, et les impacts socio-économiques tels que l'âge des producteurs ou dans la ferme cultivent la diversité. Épidémies récurrentes d'anthracnose puisque son début historique pendant les années 70 n'a pas changé le chiffre d'affaires variétal trop fortement, mais résulté dans la transition de dioscorea alata aux espèces moins susceptibles ou dans une diminution de culture d'igname particulièrement pour des agriculteurs avec mécontentement financier.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V16259
V16259

Éditeur(s) : Actes du 6e colloque national BRG, La Rochelle, 2-3-4 octobre 2006
Résumé : Previous studies have shown heritable variation in larval developmental traits in the Pacific oyster Crassostrea gigas. In order to study the genetic consequences of production of oyster larvae in hatcheries, two factors, specific to hatcheries, were examined: the effect of discarding the smallest larvae (i.e. culling) and the effect of temperature (20°C versus 26°C). A mixed-family approach was used in order to infer the genetic composition of larval populations and family assignment, limiting possible environmental bias and allowing the study of a relatively large number of families using a limited number of larval tanks. Our results show that three multiplexed highly polymorphic microsatellite markers are a powerful tool for family assignment and, consequently, for the study of bivalve larvae genetics. Culling, by selective sieving of the smallest larvae is an advantageous practice at a phenotypic scale as it reduced variance in larval size, variance of developmental rate and time to settlement. Culling of 50% of the larval population only led to 15% less spat, showing a positive phenotypic correlation between larval growth and settlement success. However, culling represents a substantial risk for diversity loss, because it increases the variance of reproductive success among parental oysters. The effective population sizes of early settling cohorts of settlement were lower than those of later ones. Our results show that the settlement of slow growing larvae significantly contributes to minimizing the variability of reproductive success and therefore to maximizing genetic diversity. These results corroborate the low estimations of variability of broodstocks sampled in several French commercial hatcheries, relative to natural populations. The genetic composition of the larval population and the resulting spat was significantly different between the two tested temperatures, revealing genotype x environment interaction for survival. Similarly, genotype x environment interaction was also observed for larval growth as a higher temperature exerted a positive influence on the expression of genetic variability for this trait. Consequently, we can conclude that a temperature of 26°C coupled with culling, to common practice in oyster hatcheries, is likely to amplify the selection pressure for fast growing larvae. To test for this hypothesis, we compared larval developmental traits in the progeny of a hatchery broodstock closed for 7 generations, with the progeny of wild oysters and the two possible hybrids. Our results show that selection of fast growing larvae can counteract presumed inbreeding depression, due to higher mean relatedness among hatchery broodstock than in the wild. Genetic effects of intensive rearing conditions at larval stage are significant and should be taken into account in hatchery practices, especially in terms of genetic diversity management.
Afin d'étudier les conséquences génétiques des pratiques de production en écloserie d'huître creuse, deux facteurs ont été examinés : l'élimination des petites larves et la température. Nos résultats montrent que l'assignation de parenté par marqueurs microsatellites est un outil performant pour les études génétiques en phase larvaire de familles élevées en mélange. Bien qu'avantageux d'un point de vue phénotypique, le tamisage sélectif représente un risque de perte de diversité. La fixation des larves à croissance lente permet en effet de minimiser la variabilité du succès reproducteur et de fait, de maximiser la variabilité génétique. Ces résultats corroborent les estimations de variabilité sur les stocks d'écloseries françaises où l'on constate une diversité allélique inférieure à celle de populations issues du milieu naturel. La température exerce également une influence sur la précocité de l'expression de la variabilité génétique pour la croissance larvaire. Ainsi une température élevée associée à une procédure de tamisage peut amplifier l'effet sélectif. Enfin, la sélection de larves à croissance rapide semble démontrée, s'opposant à la dépression de consanguinité présumée. Les conditions d'élevage peuvent donc avoir un effet génétique significatif qui devrait être pris en considération dans les pratiques d'écloserie, notamment dans la gestion de la diversité génétique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-1505.pdf
http://archimer.ifremer.fr/doc/00000/1505/

Éditeur(s) : INRA : Institut National de la Recherche Agronomique Université des Antilles. Service commun de la documentation
Extrait de : 52e congrès annuel de la Société caribéenne des plantes alimentaires / 52nd annual meeting of the Caribbean food crops society (CFCS), du 10 au 16 juillet 2016. INRA, CFCS
Description : In the Global South, improvement of agricultural outputs is eagerly awaited. While by 2050, its population will double areas devoted to agriculture will decrease exacerbating undernutrition of the poor. Unfortunately, the demand for fresh locally-produced meat products is not satisfied yet in the tropics. So, efficiency in animal productions is essential to allow coverage of protein nutritional needs of people, both in quality and quantity. In the Caribbean territories mixed farming systems are the most common farming systems (about 80%) and can constitute a solution to reach food sovereignty in such limited and isolated spaces. Lessons to be learned from these systems involve improving animal performance while respecting the natural balance with environment and maintaining the multi-functionality of plants and animals. Firstly, the natural (or selected) comfort zone of animal and plants must fit with the farm conditions, insuring thereby animal survival and welfare. Enhancement of adaptation to stresses (biotic, abiotic and socio- economic) in species or animal genotypes is a key element implying their equilibrium with the farm environment. This approach underpins for the farmer an integrated management of animal health, nutrition, genetics, reproduction, in close relationship with other compartments of the farming system. Secondly, animal adaptation may be completed by resilience ability within systems. Animals have to produce although facing stresses. Finally, the animal must be efficient that is to say must reconcile physiological functions of production, reproduction with adaptation functions. This optimization leads to decreased inputs and to overall efficiency of mixed farming systems at the end. The aim of the breeder is to choose the animal producing the best balance between output-reproduction-adaptation, at the individual or the flock scale combining genetic and physiological diversity. The underlying idea is to give to humans and animals their right place in the food chain taking into account the farmers? skills and wills. This idea is included in the agroecological approach and may give guidelines for food sovereignty worldwide.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V16318
V16318

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Epinephelus itajara is one of the marine fish species most threatened for extinction and it is considered to be "critically endangered" by the IUCN. The present study evaluated the genetic diversity of the species and the genetic/evolutionary relationships of its populations along the Atlantic coast of South America. The results indicate relatively reduced genetic variation, re-emphasizing the low adaptive potential of the species. One of the populations presented relatively high degrees of genetic diversity and it is evolutionary isolated from the all other populations. The evidences indicate the existence of two Evolutionarily Significant Units comprising E. itajara in the Atlantic coast of South America and the conservation prospects for the species must take these evidences into account.
Biochemical Systematics And Ecology (0305-1978) (Pergamon-elsevier Science Ltd), 2014-10 , Vol. 56 , P. 255-266

Droits : 2014 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00230/34100/34465.pdf
DOI:10.1016/j.bse.2014.06.004
http://archimer.ifremer.fr/doc/00230/34100/

Éditeur(s) : Elsevier
Résumé : Genetic variation was surveyed at 11 microsatellite loci and at 517 bp of the mitochondrial control region to investigate the presence of genetic stock structure in swordfish (Xiphias gladius) in four proximal localities of the southwest Indian Ocean. One aim of this study was to serve as a preliminary examination for congruency of structure detected by these two genetic markers, prior to conducting a more comprehensive basin-wide survey of the Indian Ocean and nearby surrounding areas. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences both revealed a great homogeneity between samples. Genetic diversity detected at the regional scale was not significantly higher than detected at the local scale. Results suggest that the southwest Indian Ocean globally functions as a unique panmictic population. However, some discrete genetic differences appeared that could possibly indicate influence from a second genetic pool in the northern part of the Indian Ocean. This structure appeared to be sex-dependent with genetic differences higher among female than among male samples. This result may indicate a higher level of spawning area fidelity for females with a subsequent sampling bias tending to homogenise male genotypic distributions. (c) 2009 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2009-05 , Vol. 97 , N. 3 , P. 263-269

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6455.pdf
DOI:10.1016/j.fishres.2009.03.004
http://archimer.ifremer.fr/doc/00000/6455/

Éditeur(s) : HAL CCSD
Résumé : il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : ACTIVITY_REPORT
Understanding genomic evolution in wild populations is of particular importance because evolution is a central process in our understanding of populations’ history and their future response to global changes. In addition to fundamental knowledge, the study of populations’ evolution has wide applications such as conservation/restoration genetics or epidemiology. Indeed, genetic diversity is the ‘fuel’ for populations’ evolution and adaptation to new conditions, and estimating the extent and the geographic structure of genetic diversity, as well as identifying the evolutionary forces behind (demography, gene flow, and adaptation) are thus major challenges in the current context of global changes. [br/]A particular attention is currently devoted to the process of genetic divergence in wild populations, with emphases on gene flow, local adaptation, and their interactions. Indeed, adaptation in wild populations is supported in many species by many kinds of experiments based on both quantitative phenotypic traits and molecular data. However, the processes governing populations’ evolution are poorly understood in the tropical rainforest of Amazonia, and the relative influence of neutral and adaptive processes are continuously discussed. [br/]I am a young scientist interested in the process of genomic divergence in wild (tree) populations. I aimed at understanding how evolution structures the genetic diversity and governs molecular divergence in wild populations, with particular emphases on gene flow and local adaptation. During five years as a young scientist, I worked on answering the following questions, focusing on two tree species occupying vulnerable areas: mainly [i]Eperua falcata[/i] in Amazonia and, to a lesser extent, [i]Abies alba[/i] in the Mediterranean area.[br/][u]Scientific questions:[/u][br/]- Which evolutionary drivers are responsible of the structure of genetic diversity in wild populations occupying wide areas? This question was addressed at different geographical scales: from large (regional) to very local (microgeographic) scales. [br/]- What is the relative influence of neutral (gene flow, inbreeding) and adaptive drivers in the process of genetic divergence?[br/]- Is microgeographic adaptation possible in spite of extensive gene flow between populations occupying the extreme boundaries of an ecological gradient? [br/]- What is the extent of natural selection in the (whole) genome of wild populations? [br/][br/]My research work is at the interface between three promising disciplines: Evolutionary genomics (i.e. the study of populations evolution and the evolutionary drivers behind), Bioinformatics (i.e. the treatment of next-generation data), and Bayesian modelling (i.e. the empirical calibration of complex mechanistic model). I intend to take advantage of the recent advances in sequencing and informatic technologies to bring up to date the field of ecological genetics and evolutionary biology, by developing modern research strategies to study the process of genomic divergence in wild populations.
https://hal.archives-ouvertes.fr/hal-01204218

hal-01204218
https://hal.archives-ouvertes.fr/hal-01204218
PRODINRA : 286326

Éditeur(s) : HAL CCSD
Résumé : In the tropical rainforest of Amazonia, the factors driving the evolution of tree species remain poorly understood, and the relative influence of neutral and adaptive processes is continuously debated. In particular, local habitat patchiness draws much attention, as profound changes in the structure and composition of forest communities occur among micro-habitats. Thus, micro-environmental variations related to topography have frequently been invoked as drivers of adaptive radiation leading to sympatric speciation in Neotropical trees. On one hand, the hypothesis of local adaptation has never been investigated at the intra-specific level, i.e. within species currently undergoing population differentiation; on the other hand, many tree species are genetically structured over local scales due to neutral processes, mainly limited gene flow (caused by restricted pollen and seed dispersal). In this study, I used populations of a common tree species of the Guiana Shield - Eperua falcata (Fabaceae) - to study how neutral and adaptive processes shape the distribution of genetic diversity across forest landscapes characterized by local micro-habitat patchiness. I asked three main questions by combining both phenotypic (quantitative genetics) and molecular (population genetics) approaches: 1) How is the genetic diversity structured in forest landscapes of French Guiana? 2) Which evolutionary drivers are relevant to explain the structure of genetic diversity at local scale? 3) Does local adaptation contribute to structure genetic diversity within continuous populations?
En forêt tropicale humide Amazonienne, les facteurs gouvernant l'évolution des espèces d'arbres restent peu connus et continuellement débattus. En particulier, les micro-variations environnementales attirent beaucoup d'attention car elles induisent de profondes modifications de structure et composition des communautés. Les variations micro-environnementales associées à la topographie ont couramment été évoquées comme facteur de radiations adaptatives chez les espèces d'arbres. Cependant, l'hypothèse de l'adaptation locale n'a jamais été testée au niveau intra-spécifique chez les arbres de forêt amazonienne alors que l'on sait que la diversité génétique des arbres tropicaux est couramment structurée à faibles échelles spatiales par des processus neutres (en particulier du fait de restrictions de flux de gènes). Dans cette étude, j'ai étudié le processus de différentiation génétique d'une espèce d'arbre (Eperua falcata, Fabaceae) dans les paysages forestiers de Guyane française grâce à la combinaison d'une approche phénotypique (génétique quantitative) et d'une approche moléculaire (génétique des populations). Je me suis attachée à répondre à trois questions principales : 1) Comment se distribue la diversité génétique dans les paysages forestiers de Guyane française ? 2) Quelles forces évolutives sont impliquées dans le processus de différentiation génétique à faible échelle spatiale ? 3) Est-ce que le processus d'adaptation locale contribue à structurer la diversité génétique à faible échelle spatiale ?
https://tel.archives-ouvertes.fr/tel-00967318

NNT : 2013LORR0188
tel-00967318
https://tel.archives-ouvertes.fr/tel-00967318
https://tel.archives-ouvertes.fr/tel-00967318/document
https://tel.archives-ouvertes.fr/tel-00967318/file/THESE_Louise_Brousseau.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
ISSN: 0737-4038

hal-01032153
https://hal.archives-ouvertes.fr/hal-01032153
DOI : 10.1093/molbev/msp043

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
ISSN: 0962-1083

hal-01681650
https://hal.archives-ouvertes.fr/hal-01681650
DOI : 10.1111/mec.14389

Éditeur(s) : Elsevier
Résumé : The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1–D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.
Harmful Algae (1568-9883) (Elsevier), 2014-12 , Vol. 40 , P. 75-91

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00225/33611/32310.pdf
DOI:10.1016/j.hal.2014.10.006
http://archimer.ifremer.fr/doc/00225/33611/

Éditeur(s) : Université de la Réunion
Résumé : The green turtle (Chelonia mydas) is an emblematic species of marine life. However, nowadays it is subject to many threats (poaching, by-catch). Even if there is deep growing measures for its protection, the green turtle still is an endangered species and it is listed in Appendix I of Washington Convention (CITES). In order to elaborate efficient conservation and management plans, perfect knowledge of green turtle biology, but also of its population structure and their characteristics, are needed. In this thesis, we have assessed genetic structure of green turtle populations in the South-Western Indian Ocean by using genetic tools. In all, 1551 tissue samples have been collected from our study zone and from our control site French Polynesia (37 samples). All kinds if individuals were sampled (except males in reproductive phase) from 15 sampling sites including nesting, foraging, and immature development site. We used both control region of mitochondrial DNA and 6 microsatellite loci to better infer maternal and paternal lineages. We identified 29 haplotypes in the South-Western Indian Ocean. They are distributed in 3 independent and highly divergent clades, including one composed with haplotypes from Atlantic Ocean. For 7 of these haplotypes, it was the first time they were detected in the study zone. Fifteen haplotypes were previously undescribed, distributed in all the 3 clades. These new haplotypes seem to be specific to the South-Western Indian Ocean, which is then an original zone. Besides, we found a high allelic richness. These results show the South-western Indian Ocean is rich and very diversified. This region plays an important role in the global diversity of the species. The South-Western Indian Ocean is one of the two contact zones presently known between the two metapopulations of green turtles (Atlantic-Mediterranean and Indo-Pacific). This contact induces a genetic cline based on CM8 (Atlantic) and C3 (Indo-Pacific) haplotype frequencies. Analysis of the microsatellite differentiation between individuals provides evidence of genetic exchanges between the two metapopulations in the region. The South-Western Indian Ocean participates to green turtle global genetic mixing. Studying the influence of several intrinsic and extrinsic factors on population structuring provides useful information for management plan elaboration. We found no significant difference between genetic structures of foraging females and males, contrary to immature turtles which seem to be organised in 'regional pools'. This organisation could be due to both immature natal homing and influence of oceanic currents. High mitochondrial differentiation of nesting females and low global microsatellite differentiation of our samples indicate male-mediated gene flow among populations of the study zone. The genetic composition of a sampling site presents no significant variation along the year, even if we could notice some trends. Nevertheless, it can be significantly different from a year to an other one. This may result from alternation of distinct populations on the same site. We noticed different evolution in 10 or 20 years of the genetic composition depending on the sampling site. Geographic distance seems not to have significant influence on population structuring concerning microsatellite markers. Nesting females of Saziley Beach (Mayotte Island, Comoros Archipelago) present genetic divergence from females nesting in the two other sampled beaches of this island. The observed population structure shows no contradiction with the organisation of oceanic currents in the South-Western Indian Ocean. Comparing the results from the two genetic markers used, we identified 8 genetic differentiated clusters of turtles in the study zone and at least 6 distinct populations. These clusters constitute 8 potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans.
La tortue verte (Chelonia mydas) constitue l'un des espèces emblématiques de la vie marine, pourtant de nombreuses menaces pèsent de nos jours encore sur sa survie (braconnage, captures accidentelles). Ainsi, malgré l'essor de mesures de protection menées à travers pour sa sauvegarde, la tortue verte constitue une espèce 'en danger d'extinction' et figure dans l'Annexe I de la Convention de Washington (CITES). Afin d'élaborer des plans de gestion et de conservation qui soient efficaces, il est important d'avoir une parfaite connaissance de la biologie de la tortue verte, mais aussi de la structure de ses populations et de leurs caractéristiques. C'est dans ce cadre que s'inscrit la présente étude. L'objectif de cette étude était d'acquérir des connaissances sur la structure des populations de tortues vertes dans le sud-ouest de l'océan Indien grâce à l'utilisation de l'outil génétique. Au total, 1551 échantillons de tissu ont été collectés dans la zone d'étude et dans notre site témoin la Polynésie française (37 échantillons). Toutes les catégories d'individus ont été échantillonnées (excepté les mâles en phase de reproduction) et les 15 sites d'échantillonnage comprennent à la fois des sites de ponte, d'alimentation et de développement pour les immatures. Deux types de marqueurs ont été utilisés : la région contrôle de l'ADN mitochondrial et 6 loci microsatellites, afin d'appréhender au mieux l'apport des lignées maternelles et paternelles. Nous avons pu mettre en évidence la présence dans le sud-ouest de l'océan Indien de 29 haplotypes distincts, appartenant à trois clades fortement divergents dont l'un constitué d'haplotypes originaires de l'océan Atlantique. Parmi ces haplotypes, 7 ont été détectés pour la première fois dans la zone d'étude, et 15 autres n'ont jamais été précédemment décrits chez cette espèce. Ils sont présents dans chacun des 3 clades d'haplotypes. Ces nouveaux haplotypes semblent spécifiques à la région, et en font une zone originale. On observe par ailleurs une grande richesse allélique dans les effectifs analysés. Ces résultats montrent que le sud-ouest de l'océan Indien est une zone riche et très diversifiée. Cette région joue un rôle important dans la diversité génétique globale de l'espèce. Le sud-ouest de l'océan Indien constitue l'une des deux seules zones connues à l'heure actuelle de contact entre les deux métapopulations de tortues vertes (Atlantique-Méditerranée et Indo-Pacifique). Ce contact a entraîné la formation d'un cline génétique portant principalement sur les fréquences relatives des haplotypes CM8 (Atlantique) et C3 (Indo-Pacifique). Les résultats obtenus lors de l'analyse microsatellite de la différenciation entre les individus originaires des deux métapopulations montrent que le sud-ouest de l'océan Indien constitue une zone d'échanges génétiques entre les deux métapopulations, participant au brasage génétique de l'espèce. L'étude de facteurs, intrinsèques et extrinsèques, pouvant influencer la structuration des populations apportent de nombreuses informations qui pourraient s'avérer utiles lors de l'élaboration de plans de gestion. La structure des femelles et des mâles en alimentation ne diffère pas, contrairement à celle des immatures qui semble s'organiser en 'pools régionaux' qui seraient le fruit de l'interaction d'un comportement de philopatrie et d'une influence des courants océaniques. La forte différenciation mitochondriale des femelles en ponte et la très faible différenciation microsatellite observée à l'échelle de la région, indiquent l'existence de flux de gènes via les mâles. La composition génétique d'un site ne varie pas de manière significative au cours de l'année. Par contre, elle peut varier d'une année à l'autre, signifiant l'alternance dans certains sites de ponte de plusieurs populations distinctes. L'évolution de la composition génétique d'un groupe, au cours de 10 ou 20 ans, diffère selon le site considéré. La distance ne semble pas influencer de manière significative la structuration des populations au niveau microsatellite. Les femelles en ponte sur la plage de Saziley (Mayotte) diffèrent génétiquement de celles pondant sur les deux autres plages de l'île. La structure observée des populations est en accord avec l'organisation des courants océanique dans la région. La confrontation des résultats obtenus à partir des deux marqueurs génétiques utilisés, permet la détermination de 8 ensembles génétiquement différenciés dans la zone d'étude et l'identification d'au moins 6 populations distinctes. Ces ensembles constituent autant d'unités de gestion (MUs) potentielles qui pourront servir de base à l'élaboration de plans de gestion et de conservation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-3532.pdf
http://archimer.ifremer.fr/doc/00000/3532/

Éditeur(s) : Inter-Research
Résumé : The widespread use of Agent Orange (a mixture of phenoxyl herbicides) over Southern Vietnam by US Forces led to the decimation of mangrove forests in the Mekong Delta. Mangrove trees Avicennia alba were sampled across the Mekong Delta; their age was assessed using models based on internode growth and samples were genotyped for 6 microsatellite loci. The evolution of genetic diversity over time elapsed since local extinction was reconstructed and compared with the genetic diversity of an unaffected population from Thailand, The results show that genetic diversity of the A. alba population is still increasing in the Mekong Delta 3 decades after the end of the Vietnam War, but is reaching an asymptotic level that is comparable to the adjacent non-affected population of Thailand. This might be a sign of genetic recovery, but may also reveal a limitation, either of genetic enrichment due to current predominance of auto-recruitment or of demographic increase due to intraspecific competition in this pioneer species. In any case, these results, although encouraging, demonstrate that genetic recovery after complete or almost complete population depletion continues over a longer time-scale than apparent demographic recovery.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2009-09 , Vol. 390 , P. 129-135

Droits : Inter-Research 2009
http://archimer.ifremer.fr/doc/2009/publication-6898.pdf
DOI:10.3354/meps08183
http://archimer.ifremer.fr/doc/00000/6898/

Résumé : Genetic consequences of production of Pacific oyster larval in hatchery: drift and selective pressures related to rearing practices. In order to study the genetic consequences of production of oyster larvae in hatcheries, two factors were examined: the effects of discarding the smallest larvae (i.e. culling) and temperature effects. A mixed-family approach was used in order to infer the genetic composition of the larval population. The results show that high polymorphic microsatellite-based family assignment is a powerful tool for the study of bivalve larvae genetics. Culling by selective sieving is an advantageous practice at a phenotypic scale, but also represents a substantial risk for diversity loss if parentage assignment is not introduced as a breeding practice. Settlement of slow growing larvae contributes to minimizing the variability of reproductive success and therefore to maximizing genetic diversity. These results corroborate the lower estimations of variability made on broodstocks from French commercial hatcheries relative to natural populations. Temperature exerts an influence on the expression of genetic variability for larval growth. A temperature of 26°C, coupled with culling could amplify the selective effect. Furthermore, selection of fast growing larvae has proven to counteract inbreeding depression at this stage. Genetic effects of intensive rearing conditions are significant and should be taken into account in hatchery practices, especially in terms of genetic diversity management.
Afin d'étudier les conséquences génétiques des pratiques de production de larves en écloserie d'huître creuse, deux facteurs ont été examinés : l'effet de l'élimination des plus petites larves et l'effet de la température. Une approche de familles élevées en mélange a été utilisée afin d'avoir accès à l'information génétique au stade larvaire. Les résultats obtenus montrent que l'assignation de parenté basée sur des marqueurs microsatellites hautement discriminants est un outil performant pour les études génétiques en phase larvaire. Bien qu'avantageuse d'un point de vue phénotypique, la pratique de tamisage sélectif représente un risque substantiel de perte de diversité si cette pratique n'est pas associée à une assignation de parentée par empreintes génétiques. La fixation des larves à croissance lente permet de minimiser la variabilité du succès reproducteur et de fait, de maximiser la variabilité génétique. Ces résultats corroborent les estimations de variabilité sur les stocks d'écloseries commerciales françaises où l'on constate une diversité allélique inférieure à celle de populations issues du milieu naturel. La température exerce également une influence sur la précocité de l'expression de la variabilité génétique pour la croissance larvaire. Ainsi une température élevée (26°C) associée à une procédure de tamisage peut amplifier l'effet sélectif. Enfin, la sélection de larves à croissance rapide semble démontrée, s'opposant à la dépression de consanguinité présumée en phase larvaire. Les conditions d'élevage peuvent donc avoir un effet génétique significatif qui devrait être pris en considération dans les pratiques d'écloserie, notamment dans la gestion de la diversité génétique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/rapport-1459.pdf
http://archimer.ifremer.fr/doc/00000/1459/

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
Key message: Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical treeV. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context: The interplay between genetic and demographic processes has major consequences on population viability. Population size affects demographic trends, while genetic diversity insures viability by reducing risks of inbreeding depression and by maintaining adaptive potential. Yet, the consequences of increases in census size (as opposed to effective size) on genetic diversity of forest populations are poorly known. Aims: We have studied the structure of genetic diversity in populations of saplings of the light-responsive tree, Virola michelii (Myristicaceae, the nutmeg family), in two plots having undergone different levels of canopy-gap opening disturbance. This allowed us to test the “intermediate disturbance” hypothesis, which generally applies to species diversity, at the intra-specific scale. Methods: Levels and distribution of genetic diversity were compared between plots and between life stages. Sapling parentage was analysed to infer each adult tree’s contribution to regeneration. Results: Genetic diversity was higher, and spatial genetic structure was stronger in the post-disturbance than in the control seedling population. Parentage analysis suggested that a limited number of parents contributed to most of the regeneration, but that efficient mixing of their progeny may have enhanced the diversity of saplings occupying canopy gaps. Conclusion: A mixture of demo-genetic processes may contribute to maintain genetic diversity in spite of, or possibly due to, ecosystem disturbance in V. michelii.
ISSN: 1286-4560

hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/file/art_10.1007_s13595-015-0508-3-1_%7B869D58F4-272C-491F-A903-DAD6CDBDC042%7D.pdf
DOI : 10.1007/s13595-015-0508-3

Éditeur(s) : HAL CCSD
Résumé :  Diffusion du document : INRA Antilles-Guyane, UMR ECOFOG, F97387 Kourou, Guyane (France)Diplôme : Master Recherche
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Origin and maintenance of species diversity is one of the main questions in evolutive biology. Species complexes, ie sister species still exchanging genes, are common in tropical forests and contribute to this diversity. This poster describes the organization of the genetic diversity in two closely related tree species, Carapa guianensis and C. procera, which are in sympatry in French Guiana. By using a clustering method based on nuclear markers (Pritchard et al. 2000), 506 trees sampled in French Guiana have been assigned to a species. Interestingly, many individuals harbored intermediate genome and we assigned to an hybrid group. The geographic distribution of these individuals revealed the presence of a contact zone between the two carapa species in the Eastern part of French Guiana. We then analysed genetic diversity at cholroplast genome and revealed a symmetrical gene flow between the two sister species. In addition, hybridization between hybrids and parental species ar likely possible but still need validations thanks to control crosses. Within species, we finally revealed the presence of a departure from the neutral equilibrium in thedirection of a population expansion likely related to Holocene perturbations. This expansion may have contributed to the hybrid zone formation in French Guiana.
L'origine et le maintien de la diversité spécifique des forêts tropicales humides est une question clé en biologie évolutive. Ce travail contribue à améliorer la compréhension de ces mécanismes à travers l'étude de la distribution de la diversité génétique de deux espèces sœurs interfertiles, le Carapa procera et C. guianensis en Guyane. L'assignation botanique des arbres échantillonnés (506) a été effectuée en adoptant une approche moléculaire qui repose sur l'analyse de la répartition des fréquences alléliques de six microsatellites nucléaires (Pritchard et al. 2000). Chaque locus présente des allèles dont les différences de fréquences entre espèces sont importantes, permettant ainsi d'envisager des outils simples de reconnaissances pour ces espèces difficilement identifiables sur la seule base de leurs caractères phénotypiques. Une zone de contact des deux espèces où les phénomènes d'hybridations sont fréquents a par ailleurs été localisée. En associant une analyse de la diversité au niveau du génome chloroplastique sur un sous ensemble d'individus (244), j'ai pu montrer que l'introgression est bidirectionnelle et que les backcross sont possibles. Les flux de gènes entre les deux espèces sont fréquents, et à l'intérieur des espèces, les populations sont peu structurées bien que la différenciation soit significative entre les sites les plus éloignés. Enfin, ce travail met en évidence que les populations de chacune des deux espèces présentent un signal d'expansion de population, avec un signal plus fort pour le C. procera, qui laisse présager une expansion récente, vraisemblablement à l'origine de la zone de contact. L'impact des évènements climatiques et/ou des activités amérindiennes des 10 000 dernières années pourrait expliquer la restriction puis l'expansion de ce genre post pionnier.
https://hal.archives-ouvertes.fr/hal-01189488

hal-01189488
https://hal.archives-ouvertes.fr/hal-01189488
PRODINRA : 42333

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adri-atic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.
ISSN: 1932-6203

hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/file/journal.pone.0167441.pdf
DOI : 10.1371/journal.pone.0167441.s009

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.
ISSN: 1567-1348

pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/document
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/file/Mercier_et_al_IGE2011.pdf
DOI : 10.1016/j.meegid.2011.05.003

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : Université de Paris 6 – Pierre et Marie Curie
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season and was named Summer Syndrome. Diseased Litopenaeus stylirostris shrimp suffer from a septicemic vibriosis which was attributed to V. nigripulchritudo. Preliminary studies based on a collection of V. nigripulchritudo strains have brought to light different virulence levels according to experimental infections results; three virulence statuses were defined: highly (HP), moderately (MP) and non pathogenic (NP). The aim of this work was to genetically characterize virulent V. nigripulchritudo strains. In a first step the genetic diversity of 58 V. nigripulchritudo strains was analyzed by MLST and AP-PCR, revealing a cluster of HP and MP strains, characterized by a low genetic variability and that includes all Summer Syndrome-associated isolates. This confirms the emergence of one cluster of pathogenic V. nigripulchritudo simultaneously with the emergence of the Summer Syndrome ; in a second step, 368 genetic markers of virulence were identified by a Suppressive Subtractive Hybridization performed between the genomes of a HP strain and a genetically close, NP isolate; the distribution of the screened SSH fragments was studied in 58 V. nigripulchritudo isolates by macro-array: 78 DNA fragments were selected, allowing to characterize clusters identified and pathogenic statuses; 13 are specific of the HP strains involved in Summer Syndrome. Interestingly, 10 of these markers are carried by a plasmid pSFn1 that contains sequences highly similar to those of a plasmid pAK1, detected in Vibrio shilonii, a coral pathogen. The origin and consequences of this plasmid acquisition are discussed.
Depuis 1997, les élevages de crevettes en Nouvelle-Calédonie sont confrontés à une nouvelle maladie, le Syndrome d'été, une vibriose septicémique dont l'agent étiologique est Vibrio nigripulchritudo. Les résultats d'infection expérimentale sur une collection de souches, ont montré l'existence de trois pathotypes distincts : hautement (HP), moyennement (MP) et non pathogène (NP). L'étude du polymorphisme génétique de 58 souches par typage moléculaire en MLST et AP-PCR, a mis en évidence un groupe phylogénétique particulier caractérisé par un très faible degré de variabilité génétique (confirmant l'émergence de ce groupe en parallèle à l'émergence du Syndrome d'été) et constitué uniquement de souches HP (dont toutes celles associées au Syndromed'été) et de souches MP. Afin d'identifier des marqueurs génétiques de la virulence des souches responsables du Syndrome d'été, et parmi ces marqueurs des gènes codant potentiellement pour des effecteurs de la virulence, une approche soustractive par SSH a été développée entre une souche HP de type Syndrome d'été et une souche NP : 368 marqueurs génétiques ont ainsi été mis en évidence ; la distribution de ces marqueurs a été étudiée chez les 58 souches de la collection par une approche en macroarray : 78 marqueurs ont été sélectionnés, qui permettent de caractériser les différents groupes phylogénétiques et les différents pathotypes, dont 13 fragments spécifiques des souches HP type Syndrome d'été. Parmi ces 13 fragments, 10 ont été localisés sur le plasmide pSFn1 qui a été entièrement séquencé. Ce même plasmide a été purifié uniquement des souches HP de type Syndrome d'été. Par ailleurs, une très forte homologie a été mise en évidence entre pSFn1 et pAK1, un autre plasmide également séquencé et retrouvé chez la souche V. shilonii AK1, responsable du blanchiment du corail Oculina patagonica en Méditerranée. Ces résultats ont ouvert la discussion sur le rôle de pSFn1 dans la virulence de V. nigripulchritudo.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-3906.pdf
http://archimer.ifremer.fr/doc/00000/3906/

Éditeur(s) : Université des Antilles. Service commun de la documentation INCA 5Instituto Nacional de Ciencias Agrícolas), Cuba
Extrait de : 52e congrès annuel de la Société caribéenne des plantes alimentaires / 52nd annual meeting of the Caribbean food crops society (CFCS), du 10 au 16 juillet 2016. INRA, CFCS
Description : The methodology is supported on the basis of the experience acquired by a group of researchers, farmers and technicians from Cuba in the implementation of Participatory Plant Breeding. The proposal presents a number of methodological considerations with the necessary flexibility to allow proper application of the method and follows a logical sequence of activities to be executed in a manner that facilitates their implementation in various contexts in which it is of interest to apply. Its implementation, as such, is a learning process in action for all actors involved in it; also enables participants to understand the scale of the needs of the producers and breeding programs and dissemination of varieties in terms of the real interest of these. The methodology has 4 main phases: 1) diagnosis, 2) Collection of plant genetic resources, 3) Establishment of demonstration plots and development diversity fairs and 4) farmer experimentation. Besides the four basic stages of Participatory Plant Breeding in Cuba other tools that allowed the PPB constitute a successful process were used, these tools are: action learning as interest Schools Farmers Festivals innovation, exchange visits and retreats, capacity building of students on stage in local innovation and creation of local seed banks.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V16317
V16317