Éditeur(s) : CNEXO
Résumé : This book constitutes the first of a series of three volumes, the purpose of which is to cover the principal methods used in fish population dynamics. It is devoted to the definition of the main concepts, ami the presentation of the usual mathematical models. The second volume will deal with the fitting of the models, and the estimation of parameters. The third will be devoted to sampling problems. These volumes will be recollections of communications presented during ad hoc seminars, hold in Brest (GSG/COB) in 1980 and 1981. The first part deals with the basic concepts related to the two components whose relationship is being described by the population dynamics, namely the fish stock, to its relations with biological populations, and to the partition of catchabtiity into its components (vulnerability, availability...). The second chapter of this part is devoted to the quantification of exploitation. This leads to a discussion of nominal and effective fishing effort and fishing intensity. A brief review of the use of catch per unit of effort as an index of abundance is followed by a discussion of the concept of fishing power. The second part starts with some general remarks on mathematical modelling (chapter III), then comes to the two classical categories of models : global (surplus production) models (chapter IV), and structural models (chapter V). Chapter IV is mainly a review, based upon the SCHAEFER and PELLATOMLINSON models. Some less classical formulas from the recent literature are also introduced. Attention is paid to the underlying hypotheses and to the limitation of such models. The reader is finally referred to papers presenting the developments that could make it possible to overcome some of these limitations. Chapter V is based upon the classical BEVERTON and HOLT and RlCKER models, and the yield per recruit concepts. This field is however inlarged. Other commonly used variants of structural models are presented with an effort being made to clarify the real differences between all these variants. Special attention is also paid to so-called regenerative models and to the use of spawing-biomass or fecundity per recruit, which are likely to become commonly used in the coming years. In all cases, special attention is paid to the presentation of the basic formulas, that the reader might have to use if faced with a practical problem. Finally, a discussion of the underlying hypotheses takes place, before a brief review of the main developments, where the reader is referred to the appropriate literature.
Ce livre constitue le premier volet d'un tryptique destiné à effectuer une revue des méthodes essentielles en dynamique des populations marines exploitées. Il est consacré à la définition des concepts de base, à la présentation des modèles courants. Dans la discussion des concepts, ce volume s'attache à clarifier les notions relatives aux deux parties dont les relations font l'objet de la dynamique des populations exploitées : le stock et la flottille de pêche. Ceci amène notamment à préciser la définition d'un stock, sa relation avec la notion de population biologique, à analyser les problèmes de définition de la capturabilité. Les concepts d'intensité, d'effort, de puissance de pêche, une analyse des relations entre abondance et capture par unité d'effort sont ensuite présentés. Après une brève réflexion générale sur la modélisation, la deuxième partie de cet ouvrage présente les modèles eux-mêmes, en abordant successivement les modèles dits globaux et structuraux. Un effort est fait pour couvrir non seulement les versions les plus anciennes, mais aussi les variantes récentes, pour détailler les relations entre ces différentes variantes, offrir un formulaire de base, enfin, discuter les hypothèses majeures et les prolongements souhaitables ou en cours.
Publications du C.N.E.X.O. Série "Rapports scientifiques et techniques" (0339-2899) (CNEXO), 1981 , N. 45 , P. 1-120

Droits : Centre National pour l'Exploitation des Océans, 1981
http://archimer.ifremer.fr/doc/1981/rapport-1126.pdf
http://archimer.ifremer.fr/doc/00000/1126/

Résumé : The management of marine fish stocks has stayed non-spatial, considering spatial distributions and their consequences on demography as implicit. But the impacts of climate change and the anthropisation of habitats now require to consider spatial procedures explicitly. The work presented here starts with the question of evaluating population abundance, which requires the modelling of spatial distributions (section 1). Then an ecological understanding of the multi-scale nature of distributions is investigated (section 2). Last, we study how demographic population dynamics depends on the spatial organisation of life cycles (section 3). In this work, the approach has been to combine data acquisition at sea with statistical characterisation and modelling. The application of geostatistics to fisheries survey data provided a solution to abundance evaluation and mapping for many different survey designs. A variety of models were implemented (stationary, non-stationary, non-linear, multivariate, spatio-temporal), depending on the statistical characteristics of the data and the problem posed. Sampling bias were identified by combining different survey methods. New procedures for assessing stocks based on indicators including spatial ones were developed, which prepared for ecosystem assessments. (...)
La gestion des stocks de poissons marins est longtemps restée a-spatiale, considérant implicites les mécanismes d’organisation spatiale qui soutiennent la distribution géographique des ressources et leur dynamique démographique. Mais l’impact du changement climatique et l’anthropisation des habitats nécessitent d’en tenir compte explicitement. Partant de questions d’évaluation qui ont nécessité la modélisation des distributions spatiales (section 1), le déterminisme écologique de ces distributions a ensuite été abordé à différentes échelles (section 2) puis ont été envisagées les conséquences de l’organisation spatiale sur la dynamique démographique des populations (section 3). L’approche scientifique suivie intègre l’acquisition de données à la mer, la caractérisation statistique et la modélisation. L’application de la géostatistique aux données des campagnes halieutiques permet de proposer une solution à l’estimation d’abondance et la cartographie pour une variété de plans d’échantillonnage. Différents modèles sont mis en oeuvre (stationnaires, non-stationnaires, non-linéaires, multivariés, spatio-temporels) en fonction du comportement des données et du problème posé. Des biais d’échantillonnage sont identifiés en combinant différentes méthodes d’échantillonnage. Des procédures nouvelles d’évaluation de stocks à partir d’indicateurs dont des indicateurs spatiaux sont développées, qui préparent à l’évaluation des écosystèmes. (...)

Droits : Ifremer, UPMC
http://archimer.ifremer.fr/doc/00013/12410/9197.pdf
http://archimer.ifremer.fr/doc/00013/12410/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences. Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured. In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence. The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.
ISSN: 0305-7364

hal-01032430
https://hal.archives-ouvertes.fr/hal-01032430
DOI : 10.1093/aob/mct176

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
While the fire coral Millepora platyphylla is an important component of Indo-Pacific reefs,where it thrives in a wide range of environments, the ecological and biological processesdriving its distribution and population structure are not well understood. Here, we quantifiedthis species' population structure in five habitats with contrasting hydrodynamic regimes inMoorea, French Polynesia; two in the fore reef: mid and upper slopes, and three in thelagoon: back, fringing and patch reefs. A total of 3651 colonies of fire corals were mappedand measured over 45,000 m2 of surveyed reef. Due to the species' sensitivity to fragmentationin response to strong water movement, hydrodynamic conditions (e.g. waves, pass andlagoonal circulation) corresponded to marked differences in colony size distributions, morphologyand recruitment dynamics among habitats. The size structure varied among reefhabitats with higher proportions of larger colonies in calm nearshore reefs (fringing andpatch reefs), while populations were dominated by smaller colonies in the exposed forereefs. The highest densities of fire corals were recorded in fore reef habitats (0.12±0.20 n.m-2) where the proportion of recruits and juveniles was higher at mid slope populations(49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, mostcolonies grew as vertical sheets on encrusting bases making them more vulnerable to colonyfragmentation, whereas fire corals were encrusting or massive in all other habitats. Thelowest densities of M. platyphylla occurred in lagoonal habitats (0.02±0.04 n.m-2) characterizedby a combination of low water movement and other physical and biological stressors.This study reports the first evidence of population structure of fire corals
ISSN: 1932-6203

hal-01561659
https://hal-univ-perp.archives-ouvertes.fr/hal-01561659
https://hal-univ-perp.archives-ouvertes.fr/hal-01561659/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01561659/file/millepora%20platyphylla.pdf
DOI : 10.1371/journal.pone.0173513

Résumé : The New-Caledonian shrimp industry is based on the controlled reproduction of the shrimp Litopenaeus stylirostris, a species which was introduced in the 80s. The major difficulty to which the industry has been faced for 10 years is the occurrence of the “Syndrome 93”, which corresponds to mortality phases when the temperature falls down in April-May-June. This mortality is associated to the pathogenic bacteria Vibrio penaecida. An experiment of genetic selection based on the criterion ofsurvival to Syndrome 93 has been conducted at the Laboratory of Aquaculture of New Caledonia. The 3rd selected generation had demonstrated very encouraging results (survival rates improved by around 20% in experimental infections with V. penaeicida). These results have not been confirmed at the 4th generation and no difference in terms of physiology and immunology appears between the selected population and the non-selected control population. The potential causes of these results are examined and proposals for protocol improvements are given.
La filière crevette de Nouvelle-Calédonie reposesur la maîtrise de la reproduction contrôlée de la crevette Litopenaeus stylirostris, espèce introduite dans les années 1980. La difficulté majeure que rencontre la filière depuis une dizaine d’années est la récurrence du « Syndrome 93 », qui s’exprime sous forme d’épisodes de mortalités lors des baisses de température aux intersaisons. Ces mortalités sont associées à la bactérie pathogène Vibrio penaeicida Une expérience de sélection sur un critère de survie à des épisodes de Syndrome 93 a été menée au Laboratoire Aquacole de Calédonie. La 3èmegénération sélectionnée avait montré des résultats très encourageants (survies améliorées de l’ordre de 20% lors d’infections expérimentales à V. penaeicida). Ces résultats ne sont pas confirmés en 4ème génération et aucune différence en termes physio-et immunologique n’apparaît entre la population sélectionnée et la population témoin non sélectionnée. Les causes potentielles de ces résultats sont examinées et des propositions d’amélioration de protocoles sont avancées.

Droits : 2004 Université de la Rochelle, Ifremer
http://archimer.ifremer.fr/doc/00204/31527/29943.pdf
http://archimer.ifremer.fr/doc/00204/31527/

Éditeur(s) : HAL CCSD Wiley
Résumé : Unveiling the genetic basis of local adaptation to environmental variation is a major goal in molecular ecology. In rugged landscapes characterized by environmental mosaics, living populations and communities can experience steep ecological gradients over very short geographical distances. In lowland tropical forests, interspecific divergence in edaphic specialization (for seasonally flooded bottomlands and seasonally dry terra firme soils) has been proven by ecological studies on adaptive traits. Some species are nevertheless capable of covering the entire span of the gradient; intraspecific variation for adaptation to contrasting conditions may explain the distribution of such ecological generalists. We investigated whether local divergence happens at small spatial scales in two stands of Eperua falcata (Fabaceae), a widespread tree species of the Guiana Shield. We investigated Single Nucleotide Polymorphisms (SNP) and sequence divergence as well as spatial genetic structure (SGS) at four genes putatively involved in stress response and three genes with unknown function. Significant genetic differentiation was observed among sub-populations within stands, and eight SNP loci showed patterns compatible with disruptive selection. SGS analysis showed genetic turnover along the gradients at three loci, and at least one haplotype was found to be in repulsion with one habitat. Taken together, these results suggest genetic differentiation at small spatial scale in spite of gene flow. We hypothesize that heterogeneous environments may cause molecular divergence, possibly associated to local adaptation in E. falcata.
ISSN: 1010-061X

hal-01032412
https://hal.archives-ouvertes.fr/hal-01032412
DOI : 10.1111/jeb.12069

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) : Elsevier
Résumé : Evidence has accumulated that climate variability influences the state and functioning of marine ecosystems. At the same time increasing pressure from exploitation and other human activities has been shown to impact exploited and non-exploited species and potentially modify ecosystem structure. There has been a tendency among marine scientists to pose the question as a dichotomy, i.e., whether (1) "natural" climate variability or (2) fishery exploitation bears the primary responsibility for population declines in fish populations and the associated ecosystem changes. However, effects of both climate and exploitation are probably substantially involved in most cases. More importantly, climate and exploitation interact in their effects, such that climate may cause failure in a fishery management scheme but that fishery exploitation may also disrupt the ability of a resource population to withstand, or adjust to, climate changes. Here, we review how exploitation, by altering the structure of populations and ecosystems, can modify their ability to respond to climate. The demographic effects of fishing (removal of large-old individuals) can have substantial consequences on the capacity of populations to buffer climate variability through various pathways (direct demographic effects, effects on migration, parental effects). In a similar way, selection of population sub-units within metapopulations may also lead to a reduction in the capacity of populations to withstand climate variability and change. At the ecosystem level, reduced complexity by elimination of species, such as might occur by fishing, may be destabilizing and could lead to reduced resilience to perturbations. Differential exploitation of marine resources could also promote increased turnover rates in marine ecosystems, which would exacerbate the effects of environmental changes. Overall (and despite the specificities of local situations) reduction in marine diversity at the individual, population and ecosystem levels will likely lead to a reduction in the resilience and an increase in the response of populations and ecosystems to future climate variability and change. Future management schemes will have to consider the structure and functioning of populations and ecosystems in a wider sense in order to maximise the ability of marine fauna to adapt to future climates. (C) 2009 Elsevier B.V. All rights reserved.
Journal of Marine Systems (0924-7963) (Elsevier), 2010-02 , Vol. 79 , N. 3-4 , P. 403-417

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2010/publication-7384.pdf
DOI:10.1016/j.jmarsys.2008.12.018
http://archimer.ifremer.fr/doc/00000/7384/

Éditeur(s) : HAL CCSD Wiley
Résumé :  
Drier periods from the late Pleistocene and early Holocene have been hypothesized to have caused the disappearance of various rainforest species over large geographical areas in South America and restricted the extant populations to mesic sites. Subsequent improvement in climatic conditions has been associated with recolonization. Changes in population size associated with these extinction-recolonization events should have affected genetic diversity within species. However, these historical hypotheses and their genetic consequences have rarely been tested in South America. Here, we examine the diversity of the chloroplast and nuclear genomes in a Neotropical rainforest tree species, Vouacapoua americana (Leguminosae, Caesalpinioideae) in French Guiana. The chloroplast diversity was analyzed using a polymerase chain reaction-restriction fragment length polymorphism method (six pairs of primers) in 29 populations distributed over most of French Guiana, and a subset of 17 populations was also analyzed at nine polymorphic microsatellite loci. To determine whether this species has experienced extinction-recolonization, we sampled populations in areas supposedly not or only slightly affected by climatic changes, where the populations would not have experienced frequent extinction, and in areas that appear to have been recently recolonized. In the putatively recolonized areas, we found patches of several thousands of hectares homogeneous for chloroplast variation that can be interpreted as the effect of recolonization processes from several geographical origins. In addition, we observed that, for both chloroplast and nuclear genomes, the populations in newly recolonized areas exhibited a significantly smaller allelic richness than others. Controlling for geographic distance, we also detected a significant correlation between chloroplast and nuclear population differentiation. This result indicates a cytonuclear disequilibrium that can be interpreted as a historical signal of a genetic divergence between fragmented populations. In conclusion, the spatial genetic structure of contemporary V. americana populations shows evidence that this species has experienced large extinction-recolonization events, which were possibly caused by past climatic change.
ISSN: 0014-3820

hal-01032194
https://hal.archives-ouvertes.fr/hal-01032194
DOI : 10.1111/j.0014-3820.2003.tb01517.x

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) : 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) : Gauthier-Villars
Résumé : Holothuria atra is the most common aspidochirotid holothurian on tropical Indo-Pacific reefs, Asexual reproduction by transverse fission, followed by regeneration, has been studied at Reunion Island (Indian Ocean) and compared with different populations of the Indo-Pacific zone, thus permitting a better identification of the most significant parameters and a better understanding of this reproductive strategy. At Reunion Island, the species is studied at two stations on the same fringing reef: 1) on the back-reef where the fission rate is high (20 % of the population), the individuals small (generally weighting less than 150 g) and the population density high (4/m(2)); and 2) on the reef front, where fission is extremely rare, the mean size of the individuals larger (up to 300 g) and the density low (0.01/m(2)), Different categories of individuals, fissioning (F), after fission, anterior and posterior parts (A and P), and regenerating (Ap and Pa) have been identified from external observations. Dissection has demonstrated the unequal allocation of organs during fission and the variability of the regenerative states, mostly in the anterior part. Concerning fission, the position of the split in an individual is in the anterior half (at 44 % of the total length). The monthly incidence of fission is higher from October to January and in June-July. Fission does not result in an increase in the density of the population. The monthly rates of regenerating individuals originating from anterior (3.7 %) and posterior (5.1 %) parts suggest that survival is higher in the latter instance. The occurrence of asexual reproduction in various populations of this species is discussed in relation to the ecology and the parameters of the populations considered. On the back-reef studied at Reunion Island, the population is subtidal and emersion cannot explain fission. Anthropogenic disturbances are possible triggers of this phenomenon.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1996 , Vol. 19 , N. 3-4 , P. 209-216

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00094/20479/18149.pdf
http://archimer.ifremer.fr/doc/00094/20479/

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting. The ISME Journal (2012) 6, 2199-2218; doi:10.1038/ismej.2012.84; published online 2 August 2012
ISSN: 1751-7362

hal-01546179
https://hal.archives-ouvertes.fr/hal-01546179
DOI : 10.1038/ismej.2012.84

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a similar to 6-km transect, to evaluate dispersal ability, and between paired bank populations along a similar to 65-km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life-history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life-history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 356373.
ISSN: 0024-4066

hal-01032422
https://hal.archives-ouvertes.fr/hal-01032422
DOI : 10.1111/j.1095-8312.2012.01871.x

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) : Elsevier
Résumé : The Latin American shrimp Litopenaeus stylirostris was introduced in three different Pacific islands (Tahiti, New Caledonia via Tahiti, and Hawaii) and hatchery-propagated for 7-25 generations to develop shrimp farming based on these domesticated stocks. Three microsatellite markers have been used in an attempt to assess the genetic bases of the populations available to start a selective breeding program. The comparison of eight hatchery stocks (five New Caledonian, two Hawaiian and one Tahitian stocks) and one wild Ecuadorian population showed a much lower variability in the domesticated stocks than in the wild population, especially in New Caledonia and Tahiti (2-3.7 vs. 14-27 alleles per locus; 20-60% vs. 90% expected heterozygosity). The Tahitian and the New Caledonian stocks share the same alleles, suggesting that the loss of alleles occurred during the common past of these populations. On the contrary, New Caledonian and Hawaiian populations share only one common allele at the three loci studied. Although the low genetic variability and the resulting inbreeding of the New Caledonian stocks do not seem to affect their present performance, the results of this study demonstrate the usefulness of the introduction of new stocks in order to increase the potential responses to new controlled or uncontrolled selective pressures. The introduction in New Caledonia of the Hawaiian domesticated stocks, which would provide the local shrimp industry with 40% of the allelic diversity of the species, is advised and preferred to the one of wild animals in order to take advantage (i) of the spontaneous selection which occurred during domestication and (ii) of their favourable sanitary "specific pathogen free" status (no presence of four viruses: WSV, YHV, IHHNV, TSV) which limits the risk of introduction of pathogens.
La crevette d'Amérique latine Litopaenus stylirostris a été introduite dans trois îles du Pacifique (à Tahiti, en Nouvelle-Calédonie via Tahiti, et à Hawaii), et a été ensuite reproduite en écloserie pendant 7 à 25 générations à des fins d'aquaculture. Trois marqueurs microsatellites ont été utilisés pour évaluer les bases génétiques des populations disponibles pour le démarrage d'un programme d'amélioration génétique. L'étude comparative de 8 populations domestiquées (cinq néo-calédoniennes, deux hawaiiennes et une tahitienne) et d'une population sauvage d'Equateur révèle une variabilité très réduite dans les populations d'élevage, en particulier en Nouvelle-Calédonie et à Tahiti (2 à 3.7 allèles par locus au lieu de 14 à 27 en population sauvage ; 20% à 60% d'hétérozygotie au lieu de 90%). Les souches tahitiennes et calédoniennes disposent des mêmes allèles, ce qui suggère que la perte d'allèles a eu lieu lors de l'histoire commune des ces populations. A l'inverse, les populations néo-calédoniennes et hawaiiennes n'ont en commun qu'un seul allèle sur les 3 locus étudiés. Bien que la très faible variabilité génétique du cheptel calédonien ne semble pas affecter ses performances actuelles, les résultats de cette étude démontrent l'utilité de l'introduction de variabilité afin d'augmenter la capacité de réponse à de nouvelles pressions de sélection (contrôlées ou non). L'introduction des souches hawaiiennes en Nouvelle-Calédonie qui permettrait à la filière locale de disposer de 40% de la diversité allélique de l'espèce) est préconisée de préférence à celle d'animaux sauvages afin de bénéficier (i) de la sélection spontanée qu'elles ont subi lors de leur domestication et (ii) de leur statut sanitaire « specific pathogen free, SPF » (absence de 4 virus : WSV, YHV, IHHNV, TSV) qui limite les risques de transferts de pathogènes.
Aquatic Living Resources (0990-7440) (Elsevier), 2003-12 , Vol. 16 , N. 6 , P. 501-508

Droits : 2003 Published by Elsevier, Paris.
http://archimer.ifremer.fr/doc/2003/publication-596.pdf
DOI:10.1016/j.aquliv.2003.07.001
http://archimer.ifremer.fr/doc/00000/596/

Éditeur(s) : HAL CCSD
Résumé : The genus Cecropia includes pioneer trees that colonize canopy gaps and cleared areas. It is widely distributed from Mexico to Northern Argentina. Cecropia trees have architecture, which corresponds to the Rauh’s architectural model. In recent studies we have found that C. obtusa/ and C. sciadophylla, in French Guiana, have a strong annual periodicity for growth, branching and flowering processes, with annual emission of 35 nodes for C. obtusa and 25 for C. sciadophylla. Those species show different life histories since C. sciadophylla has longer life expectancy. In addition, C. sciadophylla is found more frequently in forest gaps, although in French Guiana mixed populations are found. The aim of this work was to compare developmental strategies of both species in three different field stations in French Guiana and to determine how these two species coexist during its first years of life. We studied a 20-year old population of /C. sciadophylla/ at Saint Elie’s Road, a 10-year old population of /C. obtusa/ at Paracou’s field station, and a 7-year old mixed population at Counami’s Road. /C. sciadophylla /emits 25 nodes per year in both studied populations, while/ C. obtusa /emits 35 nodes in the monospecific population and 30 nodes in the mixed population. In the monocaule stage, the lower number of nodes emitted by /C. sciadophylla/ compared to /C. obtusa /is compensated with a higher internodal length, which allows finding individuals with similar ages and lengths, but different number of nodes. The branching and flowering processes start on average three years before in /C. obtusa/, however for 12-year old individuals we observed a dominancy of C. sciadophylla over C. obtusa. In the mixed population it is likely that the different life histories would decrease competition effects allowing coexistence of both species during the first stages of life
Botany 2008
Vancouver, Canada

hal-01190209
https://hal.archives-ouvertes.fr/hal-01190209
PRODINRA : 182910

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1

Éditeur(s) : Wiley-blackwell
Résumé : The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio-Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.
Marine Ecology-an Evolutionary Perspective (0173-9565) (Wiley-blackwell), 2015-09 , Vol. 36 , N. 3 , P. 447-461

Droits : 2014 Blackwell Verlag GmbH
http://archimer.ifremer.fr/doc/00189/30046/28566.pdf
DOI:10.1111/maec.12153
http://archimer.ifremer.fr/doc/00189/30046/

Éditeur(s) : HAL CCSD
Résumé : Climate change is one of the biggest public health threats in the 21th century. An increase in temperatures will lead to an increase in mortality attributable to temperature. In addition, some populations and territories are particularly vulnerable to the impact of increases in heat. It is thus necessary to identify these populations and territories as well as examine future heat-Related health impacts in order to recommend equity-Oriented policies today and in the future. The general objective of this thesis is to document current and future heat-Related vulnerability factors in the context of climate change. In order to address this general objective, the thesis involved four components: a) to conduct a systematic review and a meta-Analysis to assess the heterogeneity in the heat-Mortality associations with respect to individual and contextual population characteristics; b) to identify whether and how the magnitude of mean temperature effects on all-Cause mortality were modified by chronic air pollution exposure, social deprivation, and a combination of these two dimensions; c) to develop a method to quantify the climate change impacts on heat-Related mortality using climate modeling; d) to assess historical and future social disparities in years of life lost caused by ambient temperature in Montreal and Paris, and compare these estimates as well as the impact of climate change on social disparities between the two cities. This thesis highlights which populations are more vulnerable to heat and shows that several differences exist with regard to guidelines from international public health institutions for the identification of vulnerable populations. This thesis also identified chronic air pollution exposure as a new vulnerability factor in heat-Related mortality and that it has a double interaction with social deprivation. Furthermore, in this thesis a novel method to quantify future heat-Related mortality was developed which emphasized the strong evidence of an increase in heat-Related mortality under climate change. This method was then applied to estimate the increase in daily years of life lost social disparities in both Montreal and Paris under climate change which showed that this increase would be greater in Montreal compared to Paris in the future. Thus, this thesis which used a variety of epidemiologic methods has clarified which populations are particularly vulnerable to heat impacts and challenges guidelines for the identification of vulnerable populations from international public health institutions. It has also highlighted the climate change impacts on health inequalities and aims to reorient equity-Focused policies.
Les changements climatiques constituent l’un des enjeux les plus importants en santé publique du XXIème siècle. En effet, une hausse des températures provoquera une hausse de la mortalité attribuable à la chaleur. En outre, certaines populations et territoires sont particulièrement vulnérables aux effets de la chaleur. Il est donc nécessaire de les identifier clairement ainsi que les impacts futurs pour orienter avec équité les politiques publiques aujourd’hui et à l’avenir. L’objectif de cette thèse est de documenter les facteurs de vulnérabilité à la chaleur dans le présent et les éléments permettant leur prise en compte pour l’avenir dans le contexte des changements climatiques. Quatre étapes ont été menées pour répondre à cet objectif : a) Mener une revue systématique et une méta-Analyse des facteurs de vulnérabilité face aux risques de mortalité en lien avec la chaleur ; b) Analyser si l’exposition chronique à la pollution atmosphérique modifie la relation entre la chaleur et la mortalité dans un contexte urbain (Paris) et explorer la double interaction avec la défaveur sociale ; c) Développer une méthode de quantification des impacts liés à la chaleur en lien avec les changements climatiques en intégrant une grande diversité de simulations climatiques ; d) Estimer les inégalités d’années de vies perdues attribuables à la chaleur et leurs projections futures dans deux contextes distincts (Montréal et Paris) et comparer ces inégalités. Cette thèse a permis de mettre en évidence sur la base de la littérature épidémiologique les groupes de population qui sont les plus vulnérables face aux effets de la chaleur et de montrer qu’il y a plusieurs divergences par rapport aux recommandations émises par les institutions de santé publique vis-À-Vis de l’identification de populations vulnérables. Cette thèse a permis également d’identifier l’exposition chronique à la pollution atmosphérique comme nouveau facteur de vulnérabilité à la chaleur et que cette vulnérabilité était encore plus prononcée lorsqu’il s’agissait de populations défavorisées socialement. Puis, une méthode permettant de quantifier l’impact des changements climatiques sur les décès attribuables à la chaleur et ses sources d’incertitudes a été développée, et a permis de mettre en évidence que la probabilité que les changements climatiques conduisent à une augmentation de la mortalité en lien avec la chaleur est très forte. Cette méthode a ensuite été utilisée pour estimer que l’augmentation de la température conduira à une augmentation des inégalités sociales d’années de vie perdues à la fois à Montréal et à Paris, l’effet des changements climatiques sur l’accroissement de ces inégalités étant plus fort à Montréal qu’à Paris. Cette thèse, en se basant sur diverses méthodes épidémiologiques, a permis dans l’ensemble de clarifier quelles populations étaient particulièrement à risque face aux effets de la chaleur et de questionner les recommandations émises par les organismes tels que l’OMS. Elle a également permis de montrer l’effet des changements climatiques sur l’évolution de vulnérabilités face à la chaleur pour inciter dès aujourd’hui la mise en place de politiques publiques équitables et limiter l’impact des changements climatiques sur l’accroissement des inégalités de santé.
https://tel.archives-ouvertes.fr/tel-01456772

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2015PA11T003
tel-01456772
https://tel.archives-ouvertes.fr/tel-01456772
https://tel.archives-ouvertes.fr/tel-01456772/document
https://tel.archives-ouvertes.fr/tel-01456772/file/VA_BENMARHNIA_TARIK_05022015.pdf