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Several steps of sturgeon somatic cell nuclear transfer (SCNT) have been recently established, but improvements are needed to make it a feasible tool to preserve the natural populations of this group of endangered species. The donor cell position inside the recipient egg seems to be crucial for its reprogramming; therefore by injecting multiple donor somatic cells instead of a single cell with a single manipulation, we increased the potential for embryo development. Using the Russian sturgeon Acipenser gueldenstaedtii as a multiple cell donor and sterlet Acipenser ruthenus as the non-enucleated egg recipient, we obtained higher proportion of eggs developing into embryos than previously reported with single-SCNT. Molecular data showed the production of a specimen (0.8%) contained only the donor genome with no contribution from the recipient, while two specimens (1.6%) showed both recipient and donor genome. These findings are the first report of donor DNA integration into a sturgeon embryo after interspecific cloning. In all, we provide evidence that cloning with the multiple donor somatic cells can be feasible in the future. Despite the fact that the sturgeon cloning faces limitations, to date it is the most promising technique for their preservation.

Ce WP a fait l'objet d'une publication in Ecological Economics, Elsevier, 2018, 146, pp.607-620. 〈hal-01672020〉; Biological invasions entail massive biodiversity losses and tremendous economic impacts that justify significant management efforts. Because the funds available to control biological invasions are limited, there is a need to identify priority species. This paper first review current invasive species prioritization methods and explicitly highlights their pitfalls. We then construct a cost-benefit optimization framework that incorporates species utility, ecological value, distinctiveness, and species interactions. This framework offers the theoretical foundations of a simple and operational method for the management of invasive species under a limited budget constraint. It takes the form of an algorithm for the prioritization of multiple biological invasions.

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1. Hybridization is a key evolutionary process with major consequences for conservation and speciation. However, sexual barriers interact with the local context to determine hybridization rates in a way that is still poorly explored. For instance, in the context of an expanding or introduced plant population, where a few individuals are isolated in populations dominated by heterospecific individuals, what is the hybridization potential? 2. To obtain baseline predictions on hybridization rate between two species differing in abundance and to evaluate the effect of pollen limitation, we first used a mean-field model. We then explored a spatially explicit individual-based mating model relying on pollen dispersal kernels to predict hybridization rates in a mixed-species stand, under different scenarios for (i) the strength of sexual barriers; (ii) the spatial distribution of individuals within the site; (iii) the variation in individual fecundity; and (iv) the magnitude, shape and asymmetry of pollen dispersal kernels. 3. Pollen limitation was shown to have the potential to greatly increase hybridization rates. Similarly, fine-scale variation in species composition can result in elevated hybridization rates compared to mean-field predictions, especially with strong sexual barriers. However, species clustering in combination with reduced pollen dispersal has the opposite effect, protecting from hybridization. 4. Synthesis. Our simulation results show that variation of the pollen pool composition at the scale of individuals or stigmas due to spatial configurations or pollen limitation can substantially modify hybridization rates. We explain this by the disproportionate effect of some pollen environments on average hybridization rates. This suggests thoroughly evaluating individual behaviour in terms of hybridization, especially for rare or patchy species.

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)

International audience; Introduction of nonnative cultured fish is one of the most important threats to native salmonid populations. In brown trout, more than a century of stocking practices has led to a large hybridization between initially geographically isolated lineages, threatening native populations and thereby intraspecific diversity. In the French region of Haute-Savoie, managers and scientists implemented together three management strategies (genetic refuge, direct translocation of wild spawners and stocking with native fry) on 19 test sites for more than 15 years, in the aim to recover pure or nearly pure native populations. Here we propose an assessment of the different management strategies based on a synthetic analysis of the evolution of the introgression rate. While none of the implemented strategies completely achieves the initial objective to restore pure native populations, they differ in their efficiency: introgression rates tend to decrease quickly when direct translocation of native spawners of stocking with native fry strategies are used. The genetic refuge strategy shows slower and more heterogeneous changes of introgression rates. In general, pure nonnative fish are efficiently removed but at the cost of an increased presence of hybrids. Our results imply that intraspecific dynamics react quickly to management practices and that these changes are probably fueled by evolutionary feedbacks that are not yet well understood

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Sex attractant pheromones are highly sensitive and selective tools for detecting and monitoring populations of insects, yet there has been only one reported case of pheromones being used to monitor protected species. Here, we report the identification and synthesis of the sex pheromone of a protected European moth species, Graellsia isabellae (Lepidoptera: Saturniidae), as the single component, (4E,6E,11Z)-hexadecatrienal. In preliminary field trials, lures loaded with this compound attracted male moths from populations of this species at a number of widely separated field sites in France, Switzerland, and Spain, clearly demonstrating the utility of pheromones in sampling potentially endangered insect species. Electronic supplementary material The online version of this article (doi:10.1007/s10886-010-9831-1) contains supplementary material, which is available to authorized users.

Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.

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Species' interactions and the involvement of fishermen in several fisheries may not be properly accounted for by regulatory schemes,thus making regulation suboptimal. Being the only implementable instruments, the degree of ineffciency of three second-best instruments is assessed (by using a bioeconomic multispecies model) in terms of their ability to get close to socially optimal effort and stock levels. The type of regulation and the existing biological interaction are also shown to result in different impacts on effort re-allocation: a specific regulation does not necessarily increase the pressure on the unregulated species. Finally, we discuss how the choice of which second-best policy to implement is situation-specific.

The fish fauna of French Guiana is among the best known of South America. Various fieldwork campaigns have been conducted since the publication of the "Atlas des poissons d'eau douce" de Guyane, particularly in poorly surveyed areas, leading to the discovery of new taxa, and numerous scientific publications have provided new insights concerning this fauna. An updated checklist of the fishes of French Guiana, including all of this new information, is therefore desirable. The list contains 416 species, 367 of which are strictly freshwater. Fish diversity is strongly correlated with catchment size and is, on average, higher in French Guiana than in Suriname. The largest groups are the Characiformes (41%), Siluriformes (33%) and Perciformes (13%). The relative abundance of taxonomic groups differs between catchments, probably reflecting the ecological character of the rivers. Eighty seven species, around a quarter of the ichthyofauna, are listed as endemic, but this may be an underestimate because a rather strict definition of endemism is used. The rate of endemism is strongly correlated with catchment size, with some families showing higher than average rates. Comparison of the number of species shared by the different catchments suggests a highly complex pattern of dispersal as a function of the catchment size, topography, and species. The Oyapock River seems to belong to a relatively distinct biogeographic zone influenced by the Amazon basin, but it is not possible to show a broader trend. These results provide an additional tool for environmental managers and decision makers.

In this study, natural fungal diversity in wood-decaying species was explored for biomass deconstruction. In 2007 and 2008, fungal isolates were collected in temperate forests mainly from metropolitan France and in tropical forests mainly from French Guiana. We recovered and identified 74 monomorph cultures using morphological and molecular identification tools. Following production of fungal secretomes under inductive conditions, we evaluated the capacity of these fungal strains to potentiate a commercial Trichoderma reesei cellulase cocktail for the release of soluble sugars from biomass. The secretome of 19 isolates led to an improvement in biomass conversion of at least 23%. Of the isolates, the Trametes gibbosa BRFM 952 (Banque de Ressources Fongiques de Marseille) secretome performed best, with 60% improved conversion, a feature that was not universal to the Trametes and related genera. Enzymatic characterization of the T. gibbosa BRFM 952 secretome revealed an unexpected high activity on crystalline cellulose, higher than that of the T. reesei cellulase cocktail. This report highlights the interest in a systematic high-throughput assessment of collected fungal biodiversity to improve the enzymatic conversion of lignocellulosic biomass. It enabled the unbiased identification of new fungal strains issued from biodiversity with high biotechnological potential.

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Humans frequently introduce novel organisms (e.g., non-native species and, more recently, genetically modified organisms) into ecosystems for economic or biological purposes. However, prior to this, risk analysis is an inherent part of the decision about which species to release. In this contribution we draw upon our experience with non-native species to illustrate two ways in which science can potentially misdirect policy and management of novel organisms. The first involves scientific error, and the challenges in evaluating risk in complex systems. For example, predicting the ecological impact of an evolutionary novel organism on its proposed new ecosystem carries substantial uncertainty, which, depending on how it is explained or framed, can result in different policy outcomes. The second category involves potential biases amongst scientists. As a result of their training scientists may be inclined towards particular opinions that are not necessarily shared by the larger public. Moreover, differences in values also exist among scientists due to different cultures. Examples include a predisposition among scientists against non-native species which can result in an overstatement of perceived risks, as well as an under-appreciation of potential benefits. We illustrate how both scientific and epistemological error can result in sub-optimal policy. Scientists as experts can, and should, express their personal positions, but these should be clearly distinguished from scientific analyses.

At least five marine turtles and 49 terrestrial or freshwater amphibians and reptiles have been listed from the French West Indies since the beginning of human settlement. Among terrestrial or freshwater species, two groups may be distinguished. The first group comprises 35 native species, of which seven are currently extinct or vanished. These species are often endemic to a bank and make up the initial herpetofauna of the French West Indies. Disregarding two species impossible to rule on due to lack of data, the second group includes twelve species that were introduced. Except for marine turtles and some terrestrial species for which the decline was due to human predation, the extinctions primarily involved ground living reptiles of average size and round section body shape. Habitat degradation and mammalian predator introductions have probably contributed to the extinction of these species, in addition to a possible direct impact of man. To better understand the threats to species, we suggest studying the interactions between native herpetofauna and introduced competitors or predators, taking into account the habitat structure. This would help to give the necessary information for successful management measures for conservation or restoration. As an example, the conservation of the Petite Terre (Guadeloupe) Iguana delicatissima population requires identifying both the mechanisms that regulate its population and their relationships to catastrophic climatic events. Key words: Amphibians; biological invasions; conservation; French West Indies; Guadeloupe; Iguana delicatissima; Petite Terre; Reptiles; threats.

International audience; In the native range of the brown trout (Salmo trutta L.) in Europe, the hybridization of native populations by nonnative domesticated strains introduced by stocking is one of the most serious threats to the long-term conservation of diversity within this species. With the objective of conserving and restoring the native gene pool, fishery managers are beginning to implement various management strategies at the local scale. Nevertheless, few case studies have been published that investigate the effectiveness of the various different conservation strategies for native brown trout populations. In the Chevenne Creek, a small French mountain stream, we tested the strategy of removing nonnative individuals by multiple electrofishing carried out by fishery managers in order to evaluate its feasibility and effectiveness for eliminating a nonnative population threatening a native population. Electrofishing produced major reductions in the nonnative population between 2006 and 2009, with 82–100% of nonnative individuals being removed over a period of 4 years. Nevertheless, despite multiple-electrofishing campaigns, this nonnative population was not entirely eradicated, and some natural recruitment persisted. The young of the year and subadults were less effectively removed than the adults. The results suggest that repeated electrofishing campaigns can be used by managers to reduce the nonnative brown trout population with the objective of conserving the native gene pool, but the removal operation must be continued for at least 4 consecutive years. This strategy, which is feasible in small streams, has to be followed by complementary operations to allow the restoration of a new, native, self-sustainable brown trout population.

The potential conservation value of non-native species

International audience; The conservation of biodiversity has gained prominence in ecological research for the last decades. Conservation actions require a measure of biodiversity such as species richness, but its assessment is very difficult, even for small areas and therefore the search for surrogates (i.e. indicators) of biodiversity has emerged as an active research topic. We investigated the relationships between butterfly species richness and landscape structure and composition in two pine plantation sites in Southwest France. We assessed the correlation between butterfly species richness and a set of 15 landscape metrics computed for 18 land-uses at 10 different spatial scales. Spatial scales were accounted for by computing landscape metrics for circular buffers with radius ranging from 100 to 1000 m. The joint use of the Partial Least Squares Regression (PLSR) and a stepwise regression procedure revealed strong correlations between butterfly species richness and various landscape metrics in both study sites. The selected landscape metrics differed from one site to another and mostly involved measures of landscape fragmentation. We found a very strong effect of the spatial scale of investigation upon the perception of the landscape–butterfly richness relationship. Our main conclusions are that (i) certain landscape attributes can potentially serve as indicators for butterfly species richness at the landscape scale; (ii) future indicators of biodiversity based on landscape features should consider various spatial scales.

International audience; Our study is part of a multi-disciplinary research project aimed at stimulating debate among researchers and local managers. The central question of this multi-disciplinary research project was to better understand and manage high biodiversity value open habitats threatened with shrub encroachment and landscape closure, a common problem throughout Europe. Here, we study shrub encroachment and its impact on biodiversity conservation in Mount Ventoux, a MAB Biosphere Reserve located at the southernmost tip of the French Alps. We show how using a multi-agent modelling approach provide a valuable framework to confront two potentially conflicting conservation efforts in this mountain Mediterranean landscape, that of the within-species diversity of a tree (Abies alba, the European silver fir) and that of an endangered species (Vipera ursinii ursinii, the Orsini viper). A companion modelling approach – approach which aims at transmitting and sharing knowledge, methods and tools that help understand and strengthen the collective decision making process of stakeholders sharing a common resource – was used in order to collectively represent the main activities underway on the mountain and to have a tool to address both open landscapes rehabilitation and restoration of forest environments. The co-construction of the model allowed us to build a shared representation of the territory under study and to develop and compare alternative management scenarios with local stakeholders, both to evaluate their impact on biodiversity and to provide information for forest and grazing management practice

International audience; 1. Animals facing partial habitat loss can try to survive in the remaining habitat or emigrate. Effects on survival and movements should be studied simultaneously since survival rates may be underestimated if emigrants are not considered, and since emigrants may experience reduced survival. 2. We analysed movements and survival of adult wintering oystercatcher Haematopus ostralegus in response to the 1986-1987 partial closure of the Oosterschelde in the Dutch Delta. This reduced by one-third the tidal area of this major European wintering area for waders. 3. We developed a novel variant of a multistate capture-recapture model allowing simultaneous estimation of survival and movement between sites using a mixture of data (live recaptures and dead recoveries). We used a two-step process, first estimating movements between sites followed by site-specific survival rates. 4. Most birds were faithful to their ringing site. Winter survival was negatively affected by winter severity and was lowest among birds changing wintering site (i.e. moving outside of the Oosterschelde). 5. During mild winters, survival rates were very high, and similar to before the closure in both changed and unchanged sectors of the Oosterschelde. However, the combined effect of habitat loss with severe winters decreased the survival of birds from changed sectors and induced emigration. 6. The coastal engineering project coincided with three severe winters and high food stock, making assessment of its effects difficult. However, the habitat loss seems to have had less impact on adult survival and movements than did winter severity. 7. Synthesis and applications. Human-induced habitat change may result in population decline through costly emigration or reduced survival or reproduction of individuals that stay. Long-term monitoring of marked individuals helps to understand how populations respond to environmental change, but site-specific survival and movement rates should be integrated in the same model in order to maximize the information yield. Our modelling approach facilitates this because it allows the inclusion of recoveries from outside the study area.

International audience; A heterologous in vitro system, using zona-intact sheep oocytes, was used to evaluate the relationship between sperm factors of Iberian red deer thawed epididymal sperm and the percentage of cleaved oocytes. Epididymal spermatozoa were recovered from six males, diluted with freezing extender and cryopreserved. After thawing sperm motility (SM) and acrosome and membrane integrities were evaluated. Again, these parameters were assessed after incubation in freezing extender at 37 degrees C for 2 h. After cryopreservation the values for SM and acrosome and membrane integrities were high (similar to 80, 80 and 70% respectively). However, these values significantly decreased after incubation (similar to 59, 62 and 47% respectively). Red deer thawed epididymal sperm fertilized zona-intact sheep oocytes, although the percentage of cleaved oocytes was low (similar to 22%). No relationship was found between sperm parameters assessed after thawing and the percentage of cleaved oocytes. Likewise, any sperm parameter evaluated after incubation was assessed in relation to the percentage of cleaved oocytes. However, acrosome and membrane integrities were near to significance (p = 0.06 and p = 0.09 respectively). Then, we conducted a reduced model with these two variables and both were related to the percentage of cleaved oocytes (p = 0.02 and p = 0.04 respectively). Thus, acrosome and membrane integrities were related to the percentage of cleaved oocytes negatively and positively respectively. It was concluded that the classical parameters assessed in deer thawed sperm samples can be good predictors of the ability to fertilize zona-intact sheep oocytes.

International audience; Losses of natural and semi-natural forests, mostly to agriculture, are a significant concern for biodiversity. Against this trend, the area of intensively managed plantation forests increases, and there is much debate about the implications for biodiversity. We provide a comprehensive review of the function of plantation forests as habitat compared with other land cover, examine the effects on biodiversity at the landscape scale, and synthesise context-specific effects of plantation forestry on biodiversity. Natural forests are usually more suitable as habitat for a wider range of native forest species than plantation forests but there is abundant evidence that plantation forests can provide valuable habitat, even for some threatened and endangered species, and may contribute to the conservation of biodiversity by various mechanisms. In landscapes where forest is the natural land cover, plantation forests may represent a low-contrast matrix, and afforestation of agricultural land can assist conservation by providing complementary forest habitat, buffering edge effects, and increasing connectivity. In contrast, conversion of natural forests and afforestation of natural non-forest land is detrimental. However, regional deforestation pressure for agricultural development may render plantation forestry a ‘lesser evil’ if forest managers protect indigenous vegetation remnants. We provide numerous context-specific examples and case studies to assist impact assessments of plantation forestry, and we offer a range of management recommendations. This paper also serves as an introduction and background paper to this special issue on the effects of plantation forests on biodiversity.

International audience; This paper presents a study of a nonlinear reaction–diffusion population model in fragmented environments. The model is set on RN, with periodic heterogeneous coefficients obtained using stochastic processes. Using a criterion of species persistence based on the notion of principal eigenvalue of an elliptic operator, we provided a precise numerical analysis of the interactions between habitat fragmentation and species persistence. The obtained results clearly indicated that species persistence strongly tends to decrease with habitat fragmentation. Moreover, comparing two stochastic models of landscape pattern generation, we observed that in addition to local fragmentation, amore global effect of the position of the habitat patches also influenced species persistence.

International audience

International audience

This paper presents a study of a nonlinear reaction-diffusion population model in fragmented environments. The model is set on RN, with periodic heterogeneous coefficients obtained using stochastic processes. Using a criterion of species persistence based on the notion of principal eigenvalue of an elliptic operator, we provided a precise numerical analysis of the interactions between habitat fragmentation and species persistence. The obtained results clearly indicated that species persistence strongly tends to decrease with habitat fragmentation. Moreover, comparing two stochastic models of landscape pattern generation, we observed that in addition to local fragmentation, a more global effect of the position of the habitat patches also influenced species persistence.

This paper presents a study of a nonlinear reaction-diffusion population model in fragmented environments. The model is set on RN, with periodic heterogeneous coefficients obtained using stochastic processes. Using a criterion of species persistence based on the notion of principal eigenvalue of an elliptic operator, we provided a precise numerical analysis of the interactions between habitat fragmentation and species persistence. The obtained results clearly indicated that species persistence strongly tends to decrease with habitat fragmentation. Moreover, comparing two stochastic models of landscape pattern generation, we observed that in addition to local fragmentation, a more global effect of the position of the habitat patches also influenced species persistence.

International audience

DOI: 10.1006/bojl.2001.0447; International audience

Des données originelles sont présentées concernant la découverte d'une espèce de Lémurien pratiquement éteinte, #Allocebus trichotis$, dans une région de répartition préalablement inconnue dans des forêts humides des terres hautes à l'Est de Madagascar. Les conséquences et l'intérêt aussi bien pour la biogéographie que pour la conservation sont également discutés. (Résumé d'auteur)

Previous protein studies found diagnostic alleles for Atlantic and Mediterranean brown trout populations. Lake Geneva and the upper Rhone belong to the Mediterranean drainage system. Therefore, we would expect that autochthonous brown trout populations from this area show the Mediterranean alleles. In most cases, however, we found Atlantic alleles in high frequencies (f > 0.8). Intense stocking has occurred in this area with hatchery strains originating from the Atlantic drainage system. Thus, the obvious interpretation of our data is that the, presence of Atlantic alleles results from stocking. However, if we take into account information other than present geography we may propose alternative hypotheses that would explain the Atlantic alleles, e.g., an immigration of Atlantic trout from the Rhine system after the last Ice Age. Several post-glacial colonization scenarios for Lake Geneva and its tributaries are discussed and compared to our protein data. The implications of our findings relative to conservation of the genetic diversity of brown trout in this region are also discussed.