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This study presents the fecal contamination dynamic at the two bathing sites of Aytré Bay (Charente Maritime, France). We quantified fecal indicator bacteria (FIB) abundances (Escherichia coli and enterococci) from water and sediment samples over one-year survey. Then we measured biological (bacterial abundance, chlorophyll-a), physico-chemical (dissolved nutrients and oxygen, salinity, pH …) and climatic (temperatures, rainfall and tidal coefficient) parameters. Results showed that FIB abundances were occasionally higher than the European regulatory threshold during winter, summer and fall. The "poor quality" of the bathing water was due to high enterococci abundance. We found negative significant correlations between FIB and water temperature and salinity, and positive significant correlations between FIB and rainfall, PO

Description, Old genetic variants were key to the ability of bottlenose dolphins to repeatedly adapt to coastal waters across the world., Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.

What are the mechanisms that allow species to extend their ranges and adapt to the novel environmental conditions they find in the newly available habitat? The study of parallel adaptation of pairs of populations to similar environments can provide great insights into this question. Here, we test for parallel evolution driven by niche specialization in a highly social marine mammal, the common bottlenose dolphin,Tursiops truncatus, and investigate the origins of the genetic variation driving local adaptation. Coastal ecotypes of common bottlenose dolphins have recurrently emerged in multiple regions of the world from pelagic ecotype populations, when novel habitat became available. Analyzing the whole genomes of 57 individuals using comparative population genomics approaches, we found that coastal ecotype evolution was relatively independent between the Atlantic and Pacific, but related between different regions within the Atlantic. We show that parallel adaptation to coastal habitat was facilitated by repeated selection on ancient alleles present as standing genetic variation in the pelagic populations. Genes under parallel adaptation to coastal habitats have roles in cognitive abilities and feeding. Therefore, parallel adaptation in long-lived social species may be driven by a combination of ecological opportunities, selection acting on ancient variants, and stable behavioural transmission of ecological specialisations. Tried and tested genetic variation that has been subject to repeated bouts of selection, may promote linked adaptive variants with minimal pleiotropic effects, thereby facilitating their persistence at low frequency in source populations and enabling parallel evolution.

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Funding: Fyssen post-doctoral fellowship, Fondation Total, a bridge funding from the School of Biology of the University of St Andrews and People’s Trust for Endangered Species (ML). 1. Protecting species often involves the designation of protected areas, wherein suitable management strategies are applied either at the taxon or ecosystem level. Special Areas of Conservation (SACs) have been created in European waters under the Habitats Directive to protect bottlenose dolphins, Tursiops truncatus, which forms two ecotypes, pelagic and coastal. 2. The SACs have been designated in coastal waters based on photo‐identification studies that have indicated that bottlenose dolphins have relatively high site fidelity. However, individuals can carry out long‐distance movements, which suggests potential for demographic connectivity between the SACs as well as with other areas. 3. Connectivity can be studied using genetic markers. Previous studies on the species in this area used different sets of genetic markers and therefore inference on the fine‐scale population structure and demographic connectivity has not yet been made at a large scale. A common set of microsatellite markers was used in this study to provide the first comprehensive estimate of genetic structure of bottlenose dolphins in European Atlantic waters. 4. As in previous studies, a high level of genetic differentiation was found between coastal and pelagic populations. Genetic structure was defined at an unprecedented fine‐scale level for coastal dolphins, leading to identification of five distinct coastal populations inhabiting the following areas: Shannon estuary, west coast of Ireland, English Channel, coastal Galicia, east coast of Scotland and Wales/west Scotland. Demographic connectivity was very low among most populations with

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International audience; Animal social structures are shaped by external environmental factors and individual intrinsic behavioral traits. They repre-sent a balance between the costs and benefits of group-living to maximize individual fitness. Bottlenose dolphin, Tursiops truncatus, societies are fission–fusion with high variations in association strength, grouping patterns and influence of kin-ship on social bonds throughout the wide range of habitats where they occur. Here, the drivers of social structure in resident coastal bottlenose dolphins of the Normano-Breton Gulf (English Channel) were studied using a multidisciplinary approach combining individual monitoring (photo-identification) information, genetic and ecological data. First, the ecological seg-regation of the social clusters was tested. Then, the influence of kinship, sex and ecological specializations on association patterns was evaluated. Stable isotopes revealed that the social clusters had relatively distinct ecological niches. Resource partitioning among social clusters may reduce competition and may allow the area to sustain a larger resident bottlenose dolphin population. Individuals did not preferentially associate with related individuals or individuals of the same sex. However, sample size was relatively low for females and, therefore, a role of kinship in shaping association patterns could not be totally ruled out for those individuals. Instead, dolphins preferentially associated with individuals of similar ecology. The study also emphasizes that stable isotope analysis is a promising tool to investigate the link between social structure and ecological specializations, particularly in taxa that are difficult to observe in the wild.

Α-casozepine (α-CZP) is a decapeptide that mediates the anxiolytic-like properties of the tryptic hydrolysate of bovine αs1-casein. Different properties of α-CZP leads to consider this peptide close to the benzodiazepine family, the most commonly used anxiolytic molecules. In contrast, other results suggest a distinct mode of action between α-CZP and benzodiazepines, especially the fact that the peptide does not have side effects. Although a central action remains the main hypothesis of the mode of action of α-CZP, no regulation of the brain activity has been shown before. The work achieved in this thesis displayed the fact that the anxiolytic-like properties of α-CZP, after a single intraperitoneal injection of the peptide, are associated with a modulation of cerebral activity in several regions linked to anxiety regulation in mice brains, such as the amygdala, the hippocampal formation, the accumbens nucleus and some nuclei of the hypothalamus or raphe. Besides, these modulations of neural activity are not exactly the same as those obtained after an injection of diazepam, a reference benzodiazepine, or YLGYL, a derivative of α-CZP, even though observed behaviours are similar. Eventually, it has been demonstrated that an anxiety-inducing situation is needed to trigger the central effects of α-CZP. This work allowed a better understanding of the mode of action of a bioactive peptide from alimentary origin that has a positive action on its consumer’s mood and behaviour, L’α-casozépine (α-CZP) est un décapeptide porteur des propriétés anxiolytiques de l’hydrolysat trypsique de caséine αs1 bovine. Différentes propriétés ont pu rapprocher ce peptide de la famille des benzodiazépines, les anxiolytiques les plus prescrits. Cependant, certaines différences, dont notamment une absence d’effets secondaires, permettent aussi de distinguer l’α-CZP des benzodiazépines. Bien que de nombreux éléments laissent penser qu’une action centrale reste l’hypothèse principale du mécanisme d’action de l’α-CZP, aucune régulation de l’activité de zones cérébrales n’avait été montrée jusqu’à présent. Ce travail de thèse aura donc pu montrer que les propriétés anxiolytiques de l’α-CZP sont associées à une modification de l’activité cérébrale chez la souris, après une unique injection intrapéritonéale, dans différentes régions impliquées dans la régulation de l’anxiété, notamment l’amygdale, la formation hippocampale, le noyau accumbens et certains noyaux de l’hypothalamus et du raphé. De plus, ces modifications de l’activité cérébrale ne sont pas exactement les mêmes que celles observées avec le diazépam, une benzodiazépine de référence, ni de celles obtenues avec YLGYL, un peptide dérivé de l’α-CZP, bien qu’il existe des similitudes dans le comportement de l’animal suite aux différents traitements effectués. Enfin, il a été démontré qu’une situation anxiogène est indispensable pour révéler cet effet central. L’ensemble de ce travail aura permis d’avancer dans la compréhension du mode d’action d’un peptide alimentaire ayant des effets positifs sur le comportement et les émotions de son consommateur

Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

A large, but poorly studied, bottlenose dolphin community, Tursiops truncatus, inhabits coastal waters of Normandy (Normano-Breton Gulf, English Channel, France). In this study, the social structure and abundance of this community were assessed using photo-identification techniques. Like other bottlenose dolphin communities worldwide, this resident community has a fission—fusion social structure with fluid associations among individuals (half-weight index = 0.10). Association patterns were highly variable as indicated by a high social differentiation (S = 0.95 ±0.03). The majority of associations were casual, lasting days to months. However, individuals exhibited also a smaller proportion of long-term relationships. A mean group size of 26 was large compared with other resident coastal communities, and variable, ranging from 1 to 100, which could be the results of ecological conditions, in particular resource predictability and availability. Analyses also showed that the community was organized in 3 socia...

11 páginas, 4 tablas, 5 figuras.-- Paula Méndez Fernández ... et al., Concentrations of thirty two polychlorinated biphenyls (PCBs) were determined in the blubber of five sympatric species of odontocetes stranded or by-caught along the Northwest coast of the Iberian Peninsula: common dolphin (Delphinus delphis), long-finned pilot whale (Globicephala melas), harbour porpoise (Phocoena phocoena), striped dolphin (Stenella coeruleoalba) and bottlenose dolphin (Tursiops truncatus). Multivariate analyses were applied to evaluate the ability of PCB patterns to discriminate these sympatric species and to determine which eco-biological factors influence these patterns, thus evaluating the relevance of PCB concentrations as biogeochemical tracers of feeding ecology. The five species could be separated according to their PCB patterns. Different exposure to these contaminants, a consequence of their different dietary preferences or habitats, together with potentially dissimilar metabolic capacities, likely explain these results; sex, age, habitat and the type of prey eaten were the most important eco-biological parameters of those tested. Although, no single congener has been specifically identified as a tracer of feeding ecology, 4 congeners from the 22 analysed seemed to be the most useful and around 12 congeners appear to be enough to achieve good discrimination of the cetaceans studied. Therefore, this study suggests that PCB patterns can be used as tracers for studying the feeding ecology, sources of contamination or even population structure of cetacean species from the Northwest Iberian Peninsula, P. Méndez- Fernandez was supported during the research period through a PhD grant from the Fundação do Ministério de Ciência e Tecnologia de Portugal and ANIMATE project (SFRH/BD/36766/2007) and through a Science Without Borders (CSF) young talent postdoctoral grant of the Brazilian government. G. J. Pierce acknowledges support from the EU ANIMATE project (MEXC-CT-2006-042337), University of Aveiro and Caixa Geral de Depósitos (Portugal).

International audience; Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions.

Summary. Coastal shorebird species overlap at many wintering sites or migratory stopovers. However, each species is morphologically and physiologically specialised for reducing competition for space, time or habitat. A species can encompass several populations, sometimes designated as subspecies. Differences between populations, ages and sexes within the same species can also lead to segregation between individuals in a foraging area. In this study, we explored the non-breeding spatial and temporal overlap between two subspecies of the black-tailed godwit Limosa limosa on the central Atlantic coast of France (the Pertuis Charentais). The proportions of individuals of each sex and each age within the populations were assessed to explore differences in the wintering distribution. The subspecies L.l. islandica winters in the area from July to March whereas the subspecies L.l. limosa may stopover in the area during south- and northward migration. The two subspecies occasionally overlap at some sites just afte...

International audience; Delphinid populations show highly variable patterns of genetic diversity and population structure. Previous studies indicate that habitat discontinuities and geographic isolation are major drivers of population division in cetaceans. Spinner dolphins (Stenella longirostris) are distributed in all tropical oceans, but they are particularly common around islands and atolls. This species occurs in shallow waters at daytime to rest and socialise, and feeds on offshore mesopelagic prey overnight. Here we investigated the genetic population structure of spinner dolphins in the Southwest (SW) Indian Ocean along a west-east geographical gradient, from eastern Africa to the Mascarene archipelago. We combined analyses of 12 microsatellite loci, mtDNA control region sequences, and sighting data to assess genetic differentiation and characterise habitat preferences of these populations. Significant genetic structure among the three sampled sites (Zanzibar, Mayotte and La Réunion) was observed using both types of molecular markers. Overall, our results indicate that geographic isolation, and potentially other factors such as shallow water habitats to rest and socialise, may be important drivers of the genetic population structure of insular spinner dolphins in this region.

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The aim of the study was to determine genetic diversity in the soft-shell clam Mya arenaria on a wide geographical scale using mtDNA COI gene sequences. Low levels of genetic diversity was found, which can most likely be explained by a bottleneck effect during Pleistocene glaciations and/or selection. The geographical genetic structuring of the studied populations was also very low. The star-like phylogeny of the haplotypes indicates a relatively recent, rapid population expansion following the glaciation period and repeated expansion following the founder effect(s) after the initial introduction of the soft-shell clam to Europe. North American populations are characterized by the largest number of haplotypes, including rare ones, as expected for native populations. Because of the founder effect connected with initial and repeated expansion events, European populations have significantly lower numbers of haplotypes in comparison with those of North America. We also observed subtle differentiations among populations from the North and Baltic seas. The recently founded soft-shell clam population in the Black Sea exhibited the highest genetic similarity to Baltic populations, which confirmed the hypothesis that M. arenaria was introduced to the Gulf of Odessa from the Baltic Sea. The most enigmatic results were obtained for populations from the White Sea, which were characterized by high genetic affinity with American populations.

article i nfo Among marine organisms, little is known on patterns of intra-species habitat partitioning, whereas many studies have examined niche segregation at the multi-species community level. In this study, we investigated the fine-scale population structure and patterns of within-species habitat use of Indo-Pacific bottlenose dol- phins (Tursiops aduncus) in a tropical lagoon of the Indian Ocean (Mayotte, 45°10'E/12°50'S). First, we assessed genetic population structure using mtDNA and 14 microsatellite markers to determine if bottlenose dolphins around Mayotte belong to one or several panmictic groups. The analyses revealed no mitochondrial polymorphism and the presence of a single population at Hardy-Weinberg equilibrium. Second, we assessed whether a community structure exists within the bottlenose population. A community is an assemblage of individuals using a common home range. Photo-identification data were used to assess individual home range size and habitat preferences. Home range analysis revealed the presence of at least two communities of bottlenose dolphins around Mayotte: one occurring in the shallower waters inside the lagoon and a second in the vicinity of a deeper reef bank, situated further offshore in the northern part of the island. Stable isotope analyses of δ 13 C and δ 15 N were performed to detect intra-species segregation of habitat and resource use. However, no significant structure across the population was detected. Nevertheless, this study highlights that, even at small spatial scales, individual and between community variations of habitat preferences occur in bottlenose dolphin populations. Intra-species niche partitioning may explain habitat segregation in these insular delphinids.

International audience; The degradation of water quality and the multiple conflicts of interest between users make marsh restoration very important. A Water Quality Evaluation System (WQES) was developed for river systems by the European Water Framework Directive (WFD). Some form of biologically-based, habitat-specific reference standard seems absolutely essential for wise management and stewardship of marsh ecosystems. The goal of this study was to develop a statistical method to define and to characterize a water body typology for drained marshes of the Charente-Maritime wetlands on the French Atlantic coast, placing particular emphasis on environmental factors as hydraulic functioning, human activities and pedological substratum. The Charente-Maritime marshes represent a good field study because of his high diversity of types of marshes and of anthropogenic activities in a restrictive area thus erasing spatial climatic effect (latitude effect). The statistical method developed here had permitted to define and characterize 12 different water bodies, 7 in freshwater (F1 to F7) and 5 in salt water marshes for the Charente-Maritime area. This typology demonstrated an important link between the size catchment area, nitrate concentrations, and leaching of precipitation from cultured soils. Even though the Charente-Maritime marshes are strongly impacted by humans, they may still retain the ability to remove nitrate. The increasing gradient of water renewal in the freshwater marshes from F1 to F7 explained the decreasing gradient of eutrophication. A better management of the hydrodynamic of the marshes can avoid eutrophication risk on the coastal sea area. Reliance on the WFD parameter set necessarily placed limits on the kinds of interpretations that could be made and on the study's potential contribution to the basic science of marshes. Ecologically-based insights regarding both external flows (links between ecosystems, meta-ecosystem theory) and internal flows (structure of the planktonic food web) seem an essential prerequisite for further advances in the study of marsh ecosystems.

International audience; Investigating ecological segregation among organisms of a given community is challenging, especially when these organisms share similar patterns of distribution, and similar size and morphology. Around the island of Mayotte, a diversified community of at least four sympatric delphinids is present year round within a very restricted range: the Indo-Pacific bottlenose dolphin (Tursiops aduncus), the spinner dolphin (Stenella longirostris), the pantropical spotted dolphin (Stenella attenuata), and the melon-headed whale (Peponocephala electra). In addition, the Fraser's dolphin (Lagenodelphis hosei) makes temporary incursions into peri-insular waters as well. This study aims to assess niche segregation among this tropical dolphin community. We hypothesized that each species occupies its own distinct niche, defined by the following axes: habitat, resources and time. We analysed habitat in relation to physiography, behavioural budgets and C and N stable isotope values from skin and blubber samples for each species. The results highlighted that habitat and behavioural budgets were relatively distinct among species, with few exceptions. However, in those species living on the outer reef slope where habitat and behaviour were not well discriminated, stable isotope analyses confirmed that species have different trophic levels (mostly reflected through δ15N values) and/or foraging habitat (mostly reflected through δ13C values). This study confirms that the use of multiple methodologies (habitat, behaviour and feeding ecology studies) help in discerning ecological niche segregation, especially when examining closely related species within a common restricted range.

Zooplankton assemblages were studied from January 2007 to January 2008 along the salinity gradient of the Charente estuary (France). A Lagrangian survey was performed monthly at five sampling stations defined by salinity (freshwater, 0.5, 5, 15 and 25) in order to collect zooplankton and measure the main environmental parameters (concentrations of suspended particulate matter, particulate organic carbon, chlorophyll a and phaeopigments). A combination of multivariate cluster analysis, species indicator index and canonical correspondence analysis was used to relate the spatio-temporal patterns of the zooplankton assemblages with environmental drivers. The estuary was divided into three different zones by means of environmental parameters while four zooplankton assemblages were identified along the salinity gradient. The Charente estuary appeared as one of the most turbid systems in Europe, with suspended particulate matter (SPM) concentration reaching 3.5 g l-1 in the Maximum Turbidity Zone (MTZ). Algal heterotrophy and microphytobenthos resuspension from the wide mudflats could be responsible for the relatively high chlorophyll a concentrations measured within this MTZ. Salinity and SPM affected significantly the spatial distribution of zooplankton species while temperature and river flow seemed to control their temporal variations. From a zooplanktonic viewpoint, the highly turbid Charente estuary seemed to match an "ecotone-ecocline" model: the succession of species assemblages along the salinity gradient matched the concept of ecocline while the MTZ, which is a stressful narrow area, could be considered as an ecotone. Although such ecoclinal characteristics seemed to be a general feature of estuarine biocenoses, the ecotone could be more system-specific and biological compartment-specific. © 2010 Elsevier Ltd. All rights reserved.