The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.

Estuaries are among the most anthro- pogenically degraded habitats on Earth. These shallow waters are particularly exposed to the impacts of pollution and global warming [...]

The great scallop (Pecten maximus) is of high economical value, particularly in France and UnitedKingdom. Although great scallop fisheries are mostly based on the exploitation of natural beds, some stocks are seeded with hatchery-reared spat in order to ensure the sustainability of local fisheries. This is particularly the case in the Bay of Brest (France), where hatchery-based stock enhancement of P. maximus has been developed since 1983, in order to enhance the local population. However, The release of hatchery-born seeds might significantly impact the genetic diversity of local scallop populations. In the present study, microsatellites were used to monitor the genetic variability seeded great scallop populations, in order to evaluate the possible impact of hatchery-based stock enhancement on the genetic diversity of local populations. A limited but temporally persistent erosion of the genetic variability as well as a strong alteration of the natural gene pool were found in hatchery cohorts. However, the genetic diversity of seeded populations did not seem to decrease. Furthermore, molecular marker-based pedigrees were assessed, in order to identify hatchery-born individuals released in natural beds. Hatchery-born individuals were successfully assigned to their parents, thus opening new avenues for monitoring populations enhanced with hatchery-raised spat.

The integration of population genetics in ecotoxicology may be pertinent i) to detect pos- sible differential physiological capacities or performances between individuals carrying particular alleles or genotypes, and ii) to explain their potential resistant or sensitive characters, sometimes resulting in increasing or decreasing frequencies in contaminated systems. [...]

Anthropogenic pressures in estuaries may impair not only the fitness of organisms and the evolutionary processes necessary to the survival, but also the management of exploited marine resources. In order to assess these impacts, phenotypic and genotypic data pertaining to young-of-the-year (YOY) sole (Solea solea) were screened in differentially contaminated North East Atlantic estuaries ranging from Portugal (Mondego) to the English Channel (Seine). YOY sole inhabiting each estuary was found being phenotypically distinct from each other; each of them being impacted by pollution when comparing observed phenotypic data with published literature. According to the strong pollution in the Seine estuary, the corresponding YOY sole sample showed significantly lower body mass, size and condition factor compared to other samples. Using fifteen genetic markers, the Mondego estuary demonstrated low, but significant levels of genetic differentiation with most of the samples. Using neutrality tests, two loci were found to be putatively under directional selection (Soso7 and Soso23), but only locus Soso7 demonstrated significant positive heterozygosity–fitness correlation (HFC) for body size and body mass, suggesting a possible ongoing adaptive process. The candidate locus MT associated to a detoxifying metallothionein gene did not show significant genetic differentiation, but (i) significant deficit in heterozygote in the Seine estuary as already reported in other coastal samples impacted by metallic contaminants, and (ii) significant positive HFC with body mass were found. Selective rather than demographic processes better explain an observed genetic structure in YOY sole and are predominantly associated with the heavily contaminated Seine estuary whose nursery function and capacity are degraded.

The genetic structure of European flounder Platichthys flesus populations was analysed in the southern part of the species' distribution area, from England to Portugal; samples were collected in 5 estuaries which were chosen because of their latitudinal cline, the level of contaminants and the possibility of hypoxia: the Tamar in England; the Canche, Seine and Vilaine in France; and the Mondego in Portugal. Analysing the variability of a mitochondrial marker (cytochrome c oxidase subunit I), we observed (1) a moderately higher nucleotide diversity in the Tamar and Canche, reflecting the probable existence of a major refugium in this sector during the last glacial maximum, and (2) a reduced genetic differentiation over the whole data set. The use of 8 micro satellites underlined the maintenance of genetic diversity in the peripheral population of the Mondego, located near the southern limit of the species' range; furthermore, significant pairwise differentiations of populations including Mondego underlined the particular genetic status of this Portuguese population. The polymorphism of a candidate gene involved in energetic metabolism, AMP-deaminase isoform 1, was investigated focusing on exon 1; we found the highest heterozygosities in the more polluted populations (Seine, Tamar) and marked differentiations compared to the other group of populations (Mondego, Vilaine, Canche). The pattern of variability observed for the AMP-deaminase suggests that in chronically contaminated flounder populations, cocktails of pollutants act as selective agents directly or indirectly on this locus.

The vitellogenic response in the flounder (Platichthys flesus L.) has been investigated in nature through the breeding season and following estrogen treatment. Gonadosomatic index (GSI), liversomatic index (LSI), DNA and RNA concentrations in liver, liver protein synthesis, liver dry weight, liver protein, glycogen and lipid, and serum protein, glucose and lipid, as well as phosphorylase a have been measured and related to the concentration in the blood of the egg yolk precursor protein, vitellogenin. Synthesis of vitellogenin was found to be associated with simultaneous increases in GSI, LSI, DNA, RNA and phospholipid in liver in nature. Levels of glucose and lipid in blood reached a maximum at spawning. In liver, the concentration of glycogen oscillates during vitellogenesis, and no simple correlation to blood glucose could be established. A seasonal change in the activity of phosphorylase a is observed in female flounder. Administration of exogenous estrogen to male flounders made blood glucose, liver glycogen, lipid, protein and RNA change in a dose-dependent manner. Low doses of estradiol cause the activity of liver phosphorylase a to increase.

This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus . These loci were cross‐tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.

In this study, new DNA markers were explored for the flounder Platichthys flesus. cDNA and genomic sequences of the genes encoding the glyceraldehyde-3-phosphate-deshydrogenase (GAPDH), the cytosolic creatine kinase (CK), the prostaglandin D synthase (PGDS) and the betaine homocysteine methyltransferase (BHMT) were characterized. The tumour suppressor p53 gene structure was already described. A PCR–SSCP (Single Strand Conformation Polymorphism) analysis was finally conducted to study the genetic polymorphism of different populations of flounders collected along the French Atlantic coast. Four highly contaminated French estuaries (Seine, Vilaine, Loire and Gironde) were sampled and compared to a reference estuary (Ster) to explore possible selective effect of the environment on specific allelic frequencies. Our results showed that two loci p53 and PGDS, could be potential markers of chemical stress: p53A allele frequency increased in contaminated systems compared to the reference system. In the Vilaine estuary, PGDS polymorphism could be related to pesticide stress.

An increase in individual growth rate of chub Leuciscus cephalus along a longitudinal river gradient of the Rhône River basin was observed and supported by significant differences between mean growth rates of successive river size groups. The potential implications of the results for studies on species traits variability along large-scale environmental gradients are discussed.

Turbot Psetta maxima were exposed 5 days to the dissolved fraction of fuel oil number 2, then decontaminated over 30 days in clean sea water. Biliary metabolites and ethoxyresorufin‐O‐deethylase (EROD) activity were evaluated during and after the contamination. These results were compared with chromosomal damage measured by flow cytometry (FCM). Erythrocyte nuclear abnormality, micronuclei and immaturity were also evaluated over the exposure period. Biliary metabolites and EROD analyses showed a clear and early response: biliary metabolites were detected from the first day of contamination to the 14th day of depuration, EROD activity increased during the contamination period reached a maximum 3 days after the beginning of the decontamination and decreased to the control value after 1 month of depuration. FCM showed a bimodal response: a first increase of coefficient of variation of blood cell DNA content was observed during the contamination and a second one started after 14 days of depuration and was maintained for at least 2 weeks. Erythrocyte morphology analysis showed a strong increase in nuclear abnormality during the contamination period. These results confirm previous work and show that in the context of marine accidental pollution by heavy fuel oil, the measurements of chromosomal damage by FCM allow the detection of a genotoxic response in fishes.

The genetic variability of 11 French pike Esox lucius populations from rivers or extensive aquaculture ponds was analysed using seven microsatellite markers. The fish stocking of eastern European pike in French rivers is widespread, so five supplementary populations from this region were also analysed. Genetic variability within the French population was small, and similar to that previously found in Europe for this species. French populations from stocked rivers and extensive farms formed a genetically homogeneous group, and did not diverge from most eastern European samples, which may reflect either ancestral polymorphism or a complete introgression of French populations by introduced stocks. Bayesian analysis of the admixture between populations enabled identification of the French populations that were likely to be affected by introduced stocks (of local or foreign origin). Three genetically distinct evolutionary branches were identified: continental Europe, Danube basin, and south‐western France. The last is a new finding in the species which needs to be further explored by comparisons with wild populations at other sites.

Effects of pesticide exposure on the European flounder, Platichthys flesus , were investigated using a suppression subtractive hybridization method (SSH) to identify up- and down-regulated genes after a 30-day exposure to herbicides (a cocktail of atrazine, diuron, and isoproturon, and a single herbicide, glyphosate). A total of 256 expressed gene sequences were identified as having the potential for being differentially expressed, of which 116 could be identified by homology with databased sequences. The metabolic functions with which they are associated include energy production, general metabolism, signaling, transport, immune system, and structure. Expression of 14 of these genes was analyzed in liver, muscle, and gills by reverse transcriptase-polymerase chain reaction (RT-PCR) under experimental conditions (0, 15, and 30 days of exposure) and under field conditions (sampling in two estuaries displaying different levels of pesticide contamination). This study provides a first basis for studying the response of fish to pesticide exposure and allows the characterization of new potential genetic markers of pesticide contamination in the field.

In order to investigate the relative importance of historical processes and life-history traits in shaping the present-day genetic structure of European anglerfishes, 382 Lophius piscatorius and 134 Lophius budegassa were sequenced on the 5’ end of the mitochondrial control region. Both species showed a limited genetic structure and some evidence of a demographic expansion that probably occurred not at the end of the Last Glacial Maximum, but earlier in the Pleistocene. The main discrepancy between the two anglerfishes concerned the genetic structure between Atlantic and Mediterranean populations, with weak but significant differentiation observed only in L. budegassa. This genetic structure was congruent with the existence of a phylogeographical break previously reported in several marine species across the Almeria–Oran front. The contrast observed between both anglerfishes was supposed to be induced by a possible more ancient (re)colonisation of the Mediterranean Sea by L. budegassa. Finally, the limited genetic structure and lack of isolation by distance observed in both species suggested high larval dispersal capacities that probably overwhelm the influence of the bathymetric distribution range on migrations of adults and juveniles.

Physiological and genetic responses of flounder Platichthys flesus populations were investigated along the French Atlantic Coast in one moderately contaminated estuary (Ster) and three contaminated estuaries (Seine, Loire and Gironde). The focus of this study was to explore the relationship between stress resistance and energetic trade-offs, in order to detect possible differential physiological capacities or performances between individuals carrying particular alleles or genotypes (allozyme data) characterised as “tolerant” or “sensitive”. A general reduction of the relative fecundity, the growth rate and the condition factor was highlighted in contaminated fish populations, suggesting that survival in such polluted systems implies energetic costs for fish thus reducing the energy available for particular functions. A lower observed heterozygosity was also detected in contaminated populations with respect to the Ster, suggesting a general decrease in genetic variability in response to chemical stress (with an exception for the Seine estuary). This study confirmed the previously detected relationship between PGM 85, AAT1 95 alleles and reduced DNA damage in contaminated fish [Marchand, J., Tanguy, A., Laroche, J., Quiniou, L., Moraga, D., 2003. Responses of European flounder Platichthys flesus populations to contamination in different estuaries along the Atlantic coast of France. Mar. Ecol. Prog. Ser. 260, 273–284] and furthermore suggested that, reduced fecundity and condition factor associated to the individuals carrying the previous alleles, were also reflecting the cost of resistance to stress in polluted populations. The cost of tolerance to stress as well as the high gene flow from neighbouring populations less exposed to contamination may explain the apparently moderate increase of the suspected “tolerant” alleles in contaminated flounder populations.

Zingel asper is an endemic percid of the Rhône basin considered to be critically endangered. This species was continuously distributed throughout the Rhône in 1900, but today only occupies 17% of its initial area. In the present study, five microsatellite loci were used to assess the level of genetic variability within and among populations localized in different sub-basins. Contrasting results were obtained for the three main populations from the Rhône. A reduced allelic diversity was observed for the two populations displaying the lowest patch sizes (length of the river system occupied); of these, a recent genetic bottleneck was detected for the population showing a particularly low density. However, the third population was characterized by a relatively large spatial extent, high local fish concentrations and an allelic diversity that was twice as high and associated with an equilibrium between mutation and drift. Thus, this population shows an apparently better evolutionary potential for long-term survival. Since 1930, a marked fragmentation of the whole Rhône system has appeared, related to the development of dams, and we assume that the significant genetic differentiation detected between the populations could mainly reflect the impact of this fragmentation. The high turnover of the Z. asper populations, and the major role of dispersal in population persistence (highlighted in a recent population dynamics study), indeed suggest that the differentiation observed could mainly have arisen from habitat fragmentation in recent history.

Flatfishes, turbots (Scophthalmus maximus), were injected intraperitoneally with two doses of fuel oil number 2. Biliary metabolites were evaluated by fixed fluorescence to verify the efficiency of intoxication. Ethoxyresorufin-O-deethylase (EROD) activity was compared with chromosomal damage measured by flow cytometry. The analysis of biliary metabolites showed a good dose–response relation and constitutes a clear reference for the subsequent measurements. Comparing flow cytometry and EROD results, a shorter delay of response for EROD activity was obtained, but chromosomal damage was significant only after 1 week. The persistence of the EROD response was shorter, while the genotoxic signal still persisted after 1 month. The measurement of chromosomal damage allowed a good differentiation between the two tested doses. In the case of EROD activity, the results were less clear. The results suggest that within a few weeks after exposure to fuel oil number 2, the measurements of chromosomal damage by flow cytometry can be used to detect a dose-dependant genotoxic response in fish.

The effects of pesticide contamination on the metabolism of marine molluscs are poorly documented. We investigated the response of a marine bivalve, the Pacific oyster, Crassostrea gigas, using a suppression subtractive hybridization method to identify up‐ and down‐regulated genes after a 30‐day exposure period to herbicides (a cocktail of atrazine, diuron and isoproturon, and to the single herbicide glyphosate). A total of 137 unique differentially expressed gene sequences was identified, as well as their associated physiological process. The expression of 18 of these genes was analyzed by RT‐PCR under laboratory experimental conditions. The metabolic functions they are associated with include xenobiotic detoxification, energy production, immune system response and transcription. This study provides a preliminary basis for studying the response of marine bivalves to long‐term herbicide exposure in terms of regulated gene expression and characterizes new potential genetic markers of herbicide contamination.