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Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes.

International audience; Background: European eel is a panmictic species, whose decline has been recorded since the last 20 years. Amonghuman-induced environmental factors of decline, the impact of water dams during species migration is questioned. The main issue of this study was to pinpoint phenotypic traits that predisposed glass eels to successful passage by water barriers. The approach of the study was individual-centred and without any a priori hypothesis on traits involved in the putative obstacles selective pressure. We analyzed the transcription level of 14,913 genes.Results: Transcriptome analysis of three tissues (brain, liver and muscle) from individuals sampled on three successive forebays separated by water obstacles indicated different gene transcription profiles in brain between the two upstream forebays. No differences in gene transcription levels were observed in liver and muscle samples among segments. A total of 26 genes were differentially transcribed in brain. These genes encode for, among others, keratins, cytokeratins, calcium binding proteins (S100 family), cofilin, calmodulin, claudin and thy-1 membrane glycoprotein. The functional analysis of these genes highlighted a putative role of cytoskeletal dynamics and synaptic plasticity in fish upstream migration.Conclusion: Synaptic connections in brain are solicited while eels are climbing the obstacles with poorly designedfishways. Successful passage by such barriers can be related to spatial learning and spatial orientation abilities when fish is out of the water.

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93–100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

BackgroundOnce highly abundant, the European eel (Anguilla anguilla L.; Anguillidae; Teleostei) is considered to be critically endangered and on the verge of extinction, as the stock has declined by 90-99% since the 1980s. Yet, the species is poorly characterized at molecular level with little sequence information available in public databases.ResultsThe first European eel transcriptome was obtained by 454 FLX Titanium sequencing of a normalized cDNA library, produced from a pool of 18 glass eels (juveniles) from the French Atlantic coast and two sites in the Mediterranean coast. Over 310,000 reads were assembled in a total of 19,631 transcribed contigs, with an average length of 531 nucleotides. Overall 36% of the contigs were annotated to known protein/nucleotide sequences and 35 putative miRNA identified.ConclusionsThis study represents the first transcriptome analysis for a critically endangered species. EeelBase, a dedicated database of annotated transcriptome sequences of the European eel is freely available at http://compgen.bio.unipd.it/eeelbase webcite. Considering the multiple factors potentially involved in the decline of the European eel, including anthropogenic factors such as pollution and human-introduced diseases, our results will provide a rich source of data to discover and identify new genes, characterize gene expression, as well as for identification of genetic markers scattered across the genome to be used in various applications.

The evolutionary enlightened management of species with complex life cycles often requires the development of mathematical models integrating demographic and genetic data. The genetic structure of the endangered European eel (Anguilla anguilla L.) has been thoroughly analyzed in several studies in the past years. However, the interpretation of the key demographic and biologic processes that determine the observed spatio-temporal genetic structure has been very challenging owing to the complex life cycle of this catadromous species. Here, we present the first integrated demographic-genetic model applied to the European eel that explicitly accounts for different levels of larval and adult mixing during oceanic migrations and allows us to explore alternative hypotheses on genetic differentiation. Our analyses show that (i) very low levels of mixing occurring during larval dispersal or adult migration are sufficient to erase entirely any genetic differences among sub-populations; (ii) small-scale temporal differentiation in recruitment can arise if the spawning stock is subdivided in distinct reproductive groups; and (iii) the geographic differentiation component might be overestimated if a limited number of temporal recruits are analyzed. Our study can inspire the scientific debate on the interpretation of genetic structure in other species characterized by complex life cycle and long-range migrations.

Marine organisms experience a broad range of intrinsic and extrinsic influences during their lives, which impact their population dynamics and genetic structure. Subtle interpopulation differences reflect the continuity of the marine environment, but also pose challenges to those wishing to define management units. The catadromous European eel (Anguilla anguilla) is no exception. Its spawning habitat in the Sargasso Sea and long migration across the North Atlantic qualify it as marine. However, the synergy between hydrographic variability, changing climate, and the impacts of habitat degradation and overfishing in continental waters has negatively affected stock sizes. Its protracted spawning period, variance in age-at-maturity, parental contribution and reproductive success, and the difficulty in sampling the spawning region together may mask a weak geographical genetic differentiation. Recent genetic data report evidence for spatial as well as temporal differences between populations, with the temporal heterogeneity between intra-annual recruitment and annual cohorts exceeding the spatial differences. Despite its common name of ‘fresh-water eel’, the European eel should really be managed on a North Atlantic scale. The fishery may have to be curtailed, migration routes kept open and water quality restored if it is to survive. Eel aquaculture has to focus on efficient rearing in the short term and controlled breeding in the long term. Future research on eel genetics should focus on (i) sampling and analysing spawning populations and recruitment waves to detect spatio-temporally discrete groups, and establishing a biological baseline from pre-decline historical collections for critical long-term monitoring and modelling of its genetic composition; (ii) the analysis of adaptive genetic polymorphism (genes under selection) to detect adaptive divergence between populations, perhaps requiring separate management strategies; and (iii) improving artificial reproduction to protect natural stocks from heavy exploitation, especially now the species has been categorized as endangered (Maes and Volckaert, 2007).

Otolith microchemistry, the study of the minor and trace elemental composition of otoliths (earbones), has been developing rapidly with a wide range of applications in fishery science. This is because otoliths (1) grow continuously, resulting in daily and seasonal structures, (2) have an elemental composition that reflects the environmental concentrations and conditions, (3) are metabolically inert. All of these characteristics make trace element uptake useful for reconstructing environmental histories. The elemental composition is therefore a powerful tool in stock To study connectivity among North Sea sole (Solea solea) populations and to improve our understanding of the relationship between its spawning grounds and nursery areas, genetic markers and otolith microchemistry will be used as complementary discrimination tools. We performed a pilot study to test for differences in sole otolith elemental fingerprints among three sampling locations, using LA-ICPMS. This technique makes it possible to determine composition at discrete points across the otolith (corresponding with different events in the fish’s lifetime). A hierarchical design (Basin, Sea, within Sea) enables us to assess the power of this method for the simultaneous large and small scale discrimination of populations.Preliminary results of this study will be shown and discussed in the light of current European wide research objectives. size and increasing the number of sampling locations.

The recognition of the vulnerability of marine species to environmental conditions throughout their life-cycle has broadened the scope of investigations on factors influencing their population dynamics and demographics. The European eel Anguilla anguilla (Linnaeus, 1758) stock is declining rapidly due to overfishing, pollution, habitat degradation, diseases, and oceanic conditions. We analyzed arrival waves of glass eels collected in the Bay of Biscay and the western Mediterranean area during the period 2001-2003. We observed significant differences in length, weight, and condition between Atlantic and Mediterranean samples, and among arrival waves within sites. All samples were screened for genetic variation using ten allozyme and six microsatellite loci. We observed a pattern of genetic patchiness among arrival waves, namely a highly significant genetic differentiation without a temporal grouping of samples. Although natural selection and gene flow could also play a role, we suggest that the pattern observed results from the high variance in reproductive success in each spawning season. A low effective population size might have contributed to the current decline in the abundance of European eel. A precautionary approach to fisheries should be implemented in order to preserve maximal genetic potential to cope with changing anthropogenic and environment pressures.

Several commercial marine fish stocks show signs of collapse due to the synergy between climate change and adverse human impacts, such as habitat degradation and overfishing. Besides the reduction in abundance of the exploited species, intense fishing activities have an array of additional ecological impacts. Fisheries may cause irreversible evolutionary changes in life history traits and the genetic structure of populations. One of the species for which such phenotypic-genetic changes are likely to occur is common sole (Solea solea). This project aims at studying the connectivity and demographic stability of sole populations in the North Sea and adjacent waters before and after heavy (beam trawl) fishing. First, we will characterize the spatial and temporal connectivity of the different life stages of Solea solea. Are the spawning populations of Solea solea separated in time and space or are they well mixed? Do adult fish spawn near the nursery ground where they grew up? Do they return to the same spawning ground year after year? Through the combined analysis of otolith microchemistry and neutral genetic markers, we will answer these questions and investigate the extent to which spawning grounds, nursery areas and feeding grounds are linked. The level of gene flow between different populations will be estimated and adult fish from the feeding grounds will be assigned to their nursery origin. As such, we will evaluate the relative importance of different North Sea nurseries to adult populations. Secondly, we will analyze the long-term demographic stability of the sole population in the North Sea. Using DNA extracted from historical otolith collections (1960’s-1990’s), we will investigate possible fluctuations in genetic variability through time, in relation to fishery pressure and methods. The evolution of the effective number of breeding fish will be followed through time, providing a good indicator for the ‘genetic health status’ of the North Sea stock(s). Results will improve our understanding of the population genetic structure and the connectivity of spawning grounds, nurseries and feeding grounds of common sole. This knowledge is relevant for fisheries management, in order to identify appropriate management units and to evaluate the benefits of marine protected areas.

Marine organisms usually exhibit a high genetic diversity, a subtle population structure and a low level of genetic differentiation, compared to freshwater organisms. The subtle genetic differences in time and space reflect the continuity of the marine environment. Marine organisms experience a wide range of intrinsic and extrinsic influences during their life cycle, which considerably impact their biological population size and genetic population structure. Furthermore, genetic variability is crucial for the survival of organisms as it enables evolution while maintaining fitness. Marine species however have a high genetic load, affecting the population even more during a population decline or bottleneck. The European eel Anguilla anguilla (Anguillidae; Teleostei), although inhabiting fresh- and saltwater, represents no exception. Its spawning habitat in the Sargasso Sea and extensive migrations across the North Atlantic Ocean qualify it fully as a marine species. This thesis describes the multiple evolutionary consequences of the catadromous life-strategy on the genetic structure of the European eel.Recent data based on microsatellite markers show a subtle genetic structure in the European eel following an Isolation-by-Distance (IBD) pattern. But since genetic introgression from the American eel into the European eel has been suggested in the North Atlantic Ocean, reliable tests were developed to define the species status of the European eel. In this first part the interspecific conservation of a set of microsatellites was tested on other Anguilla taxa and the power of species discrimination was assessed. We then applied this knowledge by screening Icelandic and European samples for introgression of American eel. Indications of unequal but restricted hybridisation were detected, likely maintained through selection against hybrids and the preservation of migrational cues.In the second part, the genetic variability and differentiation between various glass and silver eel populations was compared over a broad geographical range (Iceland to Morocco; Spain to Turkey) with temporal replications. In the first instance a pattern of Isolation-by- Distance was detected in adult populations using allozyme markers. Following a more extended geographical sampling, the temporal stability of this pattern could not be confirmed; the temporal differentiation between populations clearly exceeded the geographical component. By sampling recruiting glass eels over a three-year period, a stronger genetic differentiation was found between temporally separated cohorts. Inter-annual differentiation was much higher than the geographical differentiation. The population genetic structure of eel is likely determined by a double process: (I) a large scale pattern of Isolation-by-Time (IBT) among spawning cohorts, and (2) a smaller scale variance in adult reproductive success (genetic patchiness) among seasonally separated cohorts, most likely originating from oceanic and climatic influences.In the third part, the relation between multi-locus heterozygosity (MLH) and fitness components was studied. If an association exists between genetic variability and fitness traits, it is even more important to maintain the population size of European eel. The catastrophic decline of the European eel might be the consequence of an accelerated loss of genetic diversity, with extinction as possible outcome. This hypothesis was tested in a polluted natural environment and in an eel farm. Eel from three Belgian drainage basins were screened for fitness, heavy metal bioaccumulation and genetic variation. There was a strong negative correlation between MLH and bioaccumulation in highly polluted eels. In a second study, aquacultured eel were screened for fitness and genetic variation; MLH was correlated to growth rate. In both studies, this effect was mainly attributed to metabolical enzymes important in the energy cycle, which points to the importance of

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.