Résumé: Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.

Résumé: Effective conservation of marine fish stocks involves understanding the impact, on population dynamics, of intra-specific variation in nursery habitats use at the juvenile stage. In some regions, an important part of the catching effort is concentrated on a small number of marine species that colonize coastal lagoons during their first year of life. To determine the intra-specific variation in lagoon use by these fish and their potential demographic consequences, we studied diet spatiotemporal variations in the group 0 juveniles of a highly exploited sparid, the gilthead seabream (Sparus aurata L), during their similar to 6 months stay in a NW Mediterranean lagoon (N = 331, SL = 25-198 mm) and traced the origin of the organic matter in their food webs, at two lagoon sites with contrasted continental inputs. This showed that the origin (marine, lagoonal or continental) of the organic matter (OM) available in the water column and the sediment can vary substantially within the same lagoon, in line with local variations in the intensity of marine and continental inputs. The high trophic plasticity of S. aurata allows its juveniles to adapt to resulting differences in prey abundances at each site during their lagoon residency, thereby sustaining high growth irrespective of the area inhabited within the lagoon. However, continental POM incorporation by the juveniles through their diet (of 21-37% on average depending on the site) is proportional to its availability in the environment and could be responsible for the greater fish sizes (of 28 mm SL on average) and body weights (of 40.8 g on average) observed at the site under continental influence in the autumn, when the juveniles are ready to leave the lagoon. This suggests that continental inputs in particulate OM, when present, could significantly enhance fish growth within coastal lagoons, with important consequences on the local population dynamics of the fish species that use them as nurseries. As our results indicate that continental OM can represent up to 62% of the flesh of the juveniles originating from these ecosystems, particular care should be taken to preserve or improve the chemical quality of riverine inputs to coastal lagoons. (C) 2014 Elsevier Ltd. All rights reserved.

Résumé: Time-area regulations have been introduced to manage stocks of tropical tuna, given the increased use of drifting fish aggregation devices (FADs). However, the consequences in terms of changes in fishing strategies and effort reallocation may not always be as expected. For instance, in the eastern Pacific Ocean, previous studies have highlighted that the increase use of FAD-fishing following the demand for tuna caught without dolphin mortality has raised concerns about the bycatch and the capture of juvenile tuna. In the tropical eastern Atlantic and western Indian Oceans, this study aimed to (1) assess, using before-after analysis, the consequences of previous time-area regulations on FAD sets on the fishing effort allocated to megafauna associated sets, and (2) evaluate through Monte Carlo simulations the potential effect of new regulations banning whale or/and whale shark associated sets. Firstly, we showed that previous time-area regulations, which were mainly implemented during seasons with few whale and whale shark associated sets, generally had thus little effect on the number of megafauna associated sets. Secondly, some simulations, particularly when both whale and whale shark associated sets were banned, predicted consequences of changes in fishing strategy. Indeed, these types of ban could lead to an increase in the number of FAD and free school sets but no change in the tuna catch, as well as a slight decrease in bycatch. These results indicate that an ecosystem approach to fisheries, by taking into account megafauna associated sets and bycatch, should thus be adopted when implementing management or conservation measures.