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To assess aquatic habitat quality and biodiversity erosion, migratory fishes constitutes excellent biological models. They allow studying the functionality of the continuum river-estuary-ocean because, to fulfill their life cycle, this continuum needs to be of good quality. Those diadromous species are part of the biodiversity of the three environments and among them, anadromous species, which young stages are born and grow in freshwater, represent good biological indicators of river and estuarine ecosystems. During species life cycle, first months of life are a critical period where survival rate can be very low. Those small size individuals have to adapt to new environmental conditions, escape predators and find food rapidly. For anadromous fish, the young stages grow in freshwaters and migrate downstream progressively towards sea waters. Then, in addition to current risks associate to this life stage, they have to face additional risks specific for migratory species: mortality (direct or indirect) or migration delay linked to obstacles, important physico-chemical variations with osmoregulation mechanisms to implement, a large distance to cover travelling through unknown habitats involving increase exposure to predators. Alosa alosa, allis shad and Alosa fallax, twaite shad are anadromous species living in sympatry. Historically they were present on European and North African coasts. Those species did not escape from the global context of decline of diadromous species. Their distribution area has been reduced, both are classified as vulnerable, their exploitation is regulated and restauration program have been established in some rivers. According to large scale modelling studies in Europe, the predictions, within the frame of the global change scenario, suggest an extension of distribution range of twaite shad population and a reduction of the allis shad populations. However, this hypothesis do not take in account the effect of local environmental stress encountered in anthropized watersheds on individuals of the different populations; the individual plasticity being a key factor to enhance resilience capacity at the population level. In Aquitania, population status, especially for allis shad, is worrying with a huge decrease of the number of individuals. While the Gironde-Garonne-Dordogne watershed gathered the largest allis shad population in Europe at the end of the 20th century, the number of spawners dropped drastically since 2006 and a moratorium
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