Tout d'abord, je tiens à remercier Mr Éric ROCHARD et Mr Fréderic SAUDUBRAY, pour m'avoir accueillie au sein de leur établissement. J'adresse un remerciement plus particulier à Éric, qui a fait les démarches administratives nécessaires pour appuyer ma demande de CDD et ce, en dépit des difficultés rencontrées.

Je tiens à remercier également Jérémy LOBRY, directeur adjoint d'unité, pour m'avoir intégrée au sein de son équipe ; mais aussi pour avoir soutenu ma candidature aux côtés d'Éric. Et parce que, tu le vaux bien, merci pour ta gentillesse, ton sourire, ta bonne humeur permanente et contagieuse, et plus encore ! Un grand merci également à Alexis PAUMIER, et Patrick LAMBERT, mes tuteurs de stage, pour m'avoir accompagnée au cours de ces 5 mois. Pour ne pas être dans l'excès, et partir dans un trop plein d'amouuur, je vais résumer ça en quelques mots. Alexis, merci pour ta patience, ta disponibilité, ton investissement, tes conseils, et ton soutient dans ce travail comme dans les démarches de thèse. Si j'en suis là, et que R n'a pas eu raison de moi, c'est quand même un peu grâce à toi ! (Poète!). Patrick, merci pour ta disponibilité, ton expertise, et la richesse de nos échanges, qui m'ont apporté de nouveaux éclairages dans la manière d'appréhender ce sujet. Merci aussi pour tes précieux conseils et tes encouragements. L'Homme expérimental à beaucoup à apprendre de l'Homme expérimenté ! Je remercie également Maud, pour son aide précieuse sur R. Dans les moments de doutes, nos discussions sur le choix de l'analyse la plus judicieuse et pertinente, m'auront été très utiles ! Je crois que ça mérite bien un mojito framboise ça ! Françoise, directrice du projet SHADEAU-FAUNA, pour m'avoir permis de participer à la réunion de projet, et de m'avoir offert l'opportunité de voir des aloses en vrai (si si !).

David, pour nos discussions mutuelles sur les petites aloses ! Merci également d'avoir joué le jeu avec Alexis, et simuler mon entretien de thèse ! Et de manière générale, merci pour ta joie de vivre, (et ton rire qu'on entend dans tout le couloir !) qui mettent toujours de bonne humeur.

De manière plus générale, je remercie toute l'équipe administrative, pour m'avoir permis de continuer en CDD. En particulier, Mme Elodie PLAUT, qui a pris en charge mon dossier en un temps record ! Merci pour votre disponibilité et votre efficacité ! J'adresse également mes remerciements à Elodie, qui a partagé mon bureau au cours de ces 5 mois de stage. Dans les moments de panique, nos échanges mutuels sur le bidouillage du logiciel R auront été salvateurs ! J'espère pouvoir continuer à partager ce bureau avec toi, pendant encore 3 longues années. Constance et Adeline, pour la relecture de ce rapport ; et de manière générale pour leur amitié, et leur soutient infaillible au cours de ces deux années de Master.

Enfin, parce que l'aventure ne s'arrête pas là, je remercie Géraldine LASSALLE et Patrick LAMBERT, pour leur confiance : si j'en crois ce qu'on me dit, la thèse n'est pas une aventure de tout repos, mais je pense que le jeu en vaut la chandelle, que ce soit humainement ou intellectuellement parlant ! Et parce que quelques bières (avec sirop pour les petits joueurs !), ça permet de décompresser, merci à toute l'équipe EABx, pour ces soirées du vendredi soir au PMU, ou ces apéros improvisés ! (Qui ne sont pas prêts d'être terminés !)

TABLE OF FIGURES

Introduction

It is widely accepted that we are entering a period of unprecedented climate changes. Since the beginning of the Industrial Revolution, human activities have significantly impacted the Earth climate [START_REF] Steffen | The Trajectory of the Anthropocene: The Great Acceleration[END_REF]. The global average temperature has increased by approximately 0.85°C, and according to the latest IPCC report, this rise could reach +4.8°C by 2100 (IPCC report, 2014). Although natural systems have already been affected by large natural climate variations, the rapidity of current changes threatens the global biodiversity [START_REF] Root | Fingerprints of Global Warming on Wild Animals and Plants[END_REF][START_REF] Thuiller | Climate Change and the Ecologist: Biodiversity[END_REF][START_REF] Wong | Behavioral Responses to Changing Environments[END_REF]. In response to these environmental changes, species can disperse, adjust behavior to suit the conditions or adapt through genetic evolution [START_REF] Wong | Behavioral Responses to Changing Environments[END_REF][START_REF] Williams | Towards an Integrated Framework for Assessing the Vulnerability of Species to Climate Change[END_REF]. Regarding to these observations, migratory behavior can be considered as a first adaptive response in this changing environment [START_REF] Dingle | What Is Migration?[END_REF].

In the animal kingdom, migration is a ubiquitous biological feature in the life cycle of many species. It can be found in all major taxa, from microscopic crustaceans to the large sea-dwelling mammals and plays a key role in the population dynamics [START_REF] Hansson | Size-Structured Risk Assessments Govern Daphnia Migration[END_REF][START_REF] Horton | Straight as an Arrow: Humpback Whales Swim Constant Course Tracks during Long-Distance Migration[END_REF][START_REF] Brönmark | There and Back Again: Migration in Freshwater Fishes[END_REF]. Although the processes underlying migration are still poorly understood and are a matter of some debates, migration is defined as a cyclical phenomenon which occurs between two or more separate habitats and includes a movement of a large part of the population [START_REF] Begon | Ecology from Individuals to Ecosystems[END_REF]Metacalfe et al, 2002;[START_REF] Secor | Migration Ecology of Marine Fishes[END_REF]. The migratory behavior usually leads to crucial processes in the life cycle as growth, maturation and reproduction [START_REF] Northcote | Migratory strategies and production in freshwater fishes[END_REF].

As most of biological traits, migration is influenced by environmental changes, especially by temperature which plays a key role in initiating and modulating the migration movement [START_REF] Baglinière | Les aloses, Alosa alosa et Alosa fallax spp[END_REF].

Over the last decades, numerous studies have shown an impact of the global warming on a various levels of biological organization, from the individual to the ecosystem levels (H. O. [START_REF] Pörtner | Climate Change Effects on Fishes and Fisheries: Towards a Cause-and-Effect Understanding[END_REF]. It includes physiological changes at the molecular, cellular and organism scale; shift in species distribution, phenology and community (H. [START_REF] Pörtner | Climate Change and Temperature-Dependent Biogeography: Oxygen Limitation of Thermal Tolerance in Animals[END_REF]H. . Pörtner 2002;[START_REF] Hughes | Biological Consequences of Global Warming: Is the Signal Already Apparent?[END_REF][START_REF] Walther | Ecological Responses to Recent Climate Change[END_REF][START_REF] Root | Fingerprints of Global Warming on Wild Animals and Plants[END_REF]. For example, many species have modified their life cycle event, especially birds or insect, which flying, reproducing and spawning earlier in the season [START_REF] Hughes | Biological Consequences of Global Warming: Is the Signal Already Apparent?[END_REF][START_REF] Walther | Ecological Responses to Recent Climate Change[END_REF][START_REF] Root | Fingerprints of Global Warming on Wild Animals and Plants[END_REF]. Changes in migratory patterns, distribution and abundances have also been observed for a large array of fish species from the polar to tropical regions [START_REF] Roessig | Effects of Global Climate Change on Marine and Estuarine Fishes and Fisheries[END_REF]).

During their life cycle, diadromous fishes which migrate up and downstream across long distances undergo considerable pressures, from natural as well as anthropogenic pressures [START_REF] Baglinière | The Allis Shad Alosa Alosa[END_REF]. Dams construction habitat degradation, water pollution deterioration in spawning grounds and unsustainable fisheries have been widely cited as responsible causes of the observed decline in abundance of these species [START_REF] Thorstad | Factors Affecting the Within-River Spawning Migration of Atlantic Salmon, with Emphasis on Human Impacts[END_REF] 2006). The negative effects of these anthropogenic pressures have been amplified by the ongoing global warming ( [START_REF] Groot | A Review of the Past and Present Status of Anadromous Fish Species in the Netherlands: Is Restocking the Rhine Feasible?[END_REF][START_REF] Limburg | Dramatic Declines in North Atlantic Diadromous Fishes[END_REF]. Given this outlook, a better understanding of migration processes is essential for the protection of these endangered populations.

Among diadromous fishes, the Allis shad (Alosa alosa, L. 1758), is an anadromous clupeid characterized by two main migrations. Juveniles first migrate from the river to the sea to complete their growth stage, and then return to their natal river at the age of 5 years to spawn between August and December (Appendix 1). Historically, the populations ranged along the Atlantic coast from Norway to Morocco. Since the beginning of the 19th century many shads populations have declined, leading to a contraction in the species distribution [START_REF] Lassalle | Diadromous Fish Conservation Plans Need to Consider Global Warming Issues: An Approach Using Biogeographical Models[END_REF]. Consequently, the species has been classified as "vulnerable" by the French committee of the International Union for the Conservation Nature (IUCN) The Garonne population, known as the largest Allis shad population in Europe, is not spared by this global decline. Indeed, the population recently collapsed, despite the drastic fishing ban implemented in 2008 to reverse this downward trend [START_REF] Rougier | Collapse of Allis Shad, Alosa Alosa, in the Gironde System (Southwest France): Environmental Change, Fishing Mortality, or Allee Effect?[END_REF].

For a few years, several studies were carried out in the Gironde watershed to investigate the impact of temperature on the reproduction, embryos and larvae survival. These approaches allowed an estimation of the optimal thermal range of the Allis shad and defined the thermal niche of reproduction [START_REF] Jatteau | Thermal Tolerance of Allis Shad ( Alosa Alosa ) Embryos and Larvae: Modeling and Potential Applications[END_REF][START_REF] Lambert | Allis Shad Adopts an Efficient Spawning Tactic to Optimise Offspring Survival[END_REF]Paumier et al, submit). Likewise, knowledge on the factors affecting upstream migration of Allis shad has been provided in several occasions [START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF][START_REF] Acolas | An Assessment of the Upstream Migration and Reproductive Behaviour of Allis Shad ( L.) Using Acoustic Tracking[END_REF][START_REF] Acolas | Upstream Migration and Reproductive Patterns of a Population of Allis Shad in a Small River (L'Aulne, Brittany, France)[END_REF][START_REF] Boisneau | Does Global Warming Impact on Migration Patterns and Recruitment of Allis Shad (Alosa Alosa L.) Young of the Year in the Loire River, France?[END_REF]. However, no studies have characterised yet, the dynamic of this process along the main water course and have linked reproduction and migration processes. The patterns of migration determine the number and the arrival periods of spawners on the spawning grounds. A desynchronization between migration and reproduction may lead to compromise breeding success and therefore survival rate of the young stages [START_REF] Lucas | Migration of Freshwater Fishes[END_REF].

The present study aimed at (i) characterizing migratory patterns of Allis shad spawners to provide a global definition of this process (ii) understanding and evaluating how it influences the expression of the thermal niche of spawning previously established (Paumier et al, submit). Firstly, migration waves along the Garonne River were defined using a MULTIFAN-approach (D. A. [START_REF] Fournier | MULTIFAN a Likelihood-Based Method for Estimating Growth Parameters and Age Composition from Multiple Length Frequency Data Sets Illustrated Using Data for Southern Bluefin Tuna ( Thunnus Maccoyii )[END_REF], and this typology was then regarded throughout the environmental parameters. Secondly, the variability of this process and its impact on the thermal niche of spawning was assessed throughout a clustering. Finally, the impact of migration variability on the breeding success was discussed.

In a broadest sense, this present work is carried out as part of the Alexis Paumier's PhD, which investigates the adaptation of spawning in relation to the larvae and juvenile survival. The results obtained will be used to implement a mechanistic model (questions in red; Fig. 1), identifying the optimal spawning strategy in order to ensure survival of the young stages in a global warming context.

Material and methods

Study area

Migration waves were defined for the Allis shad metapopulation in the Gironde watershed (Fig. 2). The analysis was conducted from the Gironde Estuary to the spawning grounds, on the Garonne River. The Gironde estuary has a total surface area of 625 km 2 (measure at high tide) and extends over 80 km from the sea to the Bec d'Ambès, confluence point of the Garonne and Dordogne Rivers [START_REF] Girardin | Surveillance halieutique de l'estuaire de la Gironde -Suivi des captures 2005-Etude de la faune circulante[END_REF][START_REF] Castelnaud | Analyse de la tendance de l'abondance de l'alose alosa alosa en gironde à partir de l'estimation d'indicateurs halieutiques sur la période 1977-1998[END_REF]. The tide is semi-diurnal and has a 14-day period.

Data have been collected on five sections: Estuary ("EST"), tidal part of the Garonne River ("GMZ"), Garonne Fluvial Zone ("GFZ"), spawning grounds ("SPG"), and Golfech dam ("FP") on the Garonne River. Two sections ("EST" and "GMZ") are under the influence of the dynamic tide and extend over 150 km. The remains three sections ("GFZ", "SPG" and "FP") are under fluvial regulation.

In the tidal part of the river ("GMZ"), hydrodynamic is complex and results of the tide and flow effect combination [START_REF] Castelnaud | Caractéristique des petites pêches côtières et estuariennes de la côte atlantique du Sud de l'Europe . Rapport Final Sites ateliers[END_REF][START_REF] Girardin | Surveillance halieutique de l'estuaire de la Gironde -Suivi des captures 2005-Etude de la faune circulante[END_REF]. The Garonne River is characterized by seven main spawning grounds [START_REF] Carry | Suivi de la reproduction de la grande alose sur la Garonne en[END_REF]. The Golfech dam, located at 270 km from the sea, is the first barrier on this river (Fig. 2). In 1987, fish passes with videos counting equipment were installed at the dam location, to restore diadromous species free movement and ensure reproduction [START_REF] Travade | Conception d'un Ascenseur à Poissons Adapté à l'alose (Alosa Alosa) Sur Un Grand Cours d'eau : I'ascenseur de Golfech Sur La Garonne[END_REF]. Despite this effort, most of fishes reproduce below the dam due to the difficulty to cross this barrier [START_REF] Groux | Actualisation des connaissances sur l'éfficacité et la conception des dispositifs de montaison pour l'alose-Projet LIFE09NAT/DE/000008-Conservation and restoration of the Allis shad in the Gironde and Rhine watersheds -Action A1[END_REF]Paumier et al, submit).

Environmental data

Daily estimates of water temperature (°C) and flows (m 3 . s -1 ) on the Garonne River were used to related the environmental parameters and the upstream migration. Data have been collected from 2003 to 2007, at the Golfech hydroelectric power plant. The average temperature and flow were calculated for each year.

Upstream migration assessment

The migration of Allis shad spawners was estimated using three data types: (i) Catch per unit effort (CPUE) (ii) acoustic monitoring on the spawning grounds ("SPG"), (iii) observations from the fish passes. Data were available from 2003 to 2007 (moratorium, 2008) except on the tidal part of the river, where no data has been collected between 2003 and 2004.

Catches Per Unit Effort (CPUE)

CPUE (Catch per Unit Effort) is a relative abundance index, commonly defined as the ratio between the number of target fishes caught and the sampling effort (days of fishing for a trammel net in our case) (FAO). CPUE data were provided by both professional and nonprofessional fishermen in three sections: Estuary ("EST", only professional), tidal part of the Garonne River ("GMZ") and Garonne Fluvial zone ("GFZ"). Fishes were caught during their upstream migration between March and June, during the lamprey and shad fishery [START_REF] Castelnaud | Caractéristique des petites pêches côtières et estuariennes de la côte atlantique du Sud de l'Europe . Rapport Final Sites ateliers[END_REF][START_REF] Castelnaud | Analyse de la tendance de l'abondance de l'alose alosa alosa en gironde à partir de l'estimation d'indicateurs halieutiques sur la période 1977-1998[END_REF].

Acoustic survey

Population reproduction was estimated by counting the number of spawning acts for five consecutive reproductive seasons. Spawning occurs during the night following a succession of characteristic behavioral sequences characterized by a fast, circular and noisy movement at the surface (Menesson et [START_REF] Mennesson-Boisneau | Migration, répartition, reproduction et caractéristique biologiques des aloses Alosa sp. dans le bassin de la Loire[END_REF]Baglinière and Elie., 2000). Splashing emissions were recorded by direct or indirect observations to assess the spawning activity. To estimate the number of individuals on the spawning ground, we assumed that (i) spawners spread eggs in only one spawning grounds (ii) only one female is involved on a spawning act, (iii) sex ratio is balanced, (iv) each female spawn in average of 7.5 times. [START_REF] Cassou-Leins | Recherches sur la biologie et l'halieutique des migrateurs de la Garonne et principalement de l'alose[END_REF]Menesson et Boisneau, 1990;[START_REF] Chanseau | Essai d'évaluation du stock de géniteurs d'alose Alosa alosa du bassin versant Gironde-Garonne-Dordogne sur la période 1987-2001 et comparaison de différents indicateurs d'abondance[END_REF][START_REF] Acolas | Upstream Migration and Reproductive Patterns of a Population of Allis Shad in a Small River (L'Aulne, Brittany, France)[END_REF].

Fish passes

Since 1987, fish surveys were ensured by video counting equipment installed at Golfech dam. When fishes reached the crossing device, the video equipment system allowed their recorded (Travade et al,1992). An identification was then made by Migado. This monitoring provided a reliable estimation of the migration process throughout the reproductive season [START_REF] Bellariva | Contribution à l'étude Du Déroulement de La Migration et de La Reproduction de La Grande Alose (Alosa Alosa L. ) En Garonne : Étude Prospective de La Dévalaison Des Juvéniles[END_REF].

Modelling approach

Definition of migration waves

Migration wave is defined as a dense flux of fish, which migrates together approximately at the same time, in response more or less, to the same environmental cues in the neighbour area [START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF][START_REF] Baglinière | The Allis Shad Alosa Alosa[END_REF].

Migration wave can be simulated by a Gaussian curve where the mean μ i corresponds to the day of the migration peak, the standard deviation σ i, is related to the migration wave duration , and p i (t) is the proportion of migrating fishes at time t, for wave i (Fig. 3).

The proportion p i,k of migrating fishes from wave i in a site k at time t is calculated by Eq. 2

p 𝑖,𝑘 (t) = 1 √2𝜋σ 𝑘 𝑒 -( 𝑡-μ 𝑘,𝑖 σ 𝑘 ) 2 (Eq.2)
2.4.2. Gaussian mixture models (GMM)

The analysis was based on the MULTIFAN approach, a likelihood based method developed by Fournier, to estimate the growth parameters and the age composition from multiple length frequency data set (D. A. [START_REF] Fournier | MULTIFAN a Likelihood-Based Method for Estimating Growth Parameters and Age Composition from Multiple Length Frequency Data Sets Illustrated Using Data for Southern Bluefin Tuna ( Thunnus Maccoyii )[END_REF][START_REF] Fournier | MULTIFAN-CL: A Length-Based, Age-Structured Model for Fisheries Stock Assessment, with Application to South Pacific Albacore, Thunnus Alalunga[END_REF]. We considered each time series in each site for a given year as a sum of several Gaussians which can be assessed by a Gaussian mixture model. Gaussian mixture model is parametric probabilistic model mainly used to estimate parameters (π k,i , μ k,i , σ k ) of Gaussians components using the iterative expectation maximization (EM) algorithm. [START_REF] Reynolds | Gaussian Mixture Models[END_REF]. A BIC (Bayesian Information criterion) is tied to the model to select the best one. In our study, we can assess our Gaussian mixture by the Eq.3

𝑃 𝑘 (𝑡) = ∑ π 𝑖,𝑘 (𝑡, µ 𝑖,𝑘 , 𝜎 𝑘 𝑛 𝑖=1 ) (Eq.3)
where P k (t) is the relative proportion of fish in the time series from the Gaussian mixture for a site-year combination; k is the site, 𝜋 𝑖,𝑘 the relative importance of migration wave i in the time series from site k, µ i,k and σ ,k the parameters of each Gaussian i.

The model was performed on Rstudio ® software (2.1) using the function "mix" and "mixconstr" of the "Mixdist" packages (Macdonald, 2012). In view of the result of the preliminary analysis, we constrained our model to consider 5 waves and fit the same number of waves for all the time series. Considering the tides influence on the upstream migration [START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF], we considered that migration waves, at least at the start of the migration in estuary, are related to the tidal cycle and then spaced by around 14 days. We therefore constrained the waves peaks (µ) to be spaced by a 14-day period. In addition, to avoid too flat waves which did not respect our definition, the standard deviations σ were constrained to be the same for all waves in the same site for given year (see Eq.3).

Selection of migration waves

Among the 5 waves, some had very low P i values (i.e. number of individuals in the specific migration waves). In order to provide a most reliable definition of the migratory process dynamics, only the wave combination which included 95% of the total individuals has been considered. Beyond this threshold, we assumed that the remaining waves have no ecological meaning.

Stability and variability of migratory patterns

To evaluate the variability of migration waves, 3 analysis were performed: (i) the standard deviation (σ) was compared in each site using a Wilcoxon signed rank test. This first analysis allowed to estimate the signal deformation during the upstream migration. (ii) a hierarchical agglomerative clustering (HAC) based on the Euclidean distance was performed on wave's parameters (μ, σ and π), using the average linkage to assess the inter-annual and inter-site variability. (iii) Migration speeds were calculated on a section of 250 km, using the time lag between the peaks of migration observed in Estuary then, on the spawning grounds (Fig. 5).

Results

The population decline in the Gironde watershed

Since 2005, a decline in fish abundances is observed with minimal abundances recorded in 2007 (Fig. 6). The abundances of fishes were divided by more than five.

Definition of the upstream migration of Allis shad spawners

Upstream migration occurred between the beginning of April and the middle of July, from the Estuary to the spawning grounds. Figure 7 presents an example of the fits of the revised MULTIFAN model according to the fish frequency. The remaining fits are included in Appendix 2. A variable number of migration waves, ranging from 3 to 5, were observed depending on the site-year combination (Fig. 8). On the estuarine section ("EST") and tidal part of the Garonne River ("GMZ") waves were more flattening and spaced by an average of 15-18 days (Appendix 3). On the fluvial section migration period was shorter, and waves were more closely spaced in times with an average of 10 days between each wave. A summary of the definition of the upstream migration from 2003 to 2007 was presented in Figure 8.

1. Signal variability and stability

The Wilcoxon test performed on the standard deviation (σ) have shown a significant difference between the tidal part of the river "GMZ" and both sites; spawning grounds "SPG" (p-value=0.036) and fluvial zone "GFZ" (p-value=0.016. "GMZ" and "SPG" were indeed characterized by a lower average σ value and thereby a lesser dispersed migration wave (Fig. 9). A greater variability was observed on the estuary ("EST"), tidal part of the river ("GMZ") and fish pass ("FP") where σ values ranged from 3 to 8.

The HAC analysis performed on the wave's parameters (u i, day of the migration peak; σ i number of days characterising the wave and p i, proportion of individuals which migrate) , discriminated four groups of site-year combination (Fig. 10). The first group was composed by fish passes "FP" 2004 and 2007; the second by downstream area (Estuary "EST" and tidal part of the river "GMZ"), the third one by the fluvial zone "GFZ" and the last one included upstream area (spawning grounds "SPG" and fish passes "FP"). Contrary to the other site, fish pass was classified in three different groups.

Migration speed

The number of days between the main waves observed at each site varied according to the year. The peak of migration occurred approximately at the same time in the tidal and medium part of the river. It takes place earlier than in the estuary that suggested negative migration speeds. On the upstream area ("SPG" and "FP"), the main wave was occurred at the same time, in downstream area and fish passes.

The number of days between the main wave in the estuary and spawning ground ranged from 11 days in 2006 to 49 days in 2007 (Table 1). The delay allowed to estimate an average speed of 12 km/days. Annual estimate temperatures were similar and varying from 18,5 °C to 20,2 °C. On the contrary, a high inter-annual variability was observed on annual estimates of flows, which ranged from 258,9 m/s to 490 m/s.

Start End

Table 1: Number of days between the main wave observed in the estuarine section and the main wave observed on the spawning ground and estimated average speed (km/days) in relation to the annual estimates of water flows (m 3 /s -1 ) and temperature (°C).

Relationship with the thermal niche of spawning

Global rule and model output

The second HAC analysis performed on the wave's parameters (µ i , σ i and p i ) on the spawning ground allowed separating 2013 from the other years. The same observation is also noticed in the previous results from Paumier et al. The arrival on the spawning ground occurs between the 106 th (in 2015) and the 178 th Julian days (in 2012) which correspond to the 16 th of April and the 27 th of June, respectively. Despite of the inter-annual variability, 3 or 4 waves were observed on the spawning grounds (Table 2, Annexe 4). The main wave occurs between the 125 th day and the 178 th day with a proportion of migratory fishes ranged from 0.41 to 0.79.

Discussion

A new model for migration dynamics

The previous works carrying out the migration of Allis shad were hitherto assessed the upstream migration using a weighted moving average method, highlighting therefore the spawners abundance peak in the distribution. In view of these works, the upstream migration of Allis shad has been described as a dynamic of one or two peaks of migration [START_REF] Mennesson-Boisneau | Migration, répartition, reproduction et caractéristique biologiques des aloses Alosa sp. dans le bassin de la Loire[END_REF][START_REF] Bellariva | Contribution à l'étude Du Déroulement de La Migration et de La Reproduction de La Grande Alose (Alosa Alosa L. ) En Garonne : Étude Prospective de La Dévalaison Des Juvéniles[END_REF][START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF][START_REF] Acolas | An Assessment of the Upstream Migration and Reproductive Behaviour of Allis Shad ( L.) Using Acoustic Tracking[END_REF][START_REF] Acolas | Upstream Migration and Reproductive Patterns of a Population of Allis Shad in a Small River (L'Aulne, Brittany, France)[END_REF]. In the present study, the upstream migration of Allis shad was described by a new original approach. Times series were decomposed from a model originally developed for length frequency data set (MULTIFAN) and have allowed fitting migration waves using the entire distribution (D. A. [START_REF] Fournier | MULTIFAN a Likelihood-Based Method for Estimating Growth Parameters and Age Composition from Multiple Length Frequency Data Sets Illustrated Using Data for Southern Bluefin Tuna ( Thunnus Maccoyii )[END_REF][START_REF] Fournier | MULTIFAN-CL: A Length-Based, Age-Structured Model for Fisheries Stock Assessment, with Application to South Pacific Albacore, Thunnus Alalunga[END_REF]. This In Grey, the wave's parameters which have been excluded in our analysis; in bold the estimated parameters of the main wave; in red the atypical year highlighted by the clustering modelling approach allowed characterizing migration waves at the temporal and spatial scale. The upstream migration has been investigated along the entire main water course, from the Gironde estuary to the spawning grounds, providing therefore a more reliable assessment of the dynamics of this process. This study brings basic knowledge about the migration process and complete the previous works carrying out on the Gironde Estuary [START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF], and spawning grounds [START_REF] Acolas | An Assessment of the Upstream Migration and Reproductive Behaviour of Allis Shad ( L.) Using Acoustic Tracking[END_REF][START_REF] Acolas | Upstream Migration and Reproductive Patterns of a Population of Allis Shad in a Small River (L'Aulne, Brittany, France)[END_REF].

Migratory pattern of the upstream migration in the Garonne River

Our study highlighted the complexity of the migration process. The number of migration waves ranged from 3 to 5 in each site. Estimated parameters, i.e. migration day occurring (µ), duration of migration wave (σ) and its intensity (i.e. the proportion of migratory fish; pi) were variable according to the site and year combination. These results therefore suggested a high inter-annual and inter-site variability, which was confirmed by the both clustering. The inter-site variability was being expressed by (i) a difference in periodicity between the area under marine and fluvial regulation (ii) a deformation of the signal from the estuary to the spawning ground. Likewise, the inter-annual variability was translated into (i) a different number of waves among years for a same site, (ii) a difference in migratory pattern (e.g.

2013).

The migratory behavior is the outcome of internal and external cues that interact and stimulate the movement [START_REF] Lucas | Migration of Freshwater Fishes[END_REF]. It depends on the internal state of the individuals, abiotic conditions, social interactions or reproductive outcomes [START_REF] Secor | Migration Ecology of Marine Fishes[END_REF][START_REF] Nathan | A Movement Ecology Paradigm for Unifying Organismal Movement Research[END_REF]. Taking into this framework, we assumed that the differences between migratory patterns at each site might explain by different factors modulating the signal.

The influence of tide cycle in the downstream area

In the Gironde estuary and tidal part of the river ("GMZ"), migration waves periodicity ranged from 13,7 days to 25, 6 days, that could be consistent with the tidal influence. The impact of the tidal cycle on migration has been highlighted in few cases (Menesson Boisneau, Rochard 2001;Sabatié 1993). [START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF] and [START_REF] Dodson | The Behavior of Adult American Shad ( Alosa Sapidissima ) During Migration from Salt to Fresh Water as Observed by Ultrasonic Tracking Techniques[END_REF] suggested a passive behaviour with the tidal current. Unlike other species (e.g. salmons), shads did not use currents selectively and this oscillating movement would be related to the physical adaptation to freshwater before starting the riverine migration [START_REF] Dodson | The Behavior of Adult American Shad ( Alosa Sapidissima ) During Migration from Salt to Fresh Water as Observed by Ultrasonic Tracking Techniques[END_REF][START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF]. Nevertheless, the great variability observed on the Gironde Estuary, suggested the existence of other factors that modulate the migration. For example, dissolved oxygen concentrations, salinity or turbidity can be stressful for fishes. It may affect the upstream migration and lead fishes to wait more suitable conditions to start the riverine migration [START_REF] Tétard | Poor Oxic Conditions in a Large Estuary Reduce Connectivity from Marine to Freshwater Habitats of a Diadromous Fish[END_REF][START_REF] Maes | Poor Water Quality Constrains the Distribution and Movements of Twaite Shad Alosa Fallax Fallax (Lacépède, 1803) in the Watershed of River Scheldt[END_REF]. An Estuarine Turbidity Maximum (ETM), resulting from a resuspension of particles, often characterizes Macrotidal estuaries, such as the Gironde Estuary. In the Gironde estuary, the ETM is associated with hypoxic conditions under high temperature and low river flow [START_REF] Lajaunie-Salla | Modélisation de la dynamique de l'oxygène dissous dans l'estuaire de la Gironde[END_REF]. This assumption proposed by [START_REF] Tétard | Poor Oxic Conditions in a Large Estuary Reduce Connectivity from Marine to Freshwater Habitats of a Diadromous Fish[END_REF] to explain the longer pattern (18.5 days on average) exhibited by shads in the Loire estuary could be adapted to the Gironde Estuary case. It could explain the migratory pattern in the estuary and tidal part of the river, and therefore the longer periodicity observed some years. However, a further analysis of turbidity and oxygen conditions in the Gironde estuary across the study period will be requisite to confirm this hypothesis.

Importance of biological factors in the riverine stage

From the medium part of the river to the spawning grounds, waves were spaced by an average of 10 days and were less dispersal (decreasing on the standard deviation), compared to the estuary and tidal part of the river. Such migratory patterns could have resulted from (i) the tidal dissipation in the medium and higher part of the river, (ii) a difference in the nature and importance of cues modulating and triggering the movement. On the fluvial section, tidal range has no effect. The internal rhythm of migration is modulated by other external factors such as water temperature and water discharge, which are widely cited as the main factor affecting the upstream migration of Allis shad (Menesson-Boisneau et Boisneau;[START_REF] Mennesson-Boisneau | Migration, répartition, reproduction et caractéristique biologiques des aloses Alosa sp. dans le bassin de la Loire[END_REF]Sabatié, 1993;Menesson-Boisneau et al, 2000). The latter interacts with biological factors (e.g. maturity state), whose the importance increases as migration proceeds upstream (Baglinière 2001, Baglinière andElie, 2003). Some physiological and internal modifications (e.g. modification in liver and muscles structure) took place during the riverine stage to support the energetic expenditures of spawning runs and could modulate the movement at the individual scale (Baglinière, 2001). In addition, shads, like most of the migratory fishes (e.g. Herrings, sardines, salmons..) traveling in schools during the riverine stage, to facilitate social transmission and learning of migration routes; increase propulsion capacities by coordinating their movement, or evade threats (e.g. predators) [START_REF] Lucas | Migration of Freshwater Fishes[END_REF][START_REF] Secor | Migration Ecology of Marine Fishes[END_REF]. This observation could justify the shorter waves observed in these two sites. It is, however, important to consider the gap in time series on the medium part of the river, between 2003 and 2004, because it could be explained the significant difference observed between the medium and the tidal part of the river.

As we suggested before, the migration process resulted on a combination of several factors. Environmental conditions fluctuate among the year and explain the inter-annual variability. Schools are dynamic in membership and can dissipate or merge with other aggregation (e.g. Atlantic herring) [START_REF] Makris | Critical Population Density Triggers Rapid Formation of Vast Oceanic Fish Shoals[END_REF][START_REF] Secor | Migration Ecology of Marine Fishes[END_REF]. Temporal and spatial dynamic scale must be considered to explain the dynamic and intensity of waves.

The variability at the fishway

Our study highlighted a great inter-annual variability on the migratory pattern at the fish passes compared to the other site. The clustering did not classify the site-year combination in the same group (see Fig. 10). Such separation may be explained by a great variability in the wave flattening and the occurring day of the migration peak. These results differ from what has been observed in the Mondego River (Portugal), where an important proportion of fishes crossed the device at the same period, when the flow conditions became more suitable [START_REF] Stratoudakis | Exploited Anadromous Fish in Portugal: Suggested Direction for Conservation and Management[END_REF]. According to this study we should observe a lesser spread migration waves with important pi-value. These results therefore suggested a highly variable temporal window within which environmental conditions enable passage of individuals. In addition, weir fishways were documented to be stressful for shads and other fishes which traveling in schools [START_REF] Groux | Actualisation des connaissances sur l'éfficacité et la conception des dispositifs de montaison pour l'alose-Projet LIFE09NAT/DE/000008-Conservation and restoration of the Allis shad in the Gironde and Rhine watersheds -Action A1[END_REF]. The difficulty to cross these barriers may be reflected by the extents meandering movements below the dam, as well as a stationary behavior. However, some other factors should be considered to explain the migratory pattern observed at the dam. A low light intensity, unfavourable hydraulic conditions at the device, or a unsuitable fishway dimensioning has now documented to affect the behavior of shad below the dam [START_REF] Groux | Actualisation des connaissances sur l'éfficacité et la conception des dispositifs de montaison pour l'alose-Projet LIFE09NAT/DE/000008-Conservation and restoration of the Allis shad in the Gironde and Rhine watersheds -Action A1[END_REF].

The Individual Based Model implementation

This study aimed at providing a global definition of the migratory process, to implement the Individual Based Model developed by Paumier et al. (Fig. 1). The variability of the migratory patterns across the different sector emphasized the complexity of the migratory process and the difficulty to grasp it. This observation was besides confirmed by the analysis of migratory patterns on the spawning ground for 14 reproductive seasons. Despite this variability, some stability is observed and allows us to give reliable estimation of the migration process on the spawning ground. Considering our results, we can define the following general rule (i) the arrival of spawnners on the spawning ground mainly takes place in 3 or 4 successive waves, with an average of 10-day intervals. (ii) the first wave is often the smaller one and occurs around the May 4th; (iii) the intensity of migration waves (pi) is the most fluctuating parameters (iv) the standard deviation σ ranged around 4 days.

Migration cost and swimming capacity

The analysis of migration speeds showed an average speed of 12 km/day. During the observation period differences were observed, with relatively low speeds in 2005 and 2007, and a higher average speed observed in 2006. The migration speed obtained was similar to the previous monitoring in the Garonne River for the same 250 km section [START_REF] Bellariva | Contribution à l'étude Du Déroulement de La Migration et de La Reproduction de La Grande Alose (Alosa Alosa L. ) En Garonne : Étude Prospective de La Dévalaison Des Juvéniles[END_REF]). However, our estimation was lower than in the Gironde Estuary [START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF] and Loire River (Menesson, 1993), which estimated an average speed of 21km/days. Nevertheless, average speeds in these both studies were calculated for smaller sections; 70 km and 150 km respectively. These lower values may be explained by a greater expenditure of energetic stores, regarding to the distance travelled [START_REF] Bellariva | Contribution à l'étude Du Déroulement de La Migration et de La Reproduction de La Grande Alose (Alosa Alosa L. ) En Garonne : Étude Prospective de La Dévalaison Des Juvéniles[END_REF]. This assumption has been confirmed by several studies carrying out of Alosa sapidissima in the Connecticut River [START_REF] Leonard | Effects of Migration Distance on Whole-Body and Tissue-Specific Energy Use in American Shad ( Alosa Sapidissima )[END_REF][START_REF] Castro-Santos | Modeling Migratory Energetics of Connecticut River American Shad (Alosa Sapidissima): Implications for the Conservation of an Iteroparous Anadromous Fish'. Edited by Bror Jonsson[END_REF]. These studies attested of depletion in energy stores with the migration distance and emphasized the importance of hydro-climatic conditions such as water flow or temperature. Regarding to this observation, the reduction in migration speed in 2007, could be explained by two ways (i) the high-water flow recorded in 2007, may be involved in a greater energy expenditure leading to a reduction in migration speed (ii) the high-water flow interrupted the upstream migration and inducing a lower migration speed.

Nevertheless, the average swimming speed was established for each year, using the time lag between the main waves observed on the estuary, then on the spawning ground. This method, widely used in the literature to estimate swimming speeds [START_REF] Bellariva | Contribution à l'étude Du Déroulement de La Migration et de La Reproduction de La Grande Alose (Alosa Alosa L. ) En Garonne : Étude Prospective de La Dévalaison Des Juvéniles[END_REF][START_REF] Rochard | Migration anadrome estuarienne des géniteurs de grande alose Alosa alosa, allure du phénomène et influence du rythme des marées[END_REF], seems particularly simplistic given the complexity of migration processes. We indeed assumed the main wave remained the same over time, but our study emphasized that it was not evident. An approach considering all waves should be more appropriate and should allow estimating migration speeds more reliably. Due to the difficulty to perform such exercise, and owing to time constraints, we did not implement this method.

Focus on the linkage between migration and reproduction

On the spawning grounds, migration waves and migratory patterns varied depending on the year and may be related to the hydro-climatic conditions. For example, in 2013, the atypical migration may be explained by extreme-weather conditions in the Gironde watershed (significant higher flow associates with cold temperature). Thus, the atypical migration could partially explain the atypical spawning season observed in 2013 (Paumier et al, submit). For the other atypical reproduction (Garonne 2008;2014 and[START_REF] Lajaunie-Salla | Modélisation de la dynamique de l'oxygène dissous dans l'estuaire de la Gironde[END_REF], the upstream migration took place in a usual way. This observation can confirm the hypothesis assumed by Paumier, that other factors such as stream velocity blocked the reproduction (Paumier et al, submit), and did not affect the migration. In view of this, migratory process seems to be more flexible regarding to the environmental conditions.

Impact of the migration patterns on the breeding success.

As previously highlighted, phenology changes (i.e. the time delay of a process) in migration and reproductions are notably assumed to be an efficient response to environmental changes as temperature and flow fluctuations. Despite these two processes are commonly studied in a context of global warming, the effect of migration on reproduction is poorly documented. The present study demonstrated the high variability of migration waves features among years, and then reflected upon the effect of these migratory patterns on the reproductive success. A valuable way to assess this impact, would be to compute survival of the early stages [START_REF] Jatteau | Thermal Tolerance of Allis Shad ( Alosa Alosa ) Embryos and Larvae: Modeling and Potential Applications[END_REF][START_REF] Lambert | Allis Shad Adopts an Efficient Spawning Tactic to Optimise Offspring Survival[END_REF], as a measure of reproductive success according to the observed migration pattern for each year. Different hypothesis of spawning behavior (random i.e. a constant daily probability of spawn; optimal i.e. spawn in the best conditions) can be considered. To perform such analysis, we will compute early stage survival for shifted migration patterns (e.g. thermal conditions of 2007 with the migration pattern of 2015). The difference of survival between observed and shifted patterns will allow evaluating the influence of migration in reproductive success.

  1. Introduction ........................................................................................................................ 2. Material and methods ......................................................................................................... 2.1. Study area .................................................................................................................... 2.2. Environmental data ......................................................................................................... 2.3. Upstream migration assessment .................................................................................. 2.3.1. Catches Per Unit Effort (CPUE) .......................................................................... 2.3.2. Acoustic survey .................................................................................................... 2.3.3. Fish passes ........................................................................................................... 2.4. Modelling approach..................................................................................................... 2.4.1. Definition of migration waves ............................................................................. 2.4.2. Gaussian mixture models (GMM) ....................................................................... 2.4.3. Selection of migration waves ............................................................................... 2.5. Relationship with the thermal niche of spawning ....................................................... 3. Results ................................................................................................................................ 3.1. The population decline in the Gironde watershed ....................................................... 3.2. Definition of the upstream migration of Allis shad spawners ..................................... 3.2 1. Signal variability and stability ................................................................................ 3.2.2. Migration speed ........................................................................................................ 3.3. Relationship with the thermal niche of spawning ....................................................... 4. Discussion ........................................................................................................................... 4.1. A new model for migration dynamics ......................................................................... 4.2. Migratory pattern of the upstream migration in the Garonne River ........................... 4.2.1 The influence of tide cycle in the downstream area .................................................. 4.2.2. Importance of biological factors in the riverine stage .............................................. 4.2.3. The variability at the fishway .................................................................................. 4.2.4. The Individual Based Model implementation ........................................................ 4.3. Migration cost and swimming capacity .................................................................... 4.4. Focus on the linkage between migration and reproduction....................................... 5. Impact of the migration patterns on the breeding success ............................................

Figure 1 :Figure 2 :Figure 3 :Figure 4 :Figure 7 :Figure 8 :Figure 9 :Figure 11 :Figure 12 :

 12347891112 Figure 1: Conceptual diagram representing the mechanistic model developed by Paumier et al. ................................................................................................................................................ 3 Figure 2: Location of the study area in the Gironde watershed. Numbers correspond to the 3 data types used for the analysis. ................................................................................................. 4 Figure 3: Diagram of the definition of a migration wave in the present study: migration wave was approached by a Gaussian curve type. Mean (μi), squared (σi) and density probabilities (pi) corresponds to the occurring days of wave migration wave duration and the proportion of migrating fishes at time t, for wave i. ....................................................................................... 3 Figure 4: Diagram of the main steps used to construct our model. .......................................... 4 Figure 5: Diagram of the method used in the present study to assess the migration speeds from the Gironde Estuary to the spawning grounds .................................................................. 5 Figure 6: Abundance of fishes per year from 2003 to 2007. .................................................... 5 Figure 7: Example of fits obtained in 2006 by the model (red) and the associated abundance of fish (blue) for each sector. a) Estuary, b) Tidal part of the River, c) Fluvial zone, d) Spawning grounds, and e) Fish passes. The solids vertical lines indicate the estimated mean days for each wave, and the vertical broken line the means for waves excluded in this analysis. The red fill rectangle corresponds to the migration period. The dark arrow indicates the direction of migration, from downstream to upstream. ....................................................... 2 Figure 8: Estimated parameters of Allis shad migration waves in the Gironde watershed from 2003 to 2007. Means (in days) and pi (proportion of fishes which migrate) are estimated from a Gaussian mixture using the package Mixdist. The colourless circles correspond to the waves which were excluded in the present study. ..................................................................... 3 Figure 9 : Boxplot investigating the site effect on the migration wave duration. The results of the wilcoxon test are represented by the letters above the boxplot. The standard deviation (σ), in "GFZ" and "SPG" appear to be lower compared to the other sites. ...................................... 4 Figure 10: Cluster dendrogram from the agglomerative hierarchical clustering analysis (HAC) performed on the Gaussian estimated parameters. The dashed horizontal line (dissimilarity threshold) separated 4 groups. ............................................................................. 4 Figure 11: Main waves observed in each sector from 2003 to 2007. Migration speeds were calculated from the Gironde Estuary to the spawning ground, distant from 250 km. ............... 5 Figure 12: Cluster dendrogram from the agglomerative hierarchical clustering separating the site-year combination on the gaussian estimated parameters. The dashed horizontal line (dissimilarity threshold) separated 2 groups. Group 1 was composed of the SPG 2013 and group 2 by the remains site-year combination. .......................................................................... 6

Figure 1 :

 1 Figure 1: Conceptual diagram representing the mechanistic model developed by Paumier et al.

Figure 2 :

 2 Figure 2: Location of the study area in the Gironde watershed. Numbers correspond to the 3 data types used for the analysis.

Figure 3 :

 3 Figure 3: Diagram of the migration wave definition in the present study: Migration wave was approached by a Gaussian curve type. Mean (μ i ), squared (σ i ) and density probabilities (pi) corresponds to the occurring days of wave, migration wave duration, and the proportion of migratory fishes at time t, for wave i.

Figure 4 :

 4 Figure 4: Diagram of the main steps used to construct our model.

Figure 5 :

 5 Figure 5: Diagram of the method used in the present study to assess the migration speeds from the Gironde Estuary to the spawning grounds

Figure 6 :

 6 Figure 6: Abundance of fishes per year from 2003 to 2007.

Figure 7 :

 7 Figure 7: Example of fits obtained in 2006 by the model (red) and the associated abundance of fish (blue) for each sector. a) Estuary, b) Tidal part of the River, c) Fluvial zone, d) Spawning grounds, and e) Fish passes. The solids vertical lines indicate the estimated mean days for each wave, and the vertical broken line the means for waves excluded in this analysis. The red fill rectangle corresponds to the migration period. The dark arrow indicates the direction of migration, from downstream to upstream.

Figure 8 :

 8 Figure 8: Estimated parameters of Allis shad migration waves in the Gironde watershed from 2003 to 2007. Means (in days) and pi (proportion of fishes which migrate) are estimated from a Gaussian mixture using the package Mixdist. The colourless circles correspond to the waves which were excluded in the present study.

Figure 9 :

 9 Figure 9 : Boxplot investigating the site effect on the migration wave duration. The results of the wilcoxon test are represented by the letters above the boxplot. The standard deviation (σ), in "GFZ" and "SPG" appear to be lower compared to the other sites.

Figure 10 :

 10 Figure 10: Cluster dendrogram from the agglomerative hierarchical clustering analysis (HAC) performed on the Gaussian estimated parameters. The dashed horizontal line (dissimilarity threshold) separated 4 groups.

Figure 11 :

 11 Figure 11: Main waves observed in each sector from 2003 to 2007. Migration speeds were calculated from the Gironde Estuary to the spawning ground, distant from 250 km.

Figure 12 :

 12 Figure 12: Cluster dendrogram from the agglomerative hierarchical clustering separating the site-year combination on the gaussian estimated parameters. The dashed horizontal line (dissimilarity threshold) separated 2 groups. Group 1 was composed of the SPG 2013 and group 2 by the remains site-year combination.

TABLE OF CONTENTS

 OF

Table 2 :

 2 Model output table for the spawning ground data set available from 2003 to 2007.

ACKNOWLEDGEMENTS

Le stage touchant à sa fin, je tiens à remercier toutes les personnes qui m'ont apporté leur aide et leur soutien dans la réalisation de ce travail et qui ont contribué à la poursuite de celuici en CDD.


Gironde Estuary

Alain Lechêne

Laure Carassou

Éric Quinton

THE « MARSH » DATABASE : NEKTON COMMUNITY STATUS IN TWO TIDALLY RESTORED MARSHES FROM THE

The " marsh " database: nekton community status in two tidally restored marshes from the Gironde estuary, southwest France

A. Lechêne, Laure Carassou, Eric Quinton

INTRODUCTION

Natural intertidal marshes display paramount ecological functions as transition systems between marine and freshwater environments on the one hand, and between aquatic and terrestrial systems on the other hand. These ecological functions are mostly supported by an intensive primary and secondary productivity, including detritic production, and by marshes' morphological and structural habitat diversity. Intertidal marshes and adjacent mudflats also represent important nursery areas, i.e., feeding and growth habitats, for juveniles of many fish and macro-crustacean species [START_REF] Kneib | The role of tidal marshes in the ecology of estuarine nekton[END_REF]. Accordingly, intertidal marshes are considered essential habitats for sustaining adult fish and crustacean populations in coastal marine environments [START_REF] Boesch | Dependence of fishery species on salt marshes: The role of food and refuge[END_REF], among which populations of species supporting fisheries of significant economic value in Europe, such as European seabass (Dicentrarchus labrax Linnaeus, 1758), Thin lipped mullet (Liza ramada Risso, 1826), sardine (Sardina pilchardus Walbaum, 1792) and grey shrimp (Crangon crangon, Linneaus, 1758) [START_REF] Cattrijsse | European intertidal marshes: a review of their habitat functioning and value for aquatic organisms[END_REF].

Despite their recognized ecological importance, natural intertidal marshes severely regressed at a global scale. In Europe in particular, coastal marshes were massively dyked over almost a millennium, mostly with the purpose of increasing agricultural land surface. This process of dyking coastal marshes and building damming systems to drain the lands gained on the sea is designated in Europe as 'polderization', from the deutsch term 'polder', as the Netherlands historically initiated the engineering expertise on coastal marsh dyking. This historical polderization of coastal wetlands resulted in the creation of approximately 15,000 km 2 of littoral polders in Europe [START_REF] Goeldner-Gianella | Dépoldériser en Europe occidentale De-polderizing in Western Europe[END_REF]. This polderization process however stopped around the 1970s, concomitant with the adoption by many countries of the Ramsar convention on wetlands in 1971. More recently, in some countries of western Europe and north America, an inverse trend is even being observed : some polders are given back to estuaries or coastal seas. This is done sometimes accidentally through the impact of storms on deteriorated or poorly managed dykes, and sometimes deliberately through concerted restoration actions. In Europe, this tendency is nowadays designated through the term 'depolderization', which includes both accidental and deliberate cases [START_REF] Goeldner | Réouverture de polders et restauration du schorre en Angleterre : une technique paradoxale de défense contre la mer / Managed reheat programmes and the restructuring of saltmarshes in England[END_REF][START_REF] Verger | Conceptions successives de l'aménagement des vasières littorales par les société riveraines 5[END_REF]. Few of those cases actually benefit from scientific surveys aiming at monitoring the impact of depolderization on ecological functionalities of restored marshes.

When implemented, monitoring programmes often take place during the first years following the restoration of the marsh, with the duration of surveys typically limited to five years [START_REF] Simenstad | Functional Equivalency Trajectories of the Restored Gog-Le-Hi-Te Estuarine Wetland[END_REF]. The nekton in particular has been scarcely analyzed in the context of marsh restoration operations (French, 2006), and the few studies available were conducted in the United-States with very rare case studies in Europe [START_REF] Colclough | Fish utilisation of managed realignments[END_REF]. This is partly due to methodological issues related to nekton sampling in marshes where environmental conditions strongly fluctuate, and where habitat conditions and accessibility of sampling sites evolve very quickly [START_REF] Rozas | Estimating densities of small fishes and decapod crustaceans in shallow estuarine habitats: A review of sampling design with focus on gear selection[END_REF].

In the Gironde estuary, two marshes were tidally restored accidentally, and supported nekton monitoring programmes since 2008 : the Mortagne-sur-Gironde marsh and the north part of the Nouvelle island. The Mortagne-sur-Gironde marsh is located on the right side of the mesohaline section of the Gironde estuary.

Covering 191 hectares, it was dyked in 1966 and used for agricultural harvesting for more than 30 years. Its protective dyke broke off during a storm in December 1999. The north Nouvelle island marsh is located in the oligohaline section of the estuary. Its protective dyke also broke off accidentally during a storm in 2010.

Biological monitoring programmes were conducted in these two marshes between 2008 and 2016, in order to assess if the depolderization process resulted in the restoration of marshes nursery function for estuarine and coastal fishes and macrocrustaceans. The 'MARSH' database gathers all information collected during those surveys (from 2008 to 2016), including nekton samples.

MAIN FEATURES AND POTENTIAL USE OF THE DATABASE

The database identifies all technical data related to sampling methodologies (fishing techniques, conditions and dates), as well as characteristics of the samples collected (taxa, fish abundance and weight, and individual length and morphometric dimensions).

The data can potentially be used to :

-describe nekton assemblages characterizing dyked marshes and natural intertidal (natural marshes and mudflats) and subtidal areas in a macrotidal estuary; -compare nekton assemblages among anthropized, restored and natural habitats within the same estuary;

-study the temporal dynamics of nekton assemblages in tidally restored marshes;

-study the size distribution of several species (e.g. Liza ramada, Dicentrarchus labrax, Pomatoschistus microps, Palaemonetes varians, Palaemon longirostris) within diked and other intertidal habitats of the Gironde estuary;

-study length-weight relationships of multiple fish and macrocrustacean species.

STRUCTURE OF THE DATABASE

GENERAL DESCRIPTION

Fishes and crustaceans (crabs, shrimps, crayfish) are collected in the field with a specific fishing gear. A fishing operation therefore corresponds to the use of a particular fishing gear in a defined spatial ( site) and temporal (campaign) context, which results into the collection of a sub-set of individuals from multiple species present in the natural environment, this sub-set being refered to as a biological sample.

All individuals composing those biological samples are identified to the lowest taxonomic level possible (species the most often), counted, and measured. Those measurements are done directly on the field for large-sized individuals (length > 60-70 mm), or back at the laboratory for smaller individuals. In the case of very abundant species, only a sub-set of individuals is being measured. Besides length, other morphological characteristics are sometimes measured or noted, for example individual weight, sex or the presence or absence of eggs (for shrimps).

Based on this procotol, for a given fishing operation, a same species can appear in both the sample fraction directly processed on the field, and in the sample fraction processed back at the laboratory (which is being frozen for archiving purpose). In some instances, this same species can also be sub-divided in the database into categories of size, in order to keep track of potential differences in sub-sampling procedures applied to each of these size fractions. For example, sub-categories « Dicentrarchus labrax L > 60 mm » and « Dicentrarchus labrax L < 60 mm » can be recorded within the same fishing operation.

Two types of fishing operations are distinguished : stationary and trawled operations. Stationary fishing operations are performed at a recurrent and fixed location identified as a fishing station. Several replicates (i.e., fishing operations realized at a similar period and location) are often associated to a same fishing station. Fishing stations are characterized by their fixed geographic coordinates (latitude, longitude). Trawled fishing operations are mobile events, relying on the use of trawled fishing gears which trajectory (or trawl lines) cannot be exactly replicated. Trawled fishing operations are described by polylines with coordinates achieved at successive times.

Abiotic environmental measures are also collected during fishing operations : water height (for intertidal and dyked areas) or depth (for subtidal areas), water temperature and salinity, etc. For stationary fishing operations, abiotic variables are measured either directly at the fishing station, or at a close location that can be common to several stationary fishing stations. Water height is often specifically measured for each stationary fishing operation replicate (as replicates can be realized at different times). For each trawled fishing operation, abiotic factors are usually averages of several measures collected along the trawl line.

Fishing operations can be performed in the context of different research projects. Each research project (e.g., « capalest », « ile_nouvelle ») is structured in several sampling campaigns (e.g., « capalest_may11 », « ilenouv_may11»). Each fishing operation can therefore be associated to one or several fishing campaigns (as associated to one or several research projects). For instance, fishing operations conducted at the 'Ile Nouvelle' site in May 2011 are associated to both May 2011 campaign of the « ile_nouvelle » project (« ilenouv_may11 » in the database) and at the May 2011 campaign of the « capalest » project (« capalest_may11 »).

DATA SETS

The MARSH database comprises data produced by several research projects conducted between 2008 and 2016.

The sampling protocols have evolved over time during this period, with protocols being described in several reference documents (Table 1).

GEOGRAPHIC LOCATION

Fishing operations associated to GPS coordinates are illustrated in Figure 1. A total of 90 fishing stations and 100 trawls are included in the database.

NUMBER OF FISHING OPERATIONS BY RESEARCH PROJECT

Fishing operations, as included in the database, correspond to the association between a fishing station or trawl line, a fishing gear, and a date. Therefore, if a fishing operation is conducted by two fishing gears, two records will appear in the database. The number of fishing operations for each research project is detailed in Table 2. ). The total number of fishing operations is therefore 1 483 (and not 1 616 that would correspond to the addition of numbers from Table 1).

The actual number of fishing operations, without considering fishing gear used, sums to 1 009, distributed as in Table 3. The database comprises 8 620 samples (taxon × fishing operation combination), associated to 98 different taxa. A total of 80 823 biological specimens are identified and individually recorded, essentially for body length measurements.

Fishing operations cover a period from 2008 to 2016, with a frequency illustrated in Figure 2.

DESCRIPTION OF TABLES

STRUCTURE OF THE DATABASE

THE « CAMPAGNE » TABLE (CAMPAIGNS)

THE « ECHANTILLON » TABLE (SAMPLES)

List of samples collected, ordered by taxa or taxa subtypes This field specifies if the probe is immersed in water (value = « eau ») or emerged in the air (value = « air ») at the time of measurement. If this information is not available, the value is NULL. This field is needed in cases when measurement probes are installed on stationary locations submitted to tidal influences.

THE « H_EAU » TABLE (WATER HEIGHTS)

THE « INDIVIDU » TABLE (INDIVIDUALS)

THE « MESURE_PARAMETRE » TABLE (MEASUREMENT PARAMETERS)

To select values collected at high tide only (when the probe is immersed in water), select values == « water »

THE « OPERATION_PECHE » TABLE (FISHING OPERATIONS)

List of fishing operations This field only concerns samples collected with double fykes. The immersion coefficient (cim) is a ratio varying from 0 to 1, corresponding to the proportion of the fishing period during which the fyke is immersed allowing the sampling of aquatic organisms. See [START_REF] Lechêne | Trajectoire de restauration des marais intertidaux : réponse du necton à la dépoldérisation dans l'estuaire de la Gironde[END_REF].

Field

volfil Numeric Filtered water volume (m 3 ) This field only concerns some specific fishing gears : winged fyke net, pushnet or frame net [START_REF] Rimond | Étude des peuplements de poissons des habitats intertidaux de l'estuaire de la Gironde[END_REF]

THE « TRAIT_GEOM » TABLE (GEOMETRIC LINES)

GPS coordinates measured along trawl lines

Field

CONCLUSIONS

The MARSH database represents a unique source of information regarding the dynamics of nekton assemblages in restored marshes of Mortagne-sur-Gironde and Ile Nouvelle, and in the Gironde estuary in general. The large number of observations collected within a relatively short period of time in multiple habitats indeed allows for a complete picture of the Gironde estuary status. Several scientific publications are based on those data (Lechêne et al., 2018a[START_REF] Lechêne | Change in fish functional diversity and assembly rules in the course of tidal marsh restoration[END_REF], including a PhD dissertation in 2017 [START_REF] Lechêne | Trajectoire de restauration des marais intertidaux : réponse du necton à la dépoldérisation dans l'estuaire de la Gironde[END_REF].

ACKNOWLEDGEMENTS

Figure 1 :

 1 Figure 1: Fishing operations included in the MARSH database.

Illustration 3 :

 3 Figure 2: Monthly distribution of fishing operations included in the MARSH database

  operation code, made of a location abbreviation, month and year, and informations about the fishing gear Example gears used to collect the biological sample When the two parts of double fykes are considered separately, nb = 0.5 dateh_debut Timestamp Date and hour of fishing gear deployment dateh_fin Timestamp Date and time when fishing gear stops operating

  Data are provided in SQL format (export from Postgresql 9.5), allowing for their identical recovery. Data are published under Open Licence 3 , with compulsory mention of data producer at export : Irstea -50 avenue de Verdun -33612 CESTAS Cedex -France. Data freely downloadable at : https://www.zenodo.org/ record /1413514 3 https://www.etalab.gouv.fr/wp-content/uploads/2014/05/Open_Licence.pdf

Fish

  surveys were funded by the Region Nouvelle-Aquitaine, the General Council of Gironde, the Adour-Garonne Water Agency and the French Agency for Biodiversity. The General Council of Gironde (Sébastien Fourcade, Sylvain Cardonnel, Bruno Augizeau) provided technical assistance in field work on the Nouvelle island. The CEN Poitou-Charentes (Thomas Hérault) and the Conservatoire du littoral (Joël Carlu, Sabine Allou) took part in the data collection in the Mortagne marsh area. The authors are indebted to many colleagues of Irstea (Jérémy Don, Flore Rimond, Nicolas Deligne, Rémy Garnier, Stéphane Bons, Romaric Le Barh) involved in field sampling and laboratory work.

Table 1 :

 1 List of reference documents describing sampling protocols used to produce the MARSH database

	Project	Period	Reference documents	Comments
	Margo	2008-2009	(Decreton, 2009; Lechêne,	The database structure described in Decreton
			2017)	(2009) has been fully revised
	Ile Nouvelle V0 2009-2013	(Chapalain, 2013; Lechêne,	Only fishing data collected between 2011 and
			2017, 2015)	2013 were used in Lechêne (2017)
	Remob	2010-2012	(Lechêne et al., 2011, 2012)	-
	Capalest	2011-2012	(Rimond, 2013; Lechêne,	-
			2017; Lechêne et al., 2018b)
	Renomares	2013	(Carlu, 2013)	Training period realized at the 'Conservatoire
				du Littoral' and 'Conservatoire Régional des
				Espaces Naturels' (CREN) Poitou-Charentes,
				in partnership with Irstea
	Marino	2016	(Allou, 2016)	Training period realized at the 'Conservatoire
				du Littoral' and 'Conservatoire Réginal des
				Espaces Naturels' (CREN( Poitou-Charentes,
				in partnership with Irstea

Table 2 :

 2 Number of fishing operations for each research project included in the MARSH database, considering fishing gear used.

	Project	Number of fishing operations
	Capalest	757
	Ile_nouvelle_v0	340
	Margo	36
	Marino	70
	Remob	259
	Renomares	154
	A total of 133 fishing operations are common to projects « Capalest » and « Ile_nouvelle » (64 in 2011 and 69 in
	2012

Table 3 :

 3 Actual number of fishing operations for each research project, without considering fishing gear used.

	project	Number of fishing operations
	Capalest	485
	Ile_nouvelle_v0	222
	Margo	36
	Marino	12
	Remob	254
	Renomares	76

  Table of physico-chemical variables associated to fishing stations

	Field	Type	Definition
	mesure_parametre_id Serial	Incremental key
	libelle_mesure	Varchar	Measurement code, made of a station abbreviation (fk_station_id),
			month/year and optional complementary information
			Example : christoly_oct11_smp2_p2
	fk_station_id	Varchar	Station code
	Dateh	Timestamp Date-hour of measurement
	heau	Numeric	Water height (m) between bottom and surface
	heau_sonde	Numeric	Water height (m) above the pressure sensor of the probe
	temperature	Numeric	Temperature (°C) measured by the probe in air or water (see « milieu »
			field)
	conductivite	Numeric	Conductivity (mS/cm)
	conductance_sp	Numeric	Specific conductance (mS/cm) at 25°C
			As conductivity measurements depend on temperature, specific conductance
			corresponds to a « corrected » conductivity measure allowing the
			comparaison of waters with different temperature
	salinite	Numeric	Salinity (no unit)
	milieu	Varchar

THE « STATION » TABLE (STATIONS)

  .

	Field		Type	Definition
	famille		Varchar Taxonomic family, in Latin
	ordre		Varchar Taxonomic order, in French
	sousclasse		Varchar Taxonomic subclass, in French
	classe		Varchar Taxonomic class, in French
	sousphylum		Varchar Taxonomic subphylum, in French
	groupe		Varchar Taxonomic group, in french
	longueur guilde_ecologique surface longueur_type commentaire	Numeric Varchar Ecological guild, in French Examples : « especes_migratrices_amphihalines » Trawl line length (m) (diadromous species), « especes_marines_stenohalines » (marine stenohaline This field only concerns trawled fishing operations Numeric species) Sampled surface (m 2 ) Varchar Indicates the length measurement type to select for the taxa of interest (either This field only concerns trawled fishing operations Varchar fork length « lf », total length « lt », or length or width of cephalothorax for Comment on the fishing operation crustaceans « lc »)
	3.3.8 THE « PROJET » TABLE (PROJECTS) 3.3.
	List of projects codes included in the database
	Field	Type	Definition
	projet_id	Varchar	Project code, from the following list :
				-margo
				-ile_nouvelle_v0
				-remob
				-capalest
				-renomares
				-marino
	3.3.9 List of fishing or measurement stations
	Field	Type	Definition
	station_id	Varchar	Station code
	type_station	Varchar	Two possible values : « peche » (=fishing) or « mesure » (=measurement)
				A fishing station is a station which is associated with stationary fishing
				operations (table « operation_peche ») and physico-chemical measurements
				(table « mesure_parametre »).
				A measurement station is a station with only physico-chemical measurements
				(table « mesure_parametre »).
	lat_wgs84	Float	Latitude (decimal) in WGS 84 reference (EPSG: 4326)
	long_wgs84	Float	Longitude (decimal) in WGS 84 reference (EPSG: 4326)
	3.3.10 THE « TAXON » TABLE (TAXA)
	List of biological taxa
	Field		Type	Definition
	taxon_id		Varchar Taxon Latin name, in the form genera_species (when known)
				Examples: Abramis_brama, Abramis_sp
	nom_commun_taxon Varchar Taxon French common name. Spaces are replaced with '_'
	code_taxon		Char(6) Code used to abbreviate the names of taxa
	genre		Varchar Taxonomic genera, in Latin

11 THE « TRAIT » TABLE (TRAWL LINES)

	List of trawl lines for trawled fishing operations
	Field	Type	Definition
	trait_id	Varchar	Trawl line reference, composed of the date and a code of fishing zone
			Example : 2011-03-01_maubert_saintonge_tr1
	profondeur	Numeric	Average depth (m) along the trawl line
	profondeur_sonde Numeric	Average depth (m) at which the probe measuring physico-chemical parameters
			is being installed during the trawl line
	temperature	Numeric	Refer to table « mesure_parametre »
	conductivite	Numeric	Refer to table « mesure_parametre »
	conductance_sp	Numeric	Refer to table « mesure_parametre »
	salinite	Numeric	Refer to table « mesure_parametre »


S Chaffard

P Galle

Juen

Building the Information System of the OZCAR French Critical Zone

HAL is

System architecture and prototype of the web interface

Fig. 6 Architecture of the Theia/OZCAR Information System. The interface is built using Vue.js JavaScript framework. The map view is implemented using Leaflet JavaScript library. The backend is a SpringBoot application embedding a Apache Tomcat server to publish the REST API on the web and Spring Data MongoDB solution to link the database. The data persistence is ensured using MongoDB replica-set. System uses cases

•••ESSI2

  Theia: one of the French data pole dedicated to continental surfaces, exposing presently mainly remote sensing data • A need to extend the Information System (IS) to in situ data (Galle et al., 2018)  OZCAR-RI data: a complex enough case study to design and test the IS Objectives of the project • Propose a unique data portal to access in situ data documenting continental surfaces and the critical zone, that are presently scattered in various information systems • Keep the data close to data producers and make the best use of existing data management systems • Define information fluxes between observatories and the Theia/OZCAR IS (distributed architecture) • Be useful to observatories managers (identification of data users, publications using data, putting DOI on data sets, etc…) • Offer services and interoperability with other portals • Foster data discovery and exploration, their sharing and reusability, their citation (Fig. 2) • Controlled vocabulary based on hierarchized concepts of GCMD Earth Science keywords thesaurus and Sandre thesaurus for water chemistry • Harmonized variables names and categories  From about 3000 data producers names to about 250 controlled names  Publication in Skos using SKOSMOS Building strategy Definition of common controlled vocabulary based on domain-specific thesaurus • Open source softwares • Definition of common metadata based on metadata standards • Put in practice FAIR principles • Organization of data fluxes between data producer IS and Theia/OZCAR-IS using a pivot data model (Fig. 3) Continue the implementation of the information flux between the observatories and the Theia/OZCAR IS (5 observatories included up to now) • Continue the implementation of search functionalities on the web interface: adding search based on variable name thesaurus • Test if the web interface is user-friendly with future users • Put the system in production for metadata (end of 2019) and extend it to data (2020) References: Braud, I., Chaffard, V., Coussot, C., Galle, S., Juen, P. and the Theia/OZCAR ITTeam, 2019.: Building the Information System of the OZCAR French Critical Zone Observatories network, Hydrological Sciences Journal, to be submitted; Galle S., et al., 2018 : « Joint portal for THEIA-OZCAR in-situ data »; Theia bull. n°9; http:// theia-land.fr; Gaillardet J., Braud I, Hankard F. and the OZCAR team, 2018 : « OZCAR: the French network of Critical Zone Observatories », Vadose zone J., 2018, doi:10.2136/vzj2018.04.0067. Context: the OZCAR Research Infrastructure • OZCAR: a network of 22 observatories monitoring various compartments of the critical zone all over the world (about 60 sites, Fig. 1) (Gaillardet et al., VZJ, 2018) • Data presently scattered in various portals or data repositories • A large diversity of observed variables:time series, gridded and vector 2D data Water, energy, sediment and matter transport, geochemistry in catchments Transport of water, solutes and reactive elements in groundwater, fractured or karstic aquifers Glaciers, snow and permafrost processes Soil profiles/carrots and sampling specimen Geophysical data (2D) Vector GIS data Surveys (agricultural practices) Raster data and remote sensing products: Land use, land cover, high resolution DTM http://www.ozcar-ri.org/

FigFig. 3 :

 3 Fig.1: The OZCAR monitoring sites

Fig. 5 :

 5 Fig. 5: Conceptual scheme of the pivot data model with 3 main classes: producer, dataset and observation. Information in the blue square corresponds to ISO19115/Inspire information. Information in the red square corresponds to Observation and Measurement (O&M) standard.

Fig. 4 :

 4 Fig. 4: Categories retained in the controlled vocabulary of the Theia/OZCAR data portal.

Fig. 2 :

 2 Fig. 2: Illustration of the advantages of open data.

  Isabelle BRAUD 1 , Charly Coussot 2 , Véronique Chaffard 2 , Sylvie Galle 2 , Patrick Juen 2 and The Theia/OZCAR ITTeam

	• User-oriented approach: dialog between
	scientists & IT teams of the source
	observatories (working groups,
	meetings)
	• Story mapping (AGILE method)
	• Concepts and information
	based on metadata/data
	exchange standards
	(ISO19115/Inspire, DataCite,
	O&M) and some system
	functional requirements

1 : IRSTEA Riverly Lyon, France; 2: IGE Grenoble, France Acknowledgements: OZCAR-RI: French Ministry of Research, French research institutions and universities. Theia/OZCAR IS is part of the Theia land data center and Earth System Research Infrastructure. CNRS/INSU and IRD for funding human resources for the project. GCMD categories https://earthdata.nasa.gov/about/gcmd/ SANDRE Chemical categories http://id.eaufrance.fr/gpr/41 Added categories Relevant for OZCAR thematics http://in-situ.theia-land.fr/vocabularies/Skosmos/theia_ozcar_thesaurus/en/index 5. Next steps


Study of the distributed hydrologic response of the Claduègne catchment (Ardèche), prone to flash floods, using dense networks of rain and water level gauges N. Hachgenei, Guillaume Nord, Isabelle Braud

  Study of the distributed hydrologic response of the Claduègne catchment (Ardèche), prone to flash floods, using dense networks of rain and water level gauges Nico Hachgenei 1 , Guillaume Nord 1 , Isabelle Braud 2 REFERENCES: Nord, G. et al., 2017: A high space-time resolution dataset linking meteorological forcing and hydro-sedimentary response in a mesoscale Mediterranean catchment (Auzon) of the Ardèche region, France, Earth System Science Data, 9, 221-249, https://doi.org/10.5194/essd-9-221-2017. USDA-NRCS 2010: Time of Concentration, in: National Engineering Handbook Part 630 Hydrology, chap. 15, pp. 1-15, United States Department of Agriculture -Natural Resources Conservation Service Molinié, G., Ceresetti, D., Anquetin, S., Creutin, J. D., and Boudevillain, B. 2012: Rainfall regime of a mountainous mediterranean region: Statistical analysis at short time steps, Journal of Applied Meteorology and Climatology, 51, 429-448, https://doi.org/10.1175/2011JAMC2691.1.

Fig. 1

 1 Fig. 1

  Fig. 3

  Fig. 4