Modélisation spatiale multiscalaire de la structure des communautés de poissons lacustres en relation avec les facteurs environnementaux littoraux

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Seasonality in coastal macrobenthic biomass and its implications for estimating secondary production using empirical models

Macrobenthic secondary production is widely used to assess the trophic capacity, health, and functioning of marine and freshwater ecosystems. Annual production estimates are often calculated using empirical models and based on data collected during a single period of the year. Yet, many ecosystems show seasonal variations. Although ignoring seasonality may lead to biased and inaccurate estimates of annual secondary production, it has never been tested at the community level. Using time series of macrobenthic data collected seasonally at three temperate marine coastal soft-bottom sites, we assessed seasonal variations in biomass of macrobenthic invertebrates at both population and community levels. We then investigated how these seasonal variations affect the accuracy of annual benthic production when assessed using an empirical model and data from a single sampling event. Significant and consistent seasonal variations in biomass at the three study sites were highlighted. Macrobenthic biomass was significantly lower in late winter and higher in summer/early fall for 18 of the 30 populations analyzed and for all three communities studied. Seasonality led to inaccurate and often biased estimates of annual secondary production at the community level when based on data from a single sampling event. Bias varied by site and sampling period, but reached similar to 50% if biomass was sampled at its annual minimum or maximum. Since monthly sampling is rarely possible, we suggest that ecologists account for uncertainty in annual production estimates caused by seasonality.Agência financiadora EDF French Ministry of Higher Education, Research and Innovation French Ministry for the Ecological and Inclusive Transition through the Marine Strategy Framework Directive Agreement French Biodiversity Agency (Agence francaise pour la biodiversite) as part of the CAPANOUR projectinfo:eu-repo/semantics/publishedVersio

Cross-basin and cross-taxa patterns of marine community tropicalization and deborealization in warming European seas.

Ocean warming and acidification, decreases in dissolved oxygen concentrations, and changes in primary production are causing an unprecedented global redistribution of marine life. The identification of underlying ecological processes underpinning marine species turnover, particularly the prevalence of increases of warm-water species or declines of cold-water species, has been recently debated in the context of ocean warming. Here, we track changes in the mean thermal affinity of marine communities across European seas by calculating the Community Temperature Index for 65 biodiversity time series collected over four decades and containing 1,817 species from different communities (zooplankton, coastal benthos, pelagic and demersal invertebrates and fish). We show that most communities and sites have clearly responded to ongoing ocean warming via abundance increases of warm-water species (tropicalization, 54%) and decreases of cold-water species (deborealization, 18%). Tropicalization dominated Atlantic sites compared to semi-enclosed basins such as the Mediterranean and Baltic Seas, probably due to physical barrier constraints to connectivity and species colonization. Semi-enclosed basins appeared to be particularly vulnerable to ocean warming, experiencing the fastest rates of warming and biodiversity loss through deborealization

Manuel des protocoles de campagne halieutique. Campagnes « Nourriceries »

Ifremer is conducting multiple scientific surveys and in particular nurserie-dedicated surveys. The protocols of those surveys are resumed in national handbooks, providing useful information for any users whishing to implement and develop new surveys. Nurseries handbooks are meant to provide essential information on data collection, onboard organization, and data analyses. They represent a reference for the continuation of the surveys and the implementation of potential new surveys with the same objective. Since the end of 1970s, Ifremer has conducted nursery-dedicated surveys on several coastal areas. The scientific monitoring of essential habitats such as nurseries, is mainly situated in sandy coastal waters and occur in the English Channel and Atlantic coast. The objectives set by the Marine Strategy Framework Directive (MSFD) entail the development of new monitoring devices of marine waters and a standardization of existing devices at a national scale. On the basis of historical surveys NURSE, NOURSEINE and NOURSOM, this report describes standard protocols to implement in order to describe nurseries areas in sandy coastal waters. This hanbook also integrates specific adaptations required in particular geographic areas.L’Ifremer mène de nombreuses campagnes scientifiques en mer, notamment sur les zones de nourriceries. Les manuels des protocoles Ifremer fournissent à tout utilisateur potentiel des données des campagnes halieutiques toutes les informations utiles sur la nature de ces données et sur les conditions de leur recueil. Ils constituent une référence pour la pérennisation des campagnes et la mise en œuvre d’éventuelles nouvelles campagnes scientifiques visant un objectif comparable. Les suivis scientifiques d’une zone fonctionnelle telle que les nourriceries, principalement situées dans les milieux meubles côtiers, existent depuis les années 1970 sur les façades Manche et Atlantique. Les objectifs fixés par la Directive Cadre Stratégie pour le Milieu Marin (DCSMM) impliquent le développement de nouveaux dispositifs de surveillance du milieu marin et une harmonisation des dispositifs existants à l’échelle nationale. Sur la base des campagnes historiques NURSE, NOURSEINE et NOURSOM, ce rapport décrit les protocoles standards à mettre en œuvre pour décrire les zones de nourriceries en milieux meubles côtiers, en intégrant les adaptations méthodologiques spécifiques à certaines zones géographiques

Assessment of the ecological status of coastal areas and estuaries in France, using multiple fish-based indicators: a comparative analysis on the Vilaine estuary

When reviewing the various fish-based community indicators aiming at assessing the ecological status of marine communities and/or ecosystems, a typology consisting of three major components emerges. The first component highlights the choice of relevant metrics associated with a level of organization (e.g. population or community). The second relies on the method used to combine the metrics (an aggregated indicator or a synoptic table). The third refers to the type of analysis (direct or indirect) that is used to establish the link between the metrics and a given pressure. In this paper we use the Vilaine coastal-estuarine fish communities as a case study to discuss and relate two different approaches to the suggested typology. The first approach (time-trend approach) is based on historical series of data, whereas the second approach (multi-metric index, MMI) is based on a geographic series including various French estuaries. They were developed or adapted from French studies but are representative of the approaches used in Europe. When applied to the case study, they differed in their diagnosis: the time-trend approach indicated that the bay of Vilaine habitat was deteriorating, whereas the MMI, which compares many French estuaries, indicated a good environmental state. Differences and complementarities between the approaches are thoroughly discussed with respect to the three mains components of the typology. This work appears at a particular moment, when several fish-based indicators are being developed in France and the rest of Europe. It intends to serve as an element of the ongoing reflection concerning the limitations of the various approaches that can be used to develop such indicators

Evaluation de la composante de l’écosystème « Poissons et céphalopodes » du descripteur 1 « Biodiversité » en France métropolitaine.

The Marine Strategy Framework Directive (MSFD), adopted in June 2008, recommends Member States to adopt an ecosystemic approach to manage the marine environment. By this directive, France aims to achieve a good environmental status (GES) described by 11 descriptors, of its marine waters by 2020. Descriptor 1 stipulates that biological diversity is maintained. The quality and occurrence of habitats and the distribution and abundance of species are in line with prevailing physiographic, geographic and climate conditions (European Commission Decision 2017/848/UE). The ecosystem components of fish and cephalopods must be assessed in the four marine subregions (“English Channel – North Sea”, “Celtic seas”, “Bay of Biscay” and “Western Mediterranea”). The species groups assessed in this report are the demersal fish of sandy or muddy coastal areas, demersal and pelagic fish of the continental shelf, cephalopods of coastal areas and continental shelf, and fish and cephalopods of deep-sea waters. For the assessment of the species groups mentioned above, except for coastal and pelagic fish, the “Celtic seas” and “Bay of Biscay” marine subregions are united in one Assessment Geographical Unit (AGU) and the “Western Mediterranea” marine subregion is divided into two AGU: Gulf of Lion and Eastern Corsica. The approach used to assess the GES of each species group in each marine subregion is based on the availability of data from scientific surveys conducted by Ifremer and scientific proven methods for identifying thresholds. This quantitative approach is implemented for criterion D1C2 related to the abundance of populations and to the group of demersal fish of the continental shelf for which sensitivity to fishing pressure is high. It is carried out at the population and community level. However, the beginning of monitoring devices matches with a period of high fishing intensity that does not allow referring to an initial situation without pressure. For the others species groups, criterion D1C2 is indicated by the results of the assessment of desciptor 3 when stock assessments are available (i.e. D3 report – Foucher and Delaunay, 2018), this is the case of the pelagic fish of the continental shelf, or through a qualitative approach. For the other criteria, a qualitative assessment is proposed. The latter approach describes (albeit non-exhaustively) the state of scientific knowledge on those unassessed species groups. Its also suggests future methodological developments which will likely be used to inform the five criteria of the descriptor 1 for the next assessments. The assessment of GES of the demersal fish populations of the continental shelf, using the criterion D1C2, indicates that among the four AGU, the “English Channel – North Sea”, “Celtic Seas and bay of Biscay” and “Gulf of Lion” present populations that don’t achieve GES. The number of populations is particularly important in the Gulf of Lion where 28% don’t achieve GES. In addition, 30 to 50% of the populations are assessed in GES in all AGU. The community approach, whose the results are consistent with the previous ones, indicates that the “English Channel – North Sea” AGU shows increasing signals of a return to GES since the 2000s. The populations qualified in GES have doubled since the beginning of the observation series, achieving 40-45 % of the populations of sensitive species to the fishing pressure. In the “Celtic seas and bay of Biscay” AGU, the environmental status of the populations is stable over the period analysed but it is difficult to interprete that stability as no threshold value of GES formely exists. Finally, the western Mediterranea with Corsica and the Gulf of Lion have respectively a stable state and a decrease of the number of populations in GES since the end of the nineties. However, in the Gulf of Lion, signals of a return to a GES are observed for the last MSFD cycle. The qualitative approach highlights the main developments leading to future operational indicators for the next MSFD cycles. This includes work on the coastal demersal fish communities with the data provided by scientific surveys on nursery areas (D1C5), the ICES work on the size and age based on indicators of exploited fish stocks (D1C3), and research development on the geographical distribution of demersal and pelagic populations of the continental shelf (D1C4).La Directive Cadre Stratégie pour le Milieu Marin (DCSMM), adoptée en juin 2008, recommande aux Etats membres de développer une approche de gestion des milieux marins fondée sur la notion d’écosystème. Par cette directive, la France s’est engagée à atteindre ou maintenir d’ici 2020 le bon état écologique (BEE) des milieux marins décrits au travers de 11 descripteurs, pour les eaux métropolitaines sous sa juridiction. Le descripteur 1 stipule que la diversité biologique doit être maintenue. La qualité des habitats et leur nombre, ainsi que la distribution et l’abondance des espèces sont adaptés aux conditions physiographiques, géographiques et climatiques existantes (décision de la Commission européenne 2017/848/UE). Les composantes de l’écosystème des poissons et céphalopodes doivent être évaluées dans les quatre sous-régions marines (SRM) françaises (« Manche – mer du Nord », « Mers Celtiques », « Golfe de Gascogne » et « Méditerranée occidentale »). Les groupes d’espèces traités dans ce rapport sont les poissons démersaux des milieux meubles côtiers, les poissons démersaux et pélagiques du plateau continental, les céphalopodes côtiers et du plateau continental et les poissons et céphalopodes d’eaux profondes. Pour l’évaluation des groupes d’espèces cités précédemment à l’exception des poissons côtiers et pélagiques, les SRM « Mers Celtiques » et « Golfe de Gascogne » sont réunies au sein d’une unité géographique d’évaluation (UGE), et la SRM « Méditerranée occidentale » a été scindée en deux UGE : le golfe du Lion et la Corse Est. L’approche utilisée pour évaluer le BEE de chaque groupe d'espèces dans chaque SRM repose sur la disponibilité des données, provenant des campagnes scientifiques conduites par l’Ifremer, et des méthodes d'identification de seuils. Cette approche quantitative est réalisée pour le critère D1C2 relatif à l’abondance des populations et au seul groupe des poissons démersaux du plateau continental dont la sensibilité à la pression de pêche est élevée. Elle est réalisée à l’échelle de la population et de la communauté. Toutefois, le début des dispositifs de suivis correspond à une période de forte intensité de pêche ne permettant pas de se référer à une situation initiale exempt de pression. Pour les autres groupes d’espèces, ce même critère (D1C2) est renseigné par les résultats de l'évaluation du descripteur 3 lorsque des évaluations de stocks sont disponibles (i.e. rapport D3 – Foucher et Delaunay, 2018), c’est le cas des poissons pélagiques du plateau continental, ou par une approche qualitative. Pour les autres critères, une approche qualitative est proposée. Cette approche décrit de manière non exhaustive l’état des connaissances scientifiques sur les groupes d’espèces et les développements méthodologiques qui permettront éventuellement de renseigner les 5 critères du descripteur 1 lors des prochaines évaluations. L’évaluation du BEE des populations de poissons démersaux du plateau continental au regard du critère D1C2 révèle que parmi les quatre UGE, la « Manche – Mer du Nord », les « Mers Celtiques et golfe du Gascogne » et le « Golfe du Lion » présentent des populations n'atteignant pas le BEE. Le nombre de populations est particulièrement important pour le golfe du Lion où 28 % d'entre elles ne sont pas en BEE. Par ailleurs, 30 à 50 % des populations sont évaluées en BEE sur l'ensemble des UGE. L’approche par communauté, dont les résultats sont cohérents avec les précédents, indique que l’UGE « Manche – mer du Nord » montre des signes croissants de retour vers le BEE depuis les années 2000. Les populations jugées en BEE ont doublé depuis le début de la série d’observation, atteignant 40-45 % des populations d’espèces sensibles à la pression de pêche. Dans l’UGE« Mers Celtiques et golfe de Gascogne », l’état écologique des populations est stable sur l’ensemble de la période étudiée mais il est délicat de le situer par rapport à une valeur seuil de BEE. Enfin, la Méditerranée occidentale avec la Corse et le golfe du Lion présentent, respectivement, un état stable et une diminution du nombre de populations en BEE depuis la fin des années 1990. Il est à noter toutefois que pour le golfe du Lion, une amélioration de l'état écologique des espèces démersales sensibles à la pêche est observée sur la période du dernier cycle DCSMM. L’approche qualitative pointe les principales pistes de développement susceptibles de fournir des indicateurs opérationnels pour les prochains cycles de la DCSMM : les travaux sur les communautés des milieux meubles côtiers à partir des données des campagnes « Nourriceries » (D1C5), les travaux du CIEM sur les indicateurs de structure en taille et en âge des stocks de poissons exploités (D1C3), ou encore les travaux de recherche sur la distribution géographique des populations d’espèces démersales ou pélagiques du plateau continental (D1C4)

Isotopic diversity indices: how sensitive to food web structure?

Recently revisited, the concept of niche ecology has lead to the formalisation of functional and trophic niches using stable isotope ratios. Isotopic diversity indices (IDI) derived from a set of measures assessing the dispersion/distribution of points in the δ-space were recently suggested and increasingly used in the literature. However, three main critics emerge from the use of these IDI: 1) they fail to account for the isotopic sources overlap, 2) some indices are highly sensitive to the number of species and/or the presence of rare species, and 3) the lack of standardization prevents any spatial and temporal comparisons. Using simulations we investigated the ability of six commonly used IDI to discriminate among different trophic food web structures, with a focus on the first two critics. We tested the sensitivity of the IDI to five food web structures along a gradient of sources overlap, varying from two distinct food chains with differentiated sources to two superimposed food chains sharing two sources. For each of the food web structure we varied the number of species (from 10 to 100 species) and the type of species feeding behaviour (i.e. random or selective feeding). Values of IDI were generally larger in food webs with distinct basal sources and tended to decrease as the superimposition of the food chains increased. This was more pronounced when species displayed food preferences in comparison to food webs where species fed randomly on any prey. The number of species composing the food web also had strong effects on the metrics, including those that were supposedly less sensitive to small sample size. In all cases, computing IDI on food webs with low numbers of species always increases the uncertainty of the metrics. A threshold of ~20 species was detected above which several metrics can be safely used

Ability of spatial indicators to detect geographic changes (shift, shrink and split) across biomass levels and sample sizes

Spatial indicators are widely used to monitor species and are essential to management and conservation. In the present study, we tested the ability of 11 spatial indicators to quantify changes in species’ geographic patterns: (1) spatial displacement of a patch of biomass (‘shift’), (2) a spatial decrease in a patch, accompanied either by a loss of biomass (‘shrink0’) or (3) a relocation of the same biomass (‘shrink1’), and (4) splitting of a patch into smaller patches (‘split’). The geographic changes were simulated by manipulating the spatial distributions of the demersal species (observed during bottom trawl surveys). Hence, the spatial distributions of the latter being used as input data on which the manipulations were done. Additionally, other aspects of the indicators affecting the responses to the geographic changes were also tested, (1) homogeneous increase in biomass throughout the patch and (2) different sample sizes. The center of gravity (defined by latitude and longitude) was the only indicator that accurately detected the ‘shift’ in biomass. The index of aggregation identified a decrease in the area and biomass of the main biomass patch (‘shrink0’), while the Gini index, equality area and spreading area were accurately identified a decrease in the area of the main biomass patch when total biomass did not decreased (‘Shrink1′). Inertia and isotropy responded to all geographic changes, except for those in biomass or distribution area. None of the indicators successfully identified ‘split’ process. Likewise, one of the indicators were sensitive to a homogeneous increase in biomass or the type of spatial distribution. Overall, all indicators behaved similarly well when sample sizes exceeded 40 stations randomly located in the area. The framework developed provides an accessible and simple approach that can be used to evaluate the ability of spatial indicators to identify geographic processes using empirical data and can be extended to other indicators or geographic processes. We discuss perspectives of the development of spatial indicators especially within the application of EU’s Marine Strategy Framework Directive

Which spatial interpolators I should use? A case study applying to marine species

Species are spread in space, whereas sampling is sparse. Thus, to describe and map along environmental gradients, it is necessary to interpolate the species abundance. Considering the plethora of valid methods, the researcher gets easily puzzled to choose the most appropriate interpolation approach with reference to the ecological question being asked. We propose a procedure to select among alternative spatial distribution models and we illustrate it with 175 marine species distributions (35 species * 5 years). In a first step, the distribution of the variance explained by the predictive model (VEcv) given by 10-fold cross validation is estimated for each interpolation method. When the inter-quartile range of the VEcv distribution of the different methods overlap, the selection passes to a second step, using 11 measures belonging to three criteria: 1) error based measures, 2) spatial equivalence measures (center of gravity, inertia, isotropy and index of aggregation) and 3) measures based on the data integrity after interpolation, for example the percentage of area over the maximum sampled data. We applied our approach to marine species sampled using either stratified random survey (trawl) or systematic survey (acoustic). We found that 87% of all species distributions had overlapping VEcv and thus passed the first selection. In the second selection step, the best method varied with species and year, although general additive model (GAM), Thin Plate Spline (TPS), Universal Kriging (UKr) and Random Forest (Rfor) performed better for the trawl data and TPS, Ordinary Kriging (OKri) and UKr for the acoustic data. Further, the results differed within methods (e.g. kriging neighborhood and type of kriging) and small modifications on the specifications can have a large impact on the surfaces produced. The proposed approach 1) is accessible and intuitive, and does not require any complex software or sophisticated methodology; 2) shows exactly in what aspects each interpolation model is prevalent over the others and permits to make a decision accordingly to the objectives of the study; 3) takes into account different criteria to evaluate each, properties of an interpolation method; 4) is universal and does not depend on the method used or the data characteristics. A detailed review on the subject is also included

Rapport de campagne de nourriceries côtières. Campagne NOURMED 2019

Dans le cadre de la mise en œuvre du programme de surveillance de la directive cadre stratégie pour le milieu marin (DCSMM), le suivi des poissons et céphalopodes démersaux des milieux meubles côtiers a été jugé prioritaire. Pour ce faire, une série de campagnes halieutiques récurrentes doit être déployée dans les nourriceries côtières, constituant des habitats essentiels pour de nombreuses espèces marines. La caractérisation de l’état écologique des peuplements et l’étude de la fonctionnalité des habitats de nourriceries s’avèrent nécessaires au calcul des indicateurs du Bon Etat Ecologique requis par la DCSMM et primordiales pour la mise en place de mesures de gestion écosystémique garantissant des usages durables. Sur la façade méditerranéenne, une première mission explorant la faisabilité de ce suivi a été réalisée avec succès dans le golfe du Lion en 2018. La campagne Nourmed 2019 augure de la mise en place d’une série de campagnes et s'inscrit donc dans le dispositif de surveillance des « Poissons-céphalopodes ». Le présent rapport décrit les principaux objectifs et résultats acquis en 2019. Il confirme la faisabilité de la mise en place de ce suivi, et calcule l’abondance, la biomasse et la diversité de trois guildes : les poissons, les céphalopodes et les autres invertébrés. Une série d’espèces bien représentées dans les captures sont listés et pour certaines, un spectre de taille et une cartographie de leurs abondances et biomasses ont été produits. Ces analyses représentent les premiers jalons du calcul des indicateurs de la DCSMM concernés et illustrent que les données recueillies permettront sans aucun doute leurs calculs. Cependant la méconnaissance de la variabilité naturelle du milieu et des biotopes associés ainsi que la définition des valeurs seuil du bon état écologique impose de constituer une série temporelle suffisamment longue et donc, de poursuivre ce suivi