Audrey M. Darnaude

Trophodynamic linkage between river runoff and coastal fishery yield elucidated by stable isotope data in the Gulf of Lions (NW Mediterranean)

The link between climate-driven river runoff and sole fishery yields observed in the Gulf of Lions (NW Mediterranean) was analysed using carbon- and nitrogen stable isotopes along the flatfish food webs. Off the Rhone River, the main terrestrial (river POM) and marine (seawater POM) sources of carbon differed in δ13C (–26.11‰ and −22.36‰, respectively). Surface sediment and suspended POM in plume water exhibited low δ13C (–24.38‰ and −24.70‰, respectively) that differed more from the seawater POM than from river POM, demonstrating the dominance of terrestrial material in those carbon pools. Benthic invertebrates showed a wide range in δ15N (mean 4.30‰ to 9.77‰) and δ13C (mean −23.81‰ to −18.47‰), suggesting different trophic levels, diets and organic sources. Among the macroinvertebrates, the surface (mean δ13C −23.71‰) and subsurface (mean δ13C −23.81‰) deposit-feeding polychaetes were particularly 13C depleted, indicating that their carbon was mainly derived from terrestrial material. In flatfish, δ15N (mean 9.42 to 10.93‰) and δ13C (mean −19.95‰ to −17.69‰) varied among species, indicating differences in food source and terrestrial POM use. A significant negative correlation was observed between the percentage by weight of polychaetes in the diet and the δ13C of flatfish white muscle. Solea solea (the main polychaete feeder) had the lowest mean δ13C, Arnoglossus laterna and Buglossidium luteum (crustacean, mollusc and polychaete feeders) had intermediate values, and Solea impar (mollusc feeder) and Citharus linguatula (crustacean and fish feeder) exhibited the highest δ13C. Two different benthic food webs were thus identified off the Rhone River, one based on marine planktonic carbon and the other on the terrestrial POM carried by the river. Deposit-feeding polychaetes were responsible for the main transfer of terrestrial POM to upper trophic levels, linking sole population dynamics to river runoff fluctuations.

Fluctuations of macrobenthic populations: a link between climate-driven river run-off and sole fishery yields in the Gulf of Lions

Abstract. The Rhone river is the most important input to the Mediterranean Sea, responsible for 50% of the primary productivity of the Gulf of Lions. A highly variable amount of 1–23×106xa0t year–1 of terrestrial material is exported to the sea by the Rhone and stocked on the continental shelf for the most part. Soft-bottom communities off the Rhone delta were dominated by polychaetes both in species richness and abundance, and exhibited strong temporal fluctuations mainly related to flooding events. Floods caused pulses of organic matter followed, with different time lags, by peaks of polychaetes. Opportunistic, short-lived species, such as Mediomastus sp. and Aricideaclaudiae, exhibited high short-term peaks in density and biomass a few months after flooding events. Conversely, long-lived species, such as Laonicecirrata and Sternaspisscutata, peaked in density and biomass with a time lag of 1–3xa0years, and their population increase lasted for a few years. The common sole, Soleasolea, is a voracious predator of polychaetes which represent >80% of its prey. A positive correlation was found between the mean annual discharge of the Rhone river and the annual commercial landings of S.solea with a time lag of 5xa0years in the two fishing harbours (Sete and Martigues) located close to the Rhone delta. The long-term increase in food (i.e. polychaete density and biomass) after flooding events might favour the different stages of the sole life cycle, enhancing its population size for several years. Fluctuations of sole fishery yields in the Gulf of Lions could be influenced by climate, as the Rhone river flow is related to the North Atlantic Oscillation that drives precipitation over Western Europe.

Food partitioning among flatfish (Pisces: Pleuronectiforms) juveniles in a Mediterranean coastal shallow sandy area

Diets of the four main flatfish species, Arnoglossus laterna, Bothus podas (Bothidae), Buglossidium luteum and Solea solea (Soleidae), inhabiting shallow sandy bottoms near the Gulf of Fos (north-west Mediterranean) were analysed to elucidate food partitioning between their juveniles (1 + group) in nursery areas. The two Soleidae were principally active during the night, and the two Bothidae during the day. The four species all mainly fed on the three most abundant categories of prey in the area (polychaetes, molluscs and crustaceans) but showed different food preferences. Arnoglossus laterna and B . luteum mainly preyed on crustaceans and molluscs (gastropods and bivalves) whereas Bothus podas and S. solea preyed principally on polychaetes and bivalve molluscs. Food niche width was clearly higher in A. laterna and Buglossidium luteum (13·3 and 14·2 respectively) than in Bothus podas and S. solea (3·2 and 3·6 respectively). Overall food niche overlaps ( T ) obtained for each pair of fish ranged from 0·33 to 0·58. Overlap was higher between species of the same family but did not reach a significant level. Food niche overlap differed according to the period of the day but did not show any important seasonal variation. Differences in feeding rhythms, food preferences and body sizes, reduced the direct food competition between the juveniles of the four flatfish species, allowing their coexistence within the same nursery zone, despite close periods of settlement.

Selecting statistical models and variable combinations for optimal classification using otolith microchemistry

Reliable assessment of fish origin is of critical importance for exploited species, since nursery areas must be identified and protected to maintain recruitment to the adult stock. During the last two decades, otolith chemical signatures (or fingerprints) have been increasingly used as tools to discriminate between coastal habitats. However, correct assessment of fish origin from otolith fingerprints depends on various environmental and methodological parameters, including the choice of the statistical method used to assign fish to unknown origin. Among the available methods of classification, Linear Discriminant Analysis (LDA) is the most frequently used, although it assumes data are multivariate normal with homogeneous within-group dispersions, conditions that are not always met by otolith chemical data, even after transformation. Other less constrained classification methods are available, but there is a current lack of comparative analysis in applications to otolith microchemistry. Here, we assessed stock identification accuracy for four classification methods (LDA, Quadratic Discriminant Analysis [QDA], Random Forests [RF], and Artificial Neural Networks [ANN]), through the use of three distinct data sets. In each case, all possible combinations of chemical elements were examined to identify the elements to be used for optimal accuracy in fish assignment to their actual origin. Our study shows that accuracy differs according to the model and the number of elements considered. Best combinations did not include all the elements measured, and it was not possible to define an ad hoc multielement combination for accurate site discrimination. Among all the models tested, RF and ANN performed best, especially for complex data sets (e.g., with numerous fish species and/or chemical elements involved). However, for these data, RF was less time-consuming and more interpretable than ANN, and far more efficient and less demanding in terms of assumptions than LDA or QDA. Therefore, when LDA and QDA assumptions cannot be reached, the use of machine learning methods, such as RF, should be preferred for stock assessment and nursery identification based on otolith microchemistry, especially when data set include multispecific otolith signatures and/or many chemical elements.

Spatial and temporal variations of fish assemblages in a shallow Mediterranean soft-bottom area (Gulf of Fos, France)

Abstract The fish assemblages of two shallow soft-bottom areas located in the Gulf of Fos (NW Mediterranean) were studied by means of 57 trawl surveys carried out on both seasonal and diel scales between 1983 and 1985. A total of 47 fish species was recorded, with a mean density and biomass of 650xa0individualsxa0ha–1 and 2.67xa0kgxa0ha–1, respectively. Most of the fluctuations observed were on the spatial scale. Strong differences in fish assemblages were observed between the two areas, with both higher species richness and biomass in the outer part of the gulf (La Gracieuse), while a higher density of individuals characterised its inner part (Bay of Carteau). This spatial pattern was due to a small number of species, such as the gobiids Gobius niger and Pomatoschitus minutus in Carteau, and the flatfish Arnoglossus laterna, Buglossidium luteum and Solea solea in La Gracieuse. These differences were probably induced by differences in the hydrological and benthic characteristics of the two study areas. Decreases in species richness, density and/or biomass were observed in both areas over the study period, although this trend was not significant in all cases. These decreases may have been linked to interannual variations in the mean flow rate of the Rhone River (–28.1% between 1983 and 1985), which might have induced a decrease in the density of benthic invertebrate populations. We suggest that a similar reaction occurred in fish populations, as most of them are known to feed on these invertebrates. Diel patterns did not reveal any significant trends. However, an increase in density and biomass at sunset, and a decrease before sunrise were observed in summer in both areas, and the presence of certain specific species was recorded in catches at determined hours of the diel cycle. These observations were likely due to the activity cycles (diurnal vs. nocturnal) of the fish species.

Getting a Good Start in Life? A Comparative Analysis of the Quality of Lagoons as Juvenile Habitats for the Gilthead Seabream Sparus aurata in the Gulf of Lions

Temperate coastal lagoons are considered key habitats for several highly prized marine fishes, which colonise them as nurseries. Lagoons can, however, exhibit diverse abiotic and biotic conditions, with potential consequences for their quality as habitats. To investigate this, we compared size, body condition (Fulton’s condition factor K and lipid classes), past growth rate (from otoliths) and sources of food web organic matter (OM), among group 0 juveniles of the gilthead sea bream Sparus aurata L. 1758, captured at the end of their first summer of residence in four lagoons of the Gulf of Lions in the NW Mediterranean (Mauguio, Thau, Bages and Salses-Leucate). These lagoons have different environmental conditions and freshwater inputs. Although age was similar for all lagoons, juveniles from Mauguio and Bages were significantly larger and heavier than those from Thau and Salses-Leucate. They were also in better condition, with higher white muscle triacylglycerol/sterol ratio (meanu2009±u2009SD 35.7u2009±u200920.1 in Mauguio and 23.2u2009±u20099.8 in Bages versus 15.1u2009±u200915.2 in Thau and 7.4u2009±u20097.9 in Salses-Leucate). All exhibited similar otolith growth rates for their larval marine phase (2.8u2009±u20090.4xa0μmxa0day−1), but significant differences were found for the lagoon phase, with higher values in Mauguio and Bages (10.1u2009±u20090.9 and 9.7u2009±u20091.0xa0μmxa0day−1, respectively) than those in Thau and Salses-Leucate (8.4u2009±u20091.2 and 8.9u2009±u20090.8xa0μmxa0day−1, respectively). White muscle stable isotope analysis revealed that terrestrial carbon use by the juveniles was >33xa0% in Mauguio and <5xa0% in Salses-Leucate, with intermediate values (~15xa0%) in Thau and Bages. Although these effects on fish condition and growth rate may relate in part to differences in water salinity and dissolved oxygen in the four lagoons, it is probable that they are mostly related to differences in food web enrichment with terrestrial OM.

Growth, condition and metal concentration in juveniles of two Diplodus species in ports

High abundances of juvenile fish in certain ports suggest they might provide alternative nursery habitats for several species. To further investigate this possibility, post-settlement growth, metal uptake and body condition were estimated in 127 juveniles of two seabream species, collected in 2014-15, inside and outside the highly polluted ports of the Bay of Toulon. This showed that differences in local pollution levels (here in Hg, Cu, Pb and Zn) are not consistently mirrored within fish flesh. Muscle metal concentrations, below sanitary thresholds for both species, were higher in ports for Cu, Pb and V only. Otherwise, fish muscle composition principally differed by species or by year. Juvenile growth and condition were equivalent at all sites. Higher prey abundance in certain ports might therefore compensate the deleterious effects of pollution, resulting in similar sizes and body conditions for departing juvenile fish than in nearby natural habitats.

elementr: An R package for reducing elemental data from LA‐ICPMS analysis of biological calcified structures

1. Elemental analysis of biological calcified structures (e.g. fish otoliths, mollusc shelves, coral skeletons or fish and shark bones) provides invaluable information regarding ecological processes for many aquatic species. Despite this importance, the reduction of the raw data obtained through Laser-ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS) (i.e. the conversion of the machine raw signal into elemental concentrations) remains a challenge as the tools developed so far for carrying out this task have important limitations for aquatic ecologists. 2. Here, we introduce the elementr R-package which provides a handy, reliable and transparent way to reduce elemental data acquired from spot or transect LA-ICPMS analysis of biological calcified structures. This free and open-source software, implemented based on state-of-the-art literature, handles data from both standards and samples, allowing fast and simultaneous calculations of concentration for any chemical element, correction for potential machine drift, and realignment and averaging for sample replicates when needed. 3. The major attributes of elementr are: (i) its user-friendly graphical interface which provides widgets to set all the reduction settings (i.e. no programming skills are required to run it), (ii) its reactivity whereby the software continuously observes any setting change made by the user, re-calculates and displays all updated results, allowing therefore users to visually check the validity of their settings and to tune them if needed and (iii) an object oriented underlying that facilitates subsequent handling of LA-ICPMS data in R. 4. Despite the elementr design being most suited to the needs of aquatic ecologists, its use could be broadened to other research fields (i.e. geology, material engineering) due to its flexibility. Moreover, the open-source approach used for programming this software allows its expansion in order to refine calculation procedures or to add new functionalities.

Performance of maximum likelihood mixture models to estimate nursery habitat contributions to fish stocks: a case study on sea bream Sparus aurata.

Background Mixture models (MM) can be used to describe mixed stocks considering three sets of parameters: the total number of contributing sources, their chemical baseline signatures and their mixing proportions. When all nursery sources have been previously identified and sampled for juvenile fish to produce baseline nursery-signatures, mixing proportions are the only unknown set of parameters to be estimated from the mixed-stock data. Otherwise, the number of sources, as well as some/all nursery-signatures may need to be also estimated from the mixed-stock data. Our goal was to assess bias and uncertainty in these MM parameters when estimated using unconditional maximum likelihood approaches (ML-MM), under several incomplete sampling and nursery-signature separation scenarios. Methods We used a comprehensive dataset containing otolith elemental signatures of 301 juvenile Sparus aurata, sampled in three contrasting years (2008, 2010, 2011), from four distinct nursery habitats. (Mediterranean lagoons) Artificial nursery-source and mixed-stock datasets were produced considering: five different sampling scenarios where 0–4 lagoons were excluded from the nursery-source dataset and six nursery-signature separation scenarios that simulated data separated 0.5, 1.5, 2.5, 3.5, 4.5 and 5.5 standard deviations among nursery-signature centroids. Bias (BI) and uncertainty (SE) were computed to assess reliability for each of the three sets of MM parameters. Results Both bias and uncertainty in mixing proportion estimates were low (BI ≤ 0.14, SE ≤ 0.06) when all nursery-sources were sampled but exhibited large variability among cohorts and increased with the number of non-sampled sources up to BI = 0.24 and SE = 0.11. Bias and variability in baseline signature estimates also increased with the number of non-sampled sources, but tended to be less biased, and more uncertain than mixing proportion ones, across all sampling scenarios (BI < 0.13, SE < 0.29). Increasing separation among nursery signatures improved reliability of mixing proportion estimates, but lead to non-linear responses in baseline signature parameters. Low uncertainty, but a consistent underestimation bias affected the estimated number of nursery sources, across all incomplete sampling scenarios. Discussion ML-MM produced reliable estimates of mixing proportions and nursery-signatures under an important range of incomplete sampling and nursery-signature separation scenarios. This method failed, however, in estimating the true number of nursery sources, reflecting a pervasive issue affecting mixture models, within and beyond the ML framework. Large differences in bias and uncertainty found among cohorts were linked to differences in separation of chemical signatures among nursery habitats. Simulation approaches, such as those presented here, could be useful to evaluate sensitivity of MM results to separation and variability in nursery-signatures for other species, habitats or cohorts.