2019 |
Matthews, T. J., et al. "sars: an R package for fitting, evaluating and comparing species-area relationship models." Ecography. 42.8 (2019): 1446–1455.
Résumé: The species-area relationship (SAR) constitutes one of the most general ecological patterns globally. A number of different SAR models have been proposed. Recent work has shown that no single model universally provides the best fit to empirical SAR datasets: multiple models may be of practical and theoretical interest. However, there are no software packages available that a) allow users to fit the full range of published SAR models, or b) provide functions to undertake a range of additional SAR-related analyses. To address these needs, we have developed the R package 'sars' that provides a wide variety of SAR-related functionality. The package provides functions to: a) fit 20 SAR models using non-linear and linear regression, b) calculate multi-model averaged curves using various information criteria, and c) generate confidence intervals using bootstrapping. Plotting functions allow users to depict and scrutinize the fits of individual models and multi-model averaged curves. The package also provides additional SAR functionality, including functions to fit, plot and evaluate the random placement model using a species-sites abundance matrix, and to fit the general dynamic model of oceanic island biogeography. The 'sars' R package will aid future SAR research by providing a comprehensive set of simple to use tools that enable in-depth exploration of SARs and SAR-related patterns. The package has been designed to allow other researchers to add new functions and models in the future and thus the package represents a resource for future SAR work that can be built on and expanded by workers in the field.
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2018 |
Afandi, I., et al. "Trace metal distribution in pelagic fish species from the north-west African coast (Morocco)." Int Aquat Res. 10.2 (2018): 191–205.
Résumé: In the current study, ten elements contents (Fe, Zn, Mn, Cu, Cr, Co, Ni, Cd, Pb and Hg) have been measured in muscle and liver of four pelagic fish species (Engraulis encrasicolus, Sardina pilchardus, Scomber japonicus and Trachurus trachurus) from the north-west African coast (South Atlantic Moroccan coast), collected during summer and autumn seasons (July and December 2013, respectively). Significant differences in metal contents were found between the different species (p < 0.05). Metals levels were also much higher in liver than those recorded in muscle tissues. The concentrations of Fe, Zn, Cd, Co, Cu and Pb were significantly higher in mackerel liver (p < 0.05).While, in muscle, anchovy presents a higher content of Mn, Cu, Cr, Ni and Pb. A high level of cadmium was recorded in liver of the different species which can be attributed to an anthropogenic source (phosphate industry) and to natural sources (upwelling activities). The main concentration of toxic elements (Cd, Pb and Hg) recorded in the four edible muscles of pelagic fish species, under study, were below the established values by the European Commission Regulations and show that their effect on the consumers health can be considered as negligible.
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2017 |
Chouvelon, T., et al. "Chemical contaminants (trace metals, persistent organic pollutants) in albacore tuna from western Indian and south-eastern Atlantic Oceans: Trophic influence and potential as tracers of populations." Sci. Total Environ.. 596 (2017): 481–495.
Résumé: Albacore tuna (Thunnus alalunga) is a highly commercial fish species harvested in the world's Oceans. Identifying the potential links between populations is one of the key tools that can improve the current management across fisheries areas. In addition to characterising populations' contamination state, chemical compounds can help refine foraging areas, individual flows and populations' structure, especially when combined with other intrinsic biogeochemical (trophic) markers such as carbon and nitrogen stable isotopes. This study investigated the bioaccumulation of seven selected trace metals – chromium, nickel, copper (Cu), zinc (Zn), cadmium (Cd), mercury (Hg) and lead – in the muscle of 443 albacore tunas, collected over two seasons and/or years in the western Indian Ocean (WIO: Reunion Island and Seychelles) and in the south-eastern Atlantic Ocean (SEAO: South Africa). The main factor that explained metal concentration variability was the geographic origin of fish, rather than the size and the sex of individuals, or the season/year of sampling. The elements Cu, Zn, Cd and Hg indicated a segregation of the geographic groups most clearly. For similar sized-individuals, tunas from SEAO had significantly higher concentrations in Cu, Zn and Cd, but lower Hg concentrations than those from WIO. Information inferred from the analysis of trophic markers (delta C-13, delta N-15) and selected persistent organic pollutants, as well as information on stomach contents, corroborated the geographical differences obtained by trace metals. It also highlighted the influence of trophic ecology on metal bioaccumulation. Finally, this study evidenced the potential of metals and chemical contaminants in general as tracers, by segregating groups of individuals using different food webs or habitats, to better understand spatial connectivity at the population scale. Limited flows of individuals between the SEAO and the WIO are suggested. Albacore as predatory fish also provided some information on environmental and food web chemical contamination in the different study areas. (C) 2017 Elsevier B.V. All rights reserved.
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Grzebyk, D., et al. "Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene." Harmful Algae. 68 (2017): 1–16.
Résumé: This study investigated the genetic diversity of phytoplankton communities in six shallow lagoons located on the French coast of the northwestern Mediterranean Sea that represented a trophic gradient ranging from oligotrophic to hypereutrophic. The phytoplankton communities were sampled once a month from spring (May) to the beginning of autumn (September/early October) in 2012 and fractionated by size. Metabarcodes were generated from cDNAs by targeting the D1-D2 region of the 28S rRNA gene and pyrosequenced using Roche 454 technology. Examination of the annotated barcodes revealed harmful algal species not previously documented in these lagoons. Three ichthyotoxic species belonging to Pfiesteriaceae were detected: Luciella masanensis was relatively widespread and abundant in many samples, whereas Pfiesteria piscicida and Stoeckeria changwonensis were found as single barcode sequences. Furthermore, a phylogenetic analysis of barcodes annotated as belonging to Pfiesteriaceae suggested the existence of two previously undescribed clades. The other toxic or potentially harmful dinoflagellates detected through rare barcodes were Dinophysis acuminata, Vulcanodinium rugosum, Alexandrium andersonii and A. ostenfeldii. The two most abundant dinoflagellate taxa were Gymnodinium litoralis and Akashiwo sanguinea with respect to sequence numbers. Four diatom species from the genus Pseudo-nitzschia that potentially produce domoic acid were identified (P. galaxiae, P. delicatissima, P. brasiliana and P. calliantha). These observations are discussed in terms of the literature and monitoring records related to the identified taxa in this Mediterranean area. (C) 2017 Elsevier B.V. All rights reserved.
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Sardenne, F., et al. "Trophic structures in tropical marine ecosystems: a comparative investigation using three different ecological tracers." Ecol. Indic.. 81 (2017): 315–324.
Résumé: We looked at how three ecological tracers may influence the characterization and interpretation of trophic structures in a tropical marine system, with a view to informing tracer(s) selection in future trophic ecology studies. We compared the trophic structures described by stable isotope compositions (carbon and nitrogen), the total mercury concentration (THg) and levels of essential fatty acids (EFA) at both the individual and species level. Analyses were undertaken on muscle tissue samples from fish and crustacean species caught in the waters surrounding the Seychelles. The carbon isotope composition (delta C-13) correlated to the proportion of arachidonic acid (ARA), whereas the nitrogen isotope composition (delta N-15) correlated to the proportion of docosahexaenoic acid (DHA) and THg. At the individual level, trophic position obtained with these three last tracers are similar. In ' contrast, the eicosapentaenoic acid (EPA) was not clearly correlated to any of the tracers. At the species level, the use of EFA (ARA and DHA), as compared to stable isotopes, resulted in slight structural modifications, mainly in the middle trophic levels. For example, the EFA overestimated the trophic positions of Thunnus alalunga and Etelis coruscans but underestimated the trophic positions of other snappers and groupers. While ARA mainly originates from coastal/benthic areas, DHA is conserved throughout the food web and may be used as a proxy indicator of trophic position. However, metabolic disparities can affect ecological tracers and in turn, distort the trophic structures derived from their results. This is especially true for species with close trophic ecologies. Despite these caveats, we think that analysing at the individual level the wealth of ARA, DHA and THg data that has already been obtained through earlier nutrition or food security studies would enhance our understanding of trophic structures.
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2016 |
Amelineau, F., et al. "Microplastic pollution in the Greenland Sea: Background levels and selective contamination of planktivorous diving seabirds." Environ. Pollut.. 219 (2016): 1131–1139.
Résumé: Microplastics have been reported everywhere around the globe. With very limited human activities, the Arctic is distant from major sources of microplastics. However, microplastic ingestions have been found in several Arctic marine predators, confirming their presence in this region. Nonetheless, existing information for this area remains scarce, thus there is an urgent need to quantify the contamination of Arctic marine waters. In this context, we studied microplastic abundance and composition within the zooplankton community off East Greenland. For the same area, we concurrently evaluated microplastic contamination of little auks (Alle alle), an Arctic seabird feeding on zooplankton while diving between 0 and 50 m. The study took place off East Greenland in July 2005 and 2014, under strongly contrasted sea-ice conditions. Among all samples, 97.2% of the debris found were filaments. Despite the remoteness of our study area, microplastic abundances were comparable to those of other oceans, with 0.99 +/- 0.62 m(-3) in the presence of sea-ice (2005), and 2.38 +/- 1.11 m(-3) in the nearby absence of sea-ice (2014). Microplastic rise between 2005 and 2014 might be linked to an increase in plastic production worldwide or to lower sea -ice extents in 2014, as sea-ice can represent a sink for microplastic particles, which are subsequently released to the water column upon melting. Crucially, all birds had eaten plastic filaments, and they collected high levels of microplastics compared to background levels with 9.99 and 8.99 pieces per chick meal in 2005 and 2014, respectively. Importantly, we also demonstrated that little auks took more often light colored microplastics, rather than darker ones, strongly suggesting an active contamination with birds mistaking microplastics for their natural prey. Overall, our study stresses the great vulnerability of Arctic marine species to microplastic pollution in a warming Arctic, where sea-ice melting is expected to release vast volumes of trapped debris. (C) 2016 Elsevier Ltd. All rights reserved.
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Fouilland, E., et al. "Effect of mixing on the structure of a natural plankton community: a mesocosm study." Vie et Milieu. 66.3-4 (2016): 251–259.
Résumé: A plankton community (< 202 μm) from the St. Lawrence Estuary was isolated
in four outdoor mesocosms with SLOW and fast mixing regimes. Variations in the concentrations
of nutrients, chlorophyll a (Chl a), nitrogen transport rates and plankton species composition
were monitored over a 10 day period. The vertical mixing times (Tm) for the slow and
fast mixing regimes were 180 and 60 min, corresponding to a vertical eddy diffusivity (Kv) of
2.34 and 7.03 cm2 s–1, respectively. The different mixing regimes had a strong effect on the
physiology of the phytoplankton and the specific structure of the plankton assemblage. The
Slow mixing regime stimulated the development of a mixed community of flagellates, small
diatoms and proto-metazooplankton while the fast mixing regime triggered the development
of a large diatom-dominated community with lower abundances of proto-metazooplankton. At
the end of the 10 day experiment, the Chl a concentrations were 50 % higher in the mesocosms
with the fast mixing regime than in those with the slow mixing regime. These results indicate
that, under low nutrient conditions, higher turbulence gives a competitive advantage to diatoms
and decreases the zooplankton grazing pressure, resulting in net positive growth. Extrapolation
of these results to natural systems suggests that a wind-driven mixing event may increase
the net phytoplankton biomass production of a stratified water column, even if there is no external
input of nutrients.
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Matthews, T. J., et al. "Island species–area relationships and species accumulation curves are not equivalent: an analysis of habitat island datasets." Global Ecology and Biogeography. 25.5 (2016): 607–618.
Résumé: Aim The relationship between species number and area is of fundamental importance in macroecology and conservation science, yet the implications of different means of quantitative depiction of the relationship remain contentious. We set out (1) to establish the variation in form of the relationship between two distinct methods applied to the same habitat island datasets, (2) to explore the relevance of several key dataset properties for variation in the parameters of these relationships, and (3) to assess the implications for application of the resulting models. Locations Global. Methods Through literature search we compiled 97 habitat island datasets. For each we analysed the form of the island species–area relationship (ISAR) and several versions of species accumulation curve (SAC), giving priority to a randomized form (Ran-SAC). Having established the validity of the power model, we compared the slopes (z-values) between the ISAR and the SAC for each dataset. We used boosted regression tree and simulation analyses to investigate the effect of nestedness and other variables in driving observed differences in z-values between ISARs and SACs. Results The Ran-SAC was steeper than the ISAR in 77% of datasets. The differences were primarily driven by the degree of nestedness, although other variables (e.g. the number of islands in a dataset) were also important. The ISAR was often a poor predictor of archipelago species richness. Main conclusions Slopes of the ISAR and SAC for the same data set can vary substantially, revealing their non-equivalence, with implications for applications of species–area curve parameters in conservation science. For example, the ISAR was a poor predictor of archipelagic richness in datasets with a low degree of nestedness. Caution should be employed when using the ISAR for the purposes of extrapolation and prediction in habitat island systems.
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2013 |
Hess, P., et al. "Pinnatoxin G is responsible for atypical toxicity in mussels (Mytilus galloprovincialis) and clams (Venerupis decussata) from Ingril, a French Mediterranean lagoon." Toxicon. 75 (2013): 16–26.
Résumé: Following a review of official control data on shellfish in France, Ingril Lagoon had been identified as a site where positive mouse bioassays for lipophilic toxins had been repeatedly observed. These unexplained mouse bioassays, also called atypical toxicity, coincided with an absence of regulated toxins and rapid death times in mice observed in the assay. The present study describes pinnatoxin G as the main compound responsible for the toxicity observed using the mouse bioassay for lipophilic toxins. Using a well-characterised standard for pinnatoxin G, LC-MS/MS analysis of mussel samples collected from 2009 to 2012 revealed regular occurrences of pinnatoxin G at levels sufficient to account for the toxicity in the mouse bioassays. Baseline levels of pinnatoxin G from May to October usually exceeded 40 μg kg−1 in whole flesh, with a maximum in September 2010 of around 1200 μg kg−1. These concentrations were much greater than those at the other 10 sites selected for vigilance testing, where concentrations did not exceed 10 μg kg−1 in a 3-month survey from April to July 2010, and where rapid mouse deaths were not typically observed. Mussels were always more contaminated than clams, confirming that mussel is a good sentinel species for pinnatoxins. Profiles in mussels and clams were similar, with the concentration of pinnatoxin A less than 2% that of pinnatoxin G, and pteriatoxins were only present in non-quantifiable traces. Esters of pinnatoxin G could not be detected by analysis of extracts before and after alkaline hydrolysis. Analysis with a receptor-binding assay showed that natural pinnatoxin G was similarly active on the nicotinic acetylcholine receptor as chemically synthesized pinnatoxin G. Culture of Vulcanodinium rugosum, previously isolated from Ingril lagoon, confirmed that this alga is a pinnatoxin G producer (4.7 pg cell−1). Absence of this organism from the water column during prolonged periods of shellfish contamination and the dominance of non-motile life stages of V. rugosum both suggest that further studies will be required to fully describe the ecology of this organism and the accumulation of pinnatoxins in shellfish.
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2009 |
Bodiguel, X., et al. "A dynamic and mechanistic model of PCB bioaccumulation in the European hake (Merluccius merluccius)." Journal of Sea Research. 62.2-3 (2009): 124–134.
Résumé: Bioaccumulation is difficult to document because responses differ among chemical compounds, with environmental conditions, and physiological processes characteristic of each species. We use a mechanistic model, based on the Dynamic Energy Budget (DEB) theory, to take into account this complexity and study factors impacting accumulation of organic pollutants in fish through ontogeny. The bioaccumulation model proposed is a comprehensive approach that relates evolution of hake PCB contamination to physiological information about the fish, such as diet, metabolism, reserve and reproduction status. The species studied is the European hake (Merluccius merluccius, L. 1758). The model is applied to study the total concentration and the lipid normalised concentration of 4 PCB congeners in male and female hakes from the Gulf of Lions (NW Mediterranean sea) and the Bay of Biscay (NE Atlantic ocean). Outputs of the model compare consistently to measurements over the life span of fish. Simulation results clearly demonstrate the relative effects of food contamination, growth and reproduction on the PCB bioaccumulation in hake. The same species living in different habitats and exposed to different PCB prey concentrations exhibit marked difference in the body accumulation of PCBs. At the adult stage, female hakes have a lower PCB concentration compared to males for a given length. We successfully simulated these sex-specific PCB concentrations by considering two mechanisms: a higher energy allocation to growth for females and a transfer of PCBs from the female to its eggs when allocating lipids from reserve to eggs. Finally, by its mechanistic description of physiological processes, the model is relevant for other species and sets the stage for a mechanistic understanding of toxicity and ecological effects of organic contaminants in marine organisms.
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