Metallic trace element contamination of the giant clam Tridacna maxima in French Polynesia.

This study is a first assessment of Metallic Trace Elements (MTE) contamination of four lagoons in French Polynesia, chosen because their main anthropic uses are potential sources of MTE (military, agriculture, maritime). We used the giant clam Tridacna maxima as a biointegrator of fifteen MTE to assess the environmental footprint of human activities. The study of organotropism showed that not only the kidney but also the gonad and digestive system (GDS) are accumulator organs of interest for ETM biomonitoring. This result confirms that heterotrophic feeding is the pathway of ETM accumulation. Here, T. maxima appeared to be a super-accumulator of Ni (2700 ppm.dw), but also revealed at Tubuai (As, Fe, Mn) and Arutua (Cd, Zn) the environmental footprint of agricultural and maritime activities. The concentration of Cd recorded in Arutua (5 ppm.dw) both in KID and GDS, also underline the need for better control of effluents resulting from human activities.

Assessment of congruence between co-occurrence and functional networks: A new framework for revealing community assembly rules.

Describing how communities change over space and time is crucial to better understand and predict the functioning of ecosystems. We propose a new methodological framework, based on network theory and modularity concept, to determine which type of mechanisms (i.e. deterministic versus stochastic processes) has the strongest influence on structuring communities. This framework is based on the computation and comparison of two networks: the co-occurrence (based on species abundances) and the functional networks (based on the species traits values). In this way we can assess whether the species belonging to a given functional group also belong to the same co-occurrence group. We adapted the Dg index of Gauzens et al. (2015) to analyze congruence between both networks. This offers the opportunity to identify which assembly rule(s) play(s) the major role in structuring the community. We illustrate our framework with two datasets corresponding to different faunal groups and ecosystems, and characterized by different scales (spatial and temporal scales). By considering both species abundance and multiple functional traits, our framework improves significantly the ability to discriminate the main assembly rules structuring the communities. This point is critical not only to understand community structuring but also its response to global changes and other disturbances.

Double trouble in the South Pacific subtropical gyre: Increased plastic ingestion by fish in the oceanic accumulation zone.

Fish are an important food source for South Pacific (SP) island countries, yet there is little information on contamination of commercial marine fish species by plastic. The aim of our study was to perform a broad-scale assessment of plastic ingestion by fish common in the diet of SP inhabitants. We examined 932 specimens from 34 commercial fish species across four SP locations, and some of the prey they ingested, for the presence of marine plastics. Plastic was found in 33 species, with an average ingestion rate (IR) of 24.3 ±â€¯1.4% and plastic load of 2.4 ±â€¯0.2 particles per fish. Rapa Nui fish exhibited the greatest IR (50.0%), significantly greater than in other three locations. Rapa Nui is located within the SP subtropical gyre, where the concentration of marine plastics is high and food is limited. Plastic was also found in prey, which confirms the trophic transfer of microplastics.

Correction: Large-Scale Diversity of Slope Fishes: Pattern Inconsistency between Multiple Diversity Indices.

[This corrects the article DOI: 10.1371/journal.pone.0066753.].

Indices for assessing coral reef fish biodiversity: the need for a change in habits.

We present the first representative and quantified overview of the indices used worldwide for assessing the biodiversity of coral reef fishes. On this basis, we discuss the suitability and drawbacks of the indices most widely used in the assessment of coral fish biodiversity. An extensive and systematic survey of the literature focused on coral reef fish biodiversity was conducted from 1990 up to the present. We found that the multicomponent aspect of biodiversity, which is considered as a key feature of biodiversity for numerous terrestrial and marine ecosystems, has been poorly taken into account in coral reef fish studies. Species richness is still strongly dominant while other diversity components, such as functional diversity, are underestimated even when functional information is available. We also demonstrate that the reason for choosing particular indices is often unclear, mainly based on empirical rationales and/or the reproduction of widespread habits, but generally with no clear relevance with regard to the aims of the studies. As a result, the most widely used indices (species richness, Shannon, etc.) would appear to be poorly suited to meeting the main challenges facing the monitoring of coral reef fish biodiversity in the future. Our results clearly show that coral reef scientists should rather take advantage of the multicomponent aspect of biodiversity. To facilitate this approach, we propose general guidelines to serve as a basis for the selection of indices that provide complementary and relevant information for monitoring the response of coral reef fish biodiversity in the face of structuring factors (natural or anthropic). The aim of these guidelines was to achieve a better match between the properties of the selected indices and the context of each study (e.g. expected effect of the main structuring factors, nature of data available).

Large-scale diversity of slope fishes: pattern inconsistency between multiple diversity indices.

Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36°3'- 45°7' N; 5°3'W - 28°E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness.

On goodness-of-fit measure for dendrogram-based analyses.

Clustering methods are widely used tools in many aspects of science, such as ecology, medicine, or even market research, that commonly deal with dendrogram-based analyses. In such analyses, for a given initial dissimilarity matrix, the resulting dendrogram may strongly vary according to the selected clustering methods. However, numerous dendrogram-based analyses require adequate measurement for assessing of which of the clustering methods preserves most faithfully the initial dissimilarity matrix. While cophenetic correlation coefficient-based measures have been widely used for this purpose, we emphasize here that it is not always a suitable approach. We thus propose a measure based on a matrix norm, the 2-norm, to adequately check which of the resulting ultrametric distance matrices related to the dendrograms is the closest to the initial dissimilarity matrix. In addition, we also propose an objective way to define a benchmark value (threshold value) in order to assess whether the degree of conformity between the ultrametric distance matrix selected and the initial dissimilarity matrix is satisfactory. Our proposal may notably be incorporated within a recently proposed approach that involves the use of clustering methods in environmental science and beyond. In ecology, various functional diversity indices based on clustering species from their functional dissimilarities may benefit from this overall approach.

Assessment of the ecological quality status of soft-bottoms in Reunion Island (tropical Southwest Indian Ocean) using AZTI marine biotic indices.

The ability of the two synthetic marine biotic indices, AMBI and M-AMBI, to account for changes in the ecological quality of coastal soft bottoms of Reunion Island according to disturbances was assessed from macrobenthic samples collected in five sectors between 1994 and 2004. Samples were collected under non-perturbed conditions and at two sites subjected to heavy organic enrichment. Both indices are based on a classification of macrofauna into ecological groups (EG), and their transfer to tropical waters required some adaptations. These indices proved efficient in detecting a degradation of habitat quality. Their use resulted in the classification of all sites sampled between 1996 and 1998 as "good" or "high". M-AMBI nevertheless tended to result in the attribution of a slightly worse ecological quality status than AMBI. Together with an update of the EG species list for the Indian Ocean area, our results support the extension of both indices for the assessment of tropical soft bottoms.