Jean-Claude Gaertner

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.

Influence of oyster culture on water column characteristics in a coastal lagoon (Thau, France)

The development of shellfish farming activities causes great changes in ecosystems functioning. In the Thau lagoon, oysters are reared on long constantly submerged lines, and these become fouled by several epifaunal species. The assemblage (oysters and epifauna) is defined as Oyster Culture Unit (OCU). The aim of our study was to estimate (i) how much the composition and the abundance of the epifaunal species can influence the nutrient and oxygen fluxes recorded at the shellfish—water interface and (ii) how these fluxes modify water column characteristics. We used Principal Component Analysis with Instrumental Variables (PCAIV). Two analyses were carried out, using sets of data on fluxes, the specific composition of the cultivated communities, and on oxygen, nutrient and chlorophyll a concentrations in the water column. The highest fluxes at the OCU—water interface were measured when epifaunal species richness was maximum. However, at our measurement scale (i. e. the oyster frame) no influence of this filter-feeders assemblage was observed on the chlorophyll a level. Conversely, we found a significant influence of oyster culture on the oxygen and dissolved nitrogen concentrations in the water column. The use of this recent factorial analysis was helpful to estimate the influence of the biofouling species composition on the fluxes at the OCU—water interface, and to estimate the potential impact of oyster cultures on the conditions prevailing in the water column.

The influence of natural cycles on coral reef fish movement: implications for underwater visual census (UVC) surveys

Movement patterns of some coral reef fishes change with natural cycles (e.g., tidal, lunar and seasonal), resulting in short-term shifts in fish assemblages. We reviewed the literature on temporal changes in coral reef fish assemblages derived from underwater visual census (UVC) and found that movement was rarely considered in experimental design and analysis or as cause of change in interpretation of the results. Studies of vagile species, large individuals, species forming transient spawning aggregations and studies of fishes in contiguous habitats are most likely to be affected by such movements. Ignoring predictable patterns of movement associated with such natural cycles in survey design and analysis increases “unexplained” variation, making it more difficult to detect longer-term changes in fish assemblages and reducing the effectiveness of UVC as a monitoring tool.

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

Abstract 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).

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 ± 1.4% and plastic load of 2.4 ± 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.