1. While competition is recognized as a major factor responsible for plant community dynamics, the genetics of intra-and interspecific competitive ability of a target species (i.e. level of intra-population genetic variation, identity of phenotypic traits under selection and genetic bases) still deserves a deeper investigation at the local spatial scale by considering both numerous genotypes and several interacting species. 2.In this study, we tested whether the genetics of competitive response and effect in Arabidopsis thaliana was dependent on the competitive environment at both the intraspecific and interspecific levels. We used a mapping population of 48 accessions (i) that maximize the genetic diversity of a local population of A. thaliana and (ii) that have been genotyped for 168 503 single nucleotide polymorphisms. 3. In a common garden experiment, those 48 accessions were grown in six competitive environments: the absence of competition, intraspecific competition and interspecific competition with four species frequently associated with A. thaliana in natural plant communities (i.e. Poa annua, Stellaria media, Trifolium repens and Veronica arvensis). A suite of nine phenotypic traits, including a proxy of fitness, were scored on each target A. thaliana plant and the aboveground dry biomass of its corresponding competitor was estimated. 4. We first showed that crossing reaction norms of competitive response (A. thaliana performance) and effect (competitor biomass) might promote maintenance of genetic variation in a local population of A. thaliana and species coexistence at a fine spatial scale. By estimating genotypic gradients of selection, we then demonstrated that the optimal phenotypic strategies in response to competition depend on the identity of the competitor species. Finally, a genomewide association mapping approach highlighted that genomic regions associated with direct genetic effects were (i) dependent on the competitor species and (ii) different from genomic regions associated with interspecific indirect genetic effects. 5. While a first step, this study highlighted the power of adding ecology to genomics in A. thaliana to identify genetic bases underlying micro-geographic adaptation to competition. Nextgeneration sequencing technologies will undoubtedly facilitate the discovery of molecular and genetic mechanisms underlying competitive ability in other plant species, and thereby the prediction of evolutionary trajectories of plant communities.

The high morphological variability observed in the genus Ammonia, together with its global distribution, led to the description of a plethora of species, subspecies, and varieties. Until now, many researchers used a limited number of (morpho-)species, and considered the numerous varieties as ecophenotypes. Recently, molecular studies show that these putative ecophenotypes are, in reality, well-separated genetically and should rather be considered as separate species. This study aims to investigate the morphological characteristics of three phylotypes (T1, T2, and T6) belonging to the genus Ammonia, encountered along European coasts. For this purpose, Ammonia specimens were sampled at 22 locations between 2014 and 2016 and were imaged using an environmental SEM (Scanning Electron Microscope). For 96 specimens, images of the spiral, umbilical, and peripheral sides were obtained and pore features were investigated using 1000x magnified images of the penultimate chamber on the spiral side. Sixty-one morphometric parameters were measured for each individual. To assign specimens to their respective phylotypes, we employed molecular analyses using SSU (Small Sub-Unit) rDNA fragments. A multivariate approach (Factorial Analysis of Mixed Data, FAMD), allowing the joint analysis of quantitative and qualitative measurements, was used to determine the most reliable morphometric parameters to discriminate the three phylotypes. Our results show that the use of only two morphological characteristics is sufficient to differentiate the three pseudocryptic species: the raised or flush character of the sutures on the central part of the spiral side and the mean pore diameter. These two criteria, which can be observed with a standard stereomicroscope, provide an efficient method to discriminate T1, T2, and T6 with at least 90% accuracy. We consider that there is still insufficient information to reliably assign previously defined formal scientific names to the three phylotypes, and therefore we recommend the continued use of phylotype designations T1, T2, and T6. Our results make it possible to study the distribution of these three pseudocryptic species (T1, T2, and T6) on the basis of stereomicroscope examination alone, which means these species can also be more easily recognized in dead/fossil assemblages. Among other things, this will allow verification in sediment cores of the putative recent introduction in European coastal areas of T6, which is often considered an exotic species originating from East Asia.

Abstract. Over the last decades, hypoxia in marine coastal environments has become more and more widespread, prolonged and intense. Hypoxic events have large consequences for the functioning of benthic ecosystems. In severe cases, they may lead to complete anoxia and the presence of toxic sulfides in the sediment and bottom-water, thereby strongly affecting biological compartments of benthic marine ecosystems. Within these ecosystems, benthic foraminifera show a high diversity of ecological responses, with a wide range of adaptive life strategies. Some species are particularly resistant to hypoxia–anoxia, and consequently it is interesting to study the whole foraminiferal community as well as species-specific responses to such events. Here we investigated the temporal dynamics of living benthic foraminiferal communities (recognised by CellTracker™ Green) at two sites in the saltwater Lake Grevelingen in the Netherlands. These sites are subject to seasonal anoxia with different durations and are characterised by the presence of free sulfide (H2S) in the uppermost part of the sediment. Our results indicate that foraminiferal communities are impacted by the presence of H2S in their habitat, with a stronger response in the case of longer exposure times. At the deepest site (34 m), in summer 2012, 1 to 2 months of anoxia and free H2S in the surface sediment resulted in an almost complete disappearance of the foraminiferal community. Conversely, at the shallower site (23 m), where the duration of anoxia and free H2S was shorter (1 month or less), a dense foraminiferal community was found throughout the year except for a short period after the stressful event. Interestingly, at both sites, the foraminiferal community showed a delayed response to the onset of anoxia and free H2S, suggesting that the combination of anoxia and free H2S does not lead to increased mortality, but rather to strongly decreased reproduction rates. At the deepest site, where highly stressful conditions prevailed for 1 to 2 months, the recovery time of the community takes about half a year. In Lake Grevelingen, Elphidium selseyense and Elphidium magellanicum are much less affected by anoxia and free H2S than Ammonia sp. T6. We hypothesise that this is not due to a higher tolerance for H2S, but rather related to the seasonal availability of food sources, which could have been less suitable for Ammonia sp. T6 than for the elphidiids.

While long-term monitoring is essential to improve our knowledge of marine ecosystems health, 37 it remains challenging to summarise complex ecological data in order to characterise and understand 38 biodiversity trends. To compile monitoring data across large numbers of species, scientists and policymakers mainly rely on diversity and species richness indices. This task may prove complicated 40 however, as many indices exist and no individual metric undoubtedly emerges as the best overall. Here, 41 using data from zooplankton surveys from 1998 to 2014, we examined year-to-year changes in copepod 42 communities in two littoral ecosystems of Western Europe-the Arcachon Bay and the Gironde estuary 43-that share similar climate, but with different local ecological processes, especially hydrological 44 conditions. We tested the ability of commonly used α and ß-diversity metrics, such as species richness, 45 Pielou's evenness or Jaccard's index, to mirror year-to-year changes in species abundances and we 46 detected a synchronous change in both copepod abundances and α-diversity that took place circa 2005 47 in the two sites. In response to changes in environmental conditions such as nutrients, salinity, river 48 discharge or particulate matter, two opposite biodiversity trends were observed, with a decrease in 49 copepod diversity in the Arcachon Bay but an increase in the downstream part of the Gironde estuary. 50 Although diversity metrics allowed us to well detect trends, the use of multivariate approaches such as 51 principal component analysis provided important information on how and why diversity fluctuates. Our 52 study provides evidence that long-term monitoring programmes must be encouraged for optimising 53 management and conservation actions such as the Marine Strategy Framework Directive and that more 54 local comparative studies need to be initiated for better characterising diversity trajectories at very fine 55 scales at which ecologists often work.