Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.

Environmental DNA (eDNA) metabarcoding is a promising tool to estimate aquatic biodiversity. It is based on the capture of DNA from a water sample. The sampled water volume, a crucial aspect for efficient species detection, has been empirically variable (ranging from few centiliters to tens of liters). This results in a high variability of sampling effort across studies, making comparisons difficult and raising uncertainties about the completeness of eDNA inventories. Our aim was to determine the sampling effort (filtered water volume) needed to get optimal inventories of fish assemblages in species-rich tropical streams and rivers using eDNA. Ten DNA replicates were collected in six Guianese sites (3 streams and 3 rivers), resulting in sampling efforts ranging from 17 to 340 liters of water. We show that sampling 34 liters of water detected more than 64% of the expected fish fauna and permitted to distinguish the fauna between sites and between ecosystem types (stream versus rivers). Above 68 liters, the number of detected species per site increased slightly, with a detection rate higher than 71%. Increasing sampling effort up to 340 liters provided little additional information, testifying that filtering 34 to 68 liters is sufficient to inventory most of the fauna in highly diverse tropical aquatic ecosystems.

Aim Differences in dispersal limitation and environmental filtering have been proposed to explain differences in diversity patterns between regions. Incorporating functional traits into studies of assembly rules allows the relative strengths of such processes to be distinguished. We test the predictions that assemblages in a similar environment under strong dispersal limitation should be differentiated taxonomically but not functionally, whereas strong environmental filtering should more differentiate assemblages functionally. Location French Guiana and France. Methods We used two datasets on fish assemblage composition: one for French Guiana and one for continental France. We constrained both dataset to have similar geographical extent and similar environment using site location and topographic variables of the French Guiana dataset to select continental France data. We estimated functional diversity using a combination of 15 fish morphological traits. We computed species and functional richness at regional and local scales for both regions. We calculated taxonomic and functional turnover between sites and compared them within and between regions. Results Taxonomic and functional richness were higher in tropical fish assemblages than in temperate ones both on regional and local scales. Species richness differences between the two regions resulted in very similar functional richness. Temperate assemblages showed a higher functional turnover than tropical assemblages, but a lower taxonomic turnover. We found a stronger turnover in taxonomic diversity than in functional diversity between tropical assemblages, and the opposite pattern between temperate ones. Main conclusions The higher functional richness in tropical assemblages was mainly caused by an increased number of species compared to temperate assemblages, probably linked with an increase in available niches. Dispersal limitation was the predominant process in structuring Guianese stream fish assemblages causing strong species replacement, whereas French stream fish assemblages were mainly under strong environmental filtering resulting in local adaptations to different environments.

Freshwater ecology templates were developed in temperate streams, but whether they also apply to tropical streams that harbour a higher biological diversity than their temperate counterparts remains uncertain. This is particularly true for tropical fish assemblages inhabiting small streams that have been less studied than larger, higher‐order lowland streams. Here, we disentangled the strength of spatial (longitudinal and environmental) drivers, and scale‐specific (drainage basin, reach and local scale) determinants of species richness and composition of freshwater fish assemblages inhabiting small streams in French Guiana. We found that species richness increased from upstream to downstream but also with increasing local habitat structural diversity independently of stream position in the upstream–downstream gradient. This pattern was shared by the two most speciose fish orders (Characiformes and Siluriformes), demonstrating that species addition rather than species replacement shaped species richness in these assemblages. Species composition of fish assemblages was determined equally by their spatial structure within drainage and by the environment, and assemblages differed both with distance and along an upstream–downstream gradient. The environmental effect on species assemblages indicated by the fact that almost all environmental descriptors had slight but nonetheless significant effects on assemblage composition, probably reflecting species‐specific responses to the local environment. In contrast, despite a strong micro‐endemism between drainages for some taxa, assemblages were only slightly affected by river drainage identity, since widespread species were a common constituent of assemblages in all rivers. We identified five species assemblages characterising different local habitat features from torrential areas to lowland muddy areas. We also distinguished fish assemblages from confluence areas with larger rivers, which differed from the other five assemblages. The fish zonation patterns we report can constitute a benchmark for future studies measuring the impact of anthropogenic disturbances on Neotropical forest streams.

Environmental DNA (eDNA) methods have recently emerged as noninvasive powerful methods to inventory biodiversity in a wide range of ecosystems (reviewed in Tab erlet et al., 2018;Zinger et al., 2020). The recent striking progress in DNA sequencing technologies allowed to shift from single-species detection (eDNA barcoding) (Ficetola et al., 2008) to the simultaneous detection of entire species assemblages (eDNA metabarcoding) (Civade et al., 2016;

Environmental DNA [eDNA] metabarcoding has recently emerged as a non-destructive alternative to traditional sampling for characterising species assemblages. We here provide a consistent dataset synthetising all eDNA sampling sites in French Guiana to date. Field collections have been initiated in 2014 and have continued until 2019. This dataset is however a work in progress and will be updated after each collecting campaign. We also provide a taxon by site matrix for fishes presence / absence as inferred from eDNA. Our aim is to allow a transparent communication to the stakeholders and provide the foundation for a monitoring programme based on eDNA. The lastest version of the dataset is publicly and freely accessible through the CEBA geoportal (http://vmcebagn-dev.ird.fr) or through the French Guiana geographic portal (https://www.geoguyane.fr).

The statistical reliability of a pollen count in representing the true composition of modern and fossil pollen assemblages depends on the minimum number of pollen grains counted. In palynological literature this number varies between b150 and N1000, but very few studies have probed the question using robust statistical approaches. Here, we use the Pearson-Brown Prophecy formula and apply it to different fossil pollen counts from two large lake systems in Iran to calculate the minimum terrestrial and total pollen count necessary to obtain a reliable representativity of pollen assemblages. Our results surprisingly show that a pollen count of b150 is sufficient to achieve a reliability of 0.90 with no additional significant information obtained when counting more pollen. If the upland vegetation reconstruction is important, then terrestrial pollen counts as low as 67 could be sufficient. It seems that the statistically significant pollen counts are site-specific and vary between different environments and even within the same type of environment. We suggest that this value should be calculated for each pollen site so that the pollen analysts can more efficiently manage their time when counting pollen slides.

Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.