Office Français de la Biodiversité

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium- and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement.

Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.

White-faced sakis (Pithecia pithecia) are among the least studied neotropical primates. The combination of shy and quiet behavior, their ability to move silently, and the extreme difficulty of capturing them may explain why very few field studies have been undertaken in undisturbed habitats. During the course of a wildlife rescue in French Guiana, six individuals were captured and translocated to a safe area of primary rainforest. In this area, based on the observation of 35 groups, the average group size was 2.3 animals (SD = 1.2) and a density of 0.28 group/km(2) (0.64 individuals/km(2)) was estimated from transect censuses. Our study focused successively on three radio-collared animals (two males and one female) over a 287-day period, starting from release to the loss of the animal. From the study start, the triangulation method was used prior to habitutation to human presence, followed thereafter by 1,327 hr of visual monitoring. The translocated animals settled down, and two of them had a stable and compact home range. Two of them merged in association with members of the resident population. A resident group had a much larger home range than previously reported: 148 and 287 ha, using grid cells and 100% minimum convex polygon techniques, respectively. A group composed of two translocated individuals (one male and one female) had a home range of 68 and 135 ha using the same techniques. Additionally, two solitary animals used 152 and 162 1-ha quadrats. We observed animals (translocated and residents) moving quickly in one direction up to 11.5 km. The mean daily path length of resident animals was 1,880 m. Sakis used the lower strata of the forest more when in group, and the intermediate strata more when solitary. Allogrooming is fairly common in social groups. On average, the activity period ranged from 7:17 to 15:59 hr.

Abstract Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit ( Oryctolagus cuniculus ). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus /GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus /GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution.

In this paper two geomorphologic maps (landform level and landscape level) are presented covering the French Guianan rainforest (84,000 km2) using full-resolution Shuttle Radar Topography Mission (SRTM) data. The entire country was segmented into 224,000 landform units on the basis of an original object-oriented approach using a modified counting box algorithm. A Principal Components Analysis (PCA) followed by k-means clustering (Ward's method) identified 12 different landform types corresponding to theoretical elementary landforms. The landscape map was generated by analyzing the spatial distribution of the different landform types. The different maps and models were compared with topographic field data collected on 92 transects totaling 260 km in length. The object-focused approach is a very efficient method that preserves geomorphologic consistency and discriminates between landforms using simple descriptors that are easily understood by non-geomorphologists. Despite major noise in the data, the landform map proved to be reliable and provided a strong spatial structure for the definition of landscape units. We recommend using the landform map at scales 1: 100,000?1: 250,000. Landscape map, used on a 1:1,000,000?1:2,000,000 scale, enabled us to draw bio-geographical limits in this region and provides exhaustive relief information that usefully supplements the geological map.

Mast seeding in temperate oak populations shapes the dynamics of seed consumers and numerous communities. Mast seeding responds positively to warm spring temperatures and is therefore expected to increase under global warming. We investigated the potential effects of changes in oak mast seeding on wild boar population dynamics, a widespread and abundant consumer species. Using long-term monitoring data, we showed that abundant acorn production enhances the proportion of breeding females. With a body-mass-structured population model and a fixed hunting rate of 0.424, we showed that high acorn production over time would lead to an average wild boar population growth rate of 1.197 whereas non-acorn production would lead to a stable population. Finally, using climate projections and a mechanistic model linking weather data to oak reproduction, we predicted that mast seeding frequency might increase over the next century, which would lead to increase in both wild boar population size and the magnitude of its temporal variation. Our study provides rare evidence that some species could greatly benefit from global warming thanks to higher food availability and therefore highlights the importance of investigating the cascading effects of changing weather conditions on the dynamics of wild animal populations to reliably assess the effects of climate change.

Plastic pollution in marine ecosystems constitutes an important threat to marine life. For vertebrates, macro/microplastics can obstruct and/or transit into the airways and digestive tract whereas nanoplastics (NPs; < 1000 nm) have been observed in non-digestive tissues such as the liver and brain. Whether NPs cross the intestinal epithelium to gain access to the blood and internal organs remains controversial, however. Here, we show directly NP translocation across the intestinal barrier of a fish, the European seabass, Dicentrarchus labrax, ex vivo. The luminal side of median and distal segments of intestine were exposed to fluorescent polystyrene NPs (PS-NPs) of 50 nm diameter. PS-NPs that translocated to the serosal side were then detected quantitatively by fluorimetry, and qualitatively by scanning electron microscopy (SEM) and pyrolysis coupled to gas chromatography and high-resolution mass spectrometry (Py-GC-HRMS). Fluorescence intensity on the serosal side increased 15-90 min after PS-NP addition into the luminal side, suggesting that PS-NPs crossed the intestinal barrier; this was confirmed by both SEM and Py-GC-HRMS. This study thus evidenced conclusively that NPs beads translocate across the intestinal epithelium in this marine vertebrate.

BACKGROUND: Gastrointestinal nematodes are ubiquitous for both domestic and wild ungulates and have varying consequences for health and fitness. They exist as complex communities of multiple co-infecting species, and we have a limited understanding of how these communities vary in different hosts, regions and circumstances or of how this affects their impacts. METHODS: We have undertaken ITS2 rDNA nemabiome metabarcoding with next-generation sequencing on populations of nematode larvae isolated from 149 fecal samples of roe deer of different sex and age classes in the two isolated populations of Chizé and Trois Fontaines in France not co-grazing with any domestic ungulate species. RESULTS: We identified 100 amplified sequence variants (ASVs) that were assigned to 14 gastrointestinal nematode taxa overall at either genus (29%) or species (71%) level. These taxa were dominated by parasites classically found in cervids-e.g. Ostertagia leptospicularis, Spiculopteragia spp. Higher parasite species diversity was present in the Trois Fontaines population than in the Chizé population including the presence of species more typically seen in domestic livestock (Haemonchus contortus, Bunostomum sp., Cooperia punctata, Teladorsagia circumcincta). No differences in parasite species diversity or community composition were seen in the samples collected from three zones of differing habitat quality within the Chizé study area. Young roe deer hosted the highest diversity of gastrointestinal nematodes, with more pronounced effects of age apparent in Trois Fontaines. The effect of host age differed between gastrointestinal nematode species, e.g. there was little effect on O. leptospicularis but a large effect on Trichostrongylus spp. No effect of host sex was detected in either site. CONCLUSIONS: The presence of some livestock parasite species in the Trois Fontaines roe deer population was unexpected given the isolation of this population away from grazing domestic livestock since decades. Overall, our results illustrate the influence of host traits and the local environment on roe deer nemabiome and demonstrate the power of the nemabiome metabarcoding approach to elucidate the composition of gastrointestinal nematode communities in wildlife.

Abstract Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations 1–6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories 7 , we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.

Abstract Step selection analysis (SSA) is a fundamental technique for uncovering the drivers of animal movement decisions. Its typical use has been to view an animal as ‘selecting’ each measured location, given its current (and possibly previous) locations. Although an animal is unlikely to make decisions precisely at the times its locations are measured, if data are gathered at a relatively low frequency (every few minutes or hours) this is often the best that can be done. Nowadays, though, tracking data are increasingly gathered at very high frequencies, often ≥1 Hz, so it may be possible to exploit these data to perform more behaviourally‐meaningful step selection analysis. Here, we present a technique to do this. We first use an existing algorithm to determine the turning‐points in an animal's movement path. We define a ‘step’ to be a straight‐line movement between successive turning‐points. We then construct a generalised version of integrated SSA (iSSA), called time‐varying iSSA (tiSSA), which deals with the fact that turning‐points are usually irregularly spaced in time. We demonstrate the efficacy of tiSSA by application to data on both simulated animals and free‐ranging goats Capra aegagrus hircus , comparing our results to those of regular iSSA with locations that are separated by a constant time‐interval. Using (regular) iSSA with constant time‐steps can give results that are misleading compared to using tiSSA with the actual turns made by the animals. Furthermore, tiSSA can be used to infer covariates that are dependent on the time between turns, which is not possible with regular iSSA. As an example, we show that our study animals tend to spend less time between successive turns when the ground is rockier and/or the temperature is hotter. By constructing a step selection technique that works between observed turning‐points of animals, we enable step selection to be used on high‐frequency movement data, which are becoming increasingly prevalent in modern biologging studies. Furthermore, since turning‐points can be viewed as decisions, our method places step selection analysis on a more behaviourally‐meaningful footing compared to previous techniques.

Since 2015, annual West Nile virus (WNV) outbreaks of varying intensities have been reported in France. Recent intensification of enzootic WNV circulation was observed in the South of France with most horse cases detected in 2015 (n = 49), 2018 (n = 13), and 2019 (n = 13). A WNV lineage 1 strain was isolated from a horse suffering from West Nile neuro-invasive disease (WNND) during the 2015 episode in the Camargue area. A breaking point in WNV epidemiology was achieved in 2018, when WNV lineage 2 emerged in Southeastern areas. This virus most probably originated from WNV spread from Northern Italy and caused WNND in humans and the death of diurnal raptors. WNV lineage 2 emergence was associated with the most important human WNV epidemics identified so far in France (n = 26, including seven WNND cases and two infections in blood and organ donors). Two other major findings were the detection of WNV in areas with no or limited history of WNV circulation (Alpes-Maritimes in 2018, Corsica in 2018–2019, and Var in 2019) and distinct spatial distribution of human and horse WNV cases. These new data reinforce the necessity to enhance French WNV surveillance to better anticipate future WNV epidemics and epizootics and to improve the safety of blood and organ donations.

Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels. To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work. The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level. This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.

DNA methylation-based biomarkers of ageing (epigenetic clocks) promise to lead to new insights into evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic ageing effects in wild species. In this study, we took advantage of a unique long-term (>40 years) longitudinal monitoring of individual roe deer (Capreolus capreolus) living in two wild populations (Chizé and Trois-Fontaines, France) facing different ecological contexts, to investigate the relationship between chronological age and levels of DNA methylation (DNAm). We generated novel DNA methylation data from n = 94 blood samples, from which we extracted leucocyte DNA, using a custom methylation array (HorvathMammalMethylChip40). We present three DNA methylation-based estimators of age (DNAm or epigenetic age), which were trained in males, females, and both sexes combined. We investigated how sex differences influenced the relationship between DNAm age and chronological age using sex-specific epigenetic clocks. Our results highlight that old females may display a lower degree of biological ageing than males. Further, we identify the main sites of epigenetic alteration that have distinct ageing patterns between the two sexes. These findings open the door to promising avenues of research at the crossroads of evolutionary biology and biogerontology.

Diadromous fishes have drastically declined over the last century, especially in Europe. Several authors have highlighted the role of large dams in this decline, but in fact, its causes are potentially multiple and cumulative, including degradation of local environmental conditions and widespread fragmentation of hydrographic networks associated with the pervasive establishment of smaller barriers. Consequently, there is a need to improve the identification and prioritization of the drivers of diadromous species loss in order to identify and apply the most appropriate conservation and restoration measures. In this study, we used both historical sources (from mid-18th to early 20th century) and current data to quantify the long-term loss of diadromous taxa over 555 sites throughout the French river network. Then, we modeled the effects of several anthropogenic pressures (e.g. barriers, water quality, hydrological and river morphological alterations) on diadromous taxon loss. Lastly, we assessed the potential consequences of four different scenarios of anthropogenic pressure reduction. Due to uncertainties in historical sources, some species were grouped into taxa leading to a potential underestimation of actual species extinctions. Despite this limitation, our results showed that the decline in diadromous assemblages is widespread but with contrasting magnitudes depending on site locations. The maximum height and density of barriers appeared as the major factors of taxon loss. Over the scenarios tested, we observed that exclusively improving local conditions have much more limited effects than restoring river continuity. Focusing actions on large dam removal did not show the strongest responses compared to removing medium and small-sized barriers. For effective and sustainable restoration of diadromous fish assemblage, (1) historical occurrences of diadromous fishes should be used as an indicator for assessing recovery, and (2) undertaken measures must be adapted to each basin to target and limit the number of barriers to remove while allowing diadromous fish recovery.

Camera traps have revolutionized how ecologists monitor wildlife, but their full potential is realized only when the hundreds of thousands of collected images can be readily classified with minimal human intervention. Deep learning classification models have allowed extraordinary progress towards this end, but trained models remain rare and are only now emerging for European fauna. We report on the first milestone of the DeepFaune initiative ( https://www.deepfaune.cnrs.fr ), a large-scale collaboration between more than 50 partners involved in wildlife research, conservation and management in France. We developed a classification model trained to recognize 26 species or higher-level taxa that are common in Europe, with an emphasis on mammals. The classification model achieved 0.97 validation accuracy and often > 0.95 precision and recall for many classes. These performances were generally higher than 0.90 when tested on independent out-of-sample datasets for which we used image redundancy contained in sequences of images. We implemented our model in a software to classify images stored locally on a personal computer, so as to provide a free, user-friendly, and high-performance tool for wildlife practitioners to automatically classify camera trap images. The DeepFaune initiative is an ongoing project, with new partners joining regularly, which allows us to continuously add new species to the classification model.

Sharing space with large carnivores on a human-dominated continent like Europe results in multiple conflictful interactions with human interests, of which depredation on livestock is the most widespread. We conducted an analysis of the impact by all four European large carnivores on sheep farming in 10 European countries, during the period 2010–2015. We ran a hierarchical Simultaneous Autoregressive model, to assess the influence of several ecological factors on the reported depredation levels. About 35,000 (SD = 4110) sheep kills were compensated in the ten countries as caused by large carnivores annually, representing 0.5% of the total sheep stock. Of them, 45% were recognized as killed by wolves, 24% by wolverines, 19% by lynx and 12% by bears. We found a positive relationship between wolf distribution and the number of compensated sheep, but not for the other three species. Depredation levels were lower in the areas where large carnivore presence has been continuous compared to areas where they disappeared and returned in the last 50 years. Our study shows that a few large carnivores can produce high damage, when the contribution of environmental, social, and economic systems predisposes for it, whereas large populations can produce a limited impact when the same components of the system reduce the probability that depredations occur. Time of coexistence plays in favour of a progressive reduction in the associated costs, provided that the responsible agencies focus their attention both on compensation and co-adaptation.

Studying the factors determining the sizes of home ranges, based on body mass, feeding style, and sociality level, is a long-standing goal at the intersection of ecology and evolution. Yet, how species-specific life history traits interact with different components of the landscape to shape differences in individual home ranges at within-population level has received much less attention. Here, we review the empirical literature on ungulates to map our knowledge of the relative effects of the key environmental drivers (resource availability, landscape heterogeneity, lethal and non-lethal risks) on the sizes of individual home ranges within a population and assess whether species' characteristics (body mass, diet, and social structure), account for observed variation in the responses of the sizes of individual home ranges to local environmental drivers. Estimating the sizes of home ranges and measuring environmental variables raise a number of methodological issues, which complicate the comparison of empirical studies. Still, from an ecological point of view, we showed that (1) a majority of papers (75%) supported the habitat productivity hypothesis, (2) the support for the influence of landscape heterogeneity was less pervasive across studies, (3) the response of cattle-type to variation in food availability was stronger than the response of moose-type, and (4) species-specific body mass or sociality level had no detectable effect on the level of support to the biological hypotheses. To our surprise, our systematic review revealed a dearth of studies focusing on the ecological drivers of the variation in the sizes of individual home ranges (only about 1% of articles that dealt with home ranges), especially in the later decade where more focus has been devoted to movement. We encourage researchers to continue providing such results with sufficient sample sizes and robust methodologies, as we still need to fully understand the link between environmental drivers and individual space use while accounting for life-history constraints.

Biodiversity has undergone a major decline throughout recent decades, particularly in farmland. Agricultural practices are recognized to be an important pressure on farmland biodiversity, and pesticides are suspected to be one of the main causes of this decline in biodiversity. As part of the national plan for reduction of pesticides use (Ecophyto), the French ministry of agriculture launched the 500 ENI (nonintended effects) monitoring program in 2012 in order to assess the unintended effects of agricultural practices, including pesticide use, on biodiversity represented by several taxonomic groups of interest for farmers. This long-term program monitors the biodiversity of nontargeted species (earthworms, plants, coleoptera, and birds), together with a wide range of annual data on agricultural practices (crop rotation, soil tillage, weed control, fertilizers, chemical treatments, etc.). Other parameters (e.g., landscape and climatic characteristics) are also integrated as covariates during the analyses. This monitoring program is expected to improve our understanding of the relative contribution of the different drivers of population and community trends. Here, we present the experience of setting up the 500 ENI network for this ambitious and highly complex monitoring program, as well as the type of data it collects. The issue of data quality control and some first results are discussed. With the aim of being useful to readers who would like to set up similar monitoring schemes, we also address some questions that have arisen following the first five years of the implementation phase of the program.

Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.

Abstract Background Population size and densities are key parameters in both fundamental and applied ecology, as they affect population resilience to density-dependent processes, habitat changes and stochastic events. Efficient management measures or species conservation programs thus require accurate estimates of local population densities across time and space, especially for continuously distributed species. For social species living in groups, population density depends on different components, namely the number of groups and the group size, for which relative variations in space may originate from different environmental factors. Whether resulting spatial variations in density are mostly triggered by one component or the other remains poorly known. Here, we aimed at determining the magnitude of the spatial variation in population densities of a social, group-living species, i.e. the European badger Meles meles , in 13 different sites of around 50 km 2 across France, to decipher whether sett density, group size or proportion of occupied sett variation is the main factor explaining density variation. Besides the intrinsic factors of density variation, we also assessed whether habitat characteristics such as habitat fragmentation, urbanisation, and resource availability, drove both the spatial variation of density components and local population densities. Results We proposed a new standardised approach combining use of multiple methods, namely distance sampling for estimating the density of occupied sett clusters, i.e. group density, and camera and hair trapping for genetic identification to determine the mean social group size. The density of adult badgers was on average 3.8 per km 2 (range 1.7–7.9 per km 2 ) and was positively correlated with the density of sett clusters. The density of adult badgers per site was less related to the social group size or to the proportion of occupied sett clusters. Landscape fragmentation also explained the spatial variation of adult badger density, with highly fragmented landscapes supporting lower adult densities. Density components were linked differently to environmental variables. Conclusions These results underline the need to break down population density estimates into several components in group-living species to better understand the pattern of temporal and spatial variation in population density, as different components may vary due to different ecological factors.