Office Français de la Biodiversité

Recurring events like migrations are an important part of the biological cycles of species. Understanding the factors influencing the timing of such events is crucial for determining how species face the pervasive consequences of climate change in highly seasonal environments. Relying on data from 406 GPS‐collared Alpine ibex Capra ibex monitored across 17 populations, we investigated the environmental and individual drivers of short‐distance migrations in this mountain ungulate. We found that vegetation phenology, including spring growth and autumn senescence, along with snow dynamics—snowmelt in spring, onset of snow cover in autumn—were the main drivers of the timing of migration. In spring, ibex migration timing was synchronized with the peak of vegetation green‐up, but more in males than in females. Specifically, a peak of green‐up occurring 10 days later delayed migration by 6.4 days for males and 2.7 days for females. This led to increased differences in migration timing between sexes when the peak of green‐up occurred early or late in the season. In addition, ibex delayed migration timing when the length of the spring season was longer and when the date of snowmelt on ibex summer ranges occurred later. Similarly, in autumn, prolonged vegetation senescence and delayed onset of snow cover led to later migration. Overall, we observed a high degree of behavioural plasticity, with individuals responding to inter‐annual variations in vegetation and snow phenology, even though the extent of these adjustments in migration dates was lower than the magnitude of the interannual changes in environmental conditions. Nonetheless, females could be less plastic than males in their timing of spring migration, likely due to the parturition period following migration forcing them to trade off foraging needs with predation risk. As the identified drivers of ibex migration are known to be and will continue to be largely impacted by climate change, the capacity of ibex to respond to such rapid changes could differ between sexes.

Environmental DNA (eDNA) metabarcoding has revolutionized the biodiversity monitoring in aquatic ecosystems, giving access to taxonomic lists in a non-disruptive way. Despite limits (taxonomic resolution nor taxa quantification), the method has repeatedly proved its effectiveness and is now used as routine freshwater monitoring tool. Especially since traditional method, including electrofishing (TEF), are reputed stressful for the species, non-selective and disruptive for the ecosystem, leading to its abandonment in Martinique (F.W.I.) for regular monitoring. The aim of this project was to explore the possibility of using eDNA metabarcoding for the detection of fish and decapods in Martinique streams, by first validating it with TEF. We selected 14 stations, a representative panel of the river diversity, and performed TEF and eDNA to compare both, based on the species richness recovered. Then, from eDNA taxonomic inventories, we assessed the ecological state of the studied stations, using different biodiversity indices (Shannon, Simpson and Bray-Curtis) and investigated how stations abiotic characteristics shape assemblages. Here, we confirmed the eDNA metabarcoding method as a reliable tool for monitoring fish and decapods, confirming most of the taxa caught by TEF and revealing the presence of additional (native and/or invasive) species. We faced some issues in discriminating some genetically close species (e.g. Sicydium sp.) potentially leading to under-representation in community assemblages, but not in functional diversity. Additional efforts are needed to raise standardized protocols, but we encourage stakeholders to join such initiative to shed light on the rich biodiversity in sometimes poorly studied regions and to face invasions.

Although global change and landscape modifications have degraded natural habitats, some species are able to thrive in anthropized landscapes by exploiting agricultural subsidies. In heterogeneous agroecosystems, spatial variation in landscape composition is predicted to impact demographic performance of wildlife depending on predominant agricultural practices and the distribution of remnant fragments of semi-natural habitat. Body mass is a key driver of among-individual variation in performance which varies at a fine scale, depending on landscape structure. We tested the hypothesis that the availability of rich crops (i.e. sorghum, corn and sunflower) in heterogeneous agricultural landscapes promotes rapid first-year growth of roe deer fawns, potentially driving spatial variation in demographic performance. We used GPS data of 166 juveniles (8–10 months old) inhabiting a heterogeneous agricultural landscape to predict their home range and evaluate its composition in terms of crops that may provide complementary resources. We hypothesized that juveniles with a post-weaning home range that included these crop types would be the heaviest at the onset of winter. Winter body mass of juveniles decreased by 35 ± 5 g per percentage point increase of woodland in their home range, so that juveniles with almost no woodland in their home range were about 3.5 kg heavier than those living in pure forest. Further, individuals with at least some corn in their home range were, on average, 773 ± 237 g heavier than those with none. Agricultural food subsidies reshape the habitat-dependent body mass trajectory of large herbivores, likely driving improved reproductive performance in agricultural landscapes.

Few studies have explored population dynamics of species sharing life-history traits and common environmental drivers but living in widely separated regions or continents. Large-scale climate cycles can impact habitats and populations over broad geographic areas and may act as global forces shaping animal population dynamics. We tested for synchronous population dynamics of eight ecologically equivalent duck species in Western Europe (WEU) and central North America (NA) from 1976 to 2019. We investigated the extent to which the Atlantic Multi-Decadal Oscillation (AMO) may have induced shared climatic conditions on the breeding areas of these populations and whether the index was correlated with duck population dynamics. Evidence of annual and long-term population synchrony was assessed by estimating correlation in annual growth rates and population abundances, respectively. Shared (increasing) long-term trends in WEU and NA were found in four species-pairs, but no species-pair had synchronous population growth on an annual basis. Three species-pairs sharing trends were positively correlated with the AMO index which increased during the study period. Positive cycling of the AMO was correlated with increased temperature and precipitation in breeding areas of both continents, which may have produced favorable conditions (earlier springs, more ponds) for some duck populations. Differences in the local effects of weather on environmental conditions and other continent-specific extrinsic factors may mask annual synchrony in the response of continental populations to climate. Potential links between the AMO trends and extrinsic factors such as shared changes in anthropogenic drivers (e.g., climate and land use change) should be addressed in future studies.

In 2022, a very high number of wild bird deaths associated with the detection of highly pathogenic (HP) H5 avian influenza virus (AIV) lineage Gs/GD/96, clade 2.3.4.4b viruses were unusually observed in Europe between May and September, whereas prior to 2022 most of these HP H5 AIVs detected in wild birds in Europe were almost all detected between October and March and few between April and September. In France, wild birds affected by this virus during this unusual period were mainly seabirds, including larids and sulids. Although the abnormal mortalities in larids and sulids were reported simultaneously, sequencing of the complete genomes of the viruses identified in these seabirds showed that sulids are mainly infected with genotype EA-2020-C, whereas larids are mainly infected with genotype EA-2022-BB. The identification of these two genotypes, therefore, confirmed that there was no direct link between the abnormal mortality observed in sulids and the abnormal mortality observed in larids. These two seabird mortality events can also be distinguished by the evolutionary pattern of the number of detections. Indeed, sulid mortality associated with the EA-2020-C genotype was observed in France only between July and September, corresponding to a single epidemic wave, whereas larid mortality associated with the EA-2022-BB genotype began in France and Europe in May 2022 and then this genotype continued to spread among larids in France in the form of several successive epidemic waves until at least September 2023.

Sex chromosomes differ in their inheritance properties from autosomes, and hence may encode complementary information about past demographic events. We compiled and analysed a range-wide resequencing dataset of the red deer (Cervus elaphus), one of the few Eurasian herbivores of the Late Pleistocene megafauna still found throughout much of its historic range. Our analyses of 144 whole genomes reveal striking discrepancies between the population clusters suggested by autosomal and X-chromosomal data. We postulate that the genetic legacy of Late Glacial population structure is better captured and preserved by the X chromosome than by autosomes, for two reasons. First, X chromosomes have a lower Ne and hence lose genetic variation faster during isolation in glacial refugia, causing increased population differentiation. Second, following postglacial recolonisation and secondary contact, immigrant males pass on their X chromosomes to female offspring only, which effectively halves the migration rate when gene flow is male-mediated. Our study illustrates how a comparison between autosomal and sex chromosomal phylogeographic signals unravels past demographic processes which otherwise would remain hidden.

Identifying the wildlife reservoirs of bacterial pathogens, spatially and temporally, is important for assessing the threats to human and the rest of the biosphere. Our objective was to study Europe-wide characteristics of the fecal microbiota of four highly mobile migratory vertebrates, that is, one bat (Pipistrellus nathusii) and three bird species (Turdus merula, Anas platyrhynchos, Columba palumbus). The 351 sample PacBio data set of almost the entire 16S rRNA gene with 438,997 amplicon sequence variants (ASVs) assigned 3,277 bacterial species. A significant proportion of the ASVs were assigned to bacterial genera having species pathogenic to human or animals. These pathogen ASVs accounted for 45% of all the ASVs and statistically were more frequent at higher latitudes and in younger age groups. In 36 samples, more than >90% of all the PacBio reads were assigned to these pathogenic genera. We designate to individuals of these samples a new term, that is, a pathogen bloomer. The pathogen bloomers, which did not display apparent macroscopic disease symptoms, were detected in Nathusius bat (n = 8; Finland and Latvia), blackbird (n = 6; Finland, Latvia and Denmark), and wood pigeon (n = 22; Finland and France), but not in mallard. Key species-level taxonomic assignments in the pathogen bloomers were the two well-known enteropathogens (Campylobacter jejuni or Escherichia coli) and one emerging enteropathogen (Escherichia marmotae). Our data imply that the studied common migratory vertebrates may contribute to the transmission of bacterial pathogens across the European continent. IMPORTANCE The understanding of gut microbiota composition and dynamics in wild vertebrate populations, especially in highly mobile vertebrates, birds and bats, remains limited. Our study sheds light on the critical knowledge gap in how common pathogenic bacterial taxa of fecal microbiota are in migratory bats and birds in Europe. We found out that bacterial genera having species pathogenic to human or animals constituted a substantial portion of the fecal microbiota in all the studied host taxa. Most importantly, we identified asymptomatic individuals that were dysbiotic with bacterial pathogen overgrowth. These previously unknown pathogen bloomers appear as potent Europe-wide transmitters of bacterial pathogens, which cause, for example, diarrhea and bacteremia in human. Our findings may contribute to better understanding of seasonal disease hotspots and pathogen spillover risks related to migratory vertebrates.

Habitat degradation induced by human activities can exacerbate the spread of wildlife disease and could hinder the recovery of imperiled species. The endangered green turtle Chelonia mydas is impacted worldwide by fibropapillomatosis (FP), a neoplastic infectious disease likely triggered by the Scutavirus chelonidalpha5 with coastal anthropogenic stressors acting as cofactors in disease development. Here, we studied fibropapillomatosis dynamics and its demographic consequences using an 11-year capture-mark-recapture dataset in Anse du Bourg d’Arlet/Chaudière (ABAC) and Grande Anse d’Arlet (GA), two juvenile green turtle foraging grounds in Martinique, French West Indies. Afflicted turtles had similar mortality and permanent emigration rates to the non-afflicted ones. Fibropapillomatosis was commonly observed in large individuals and disease recovery may take several years. Consequently, permanent emigration before full recovery from the disease is suspected and might affect the developmental migration success. Additionally, the results revealed that the FP had higher prevalence and severity, and progressed two times faster in ABAC than in GA despite the proximity (< 2 km) and the similarity of the two foraging grounds. The reasons for these differences remain unidentified. Locally, further studies should be focused on the determination of the external and internal cofactors related to the observed FP dynamics. Finally, the investigations should be extended at a global regional scale to determine potential deleterious effect of the FP on the adult life-stage. These perspectives improves upon our overall understanding on the interplay between wildlife diseases, hosts and environmental factors.

Migratory species experience various conditions and events throughout their annual cycle that influence their spatial and demographic dynamics. To understand these dynamics, it is essential to describe the origin and destination of individuals. Migratory connectivity, which is defined as the geographic linkage between populations across the annual cycle, is increasingly incorporated in population models to relate population trends to environmental variables at different stages of the cycle. However, such information on migratory movements is obtained independently from the study of population dynamics despite the interaction between both processes. Expanding on the growing use of integrated modelling approaches, we developed an integrated framework that allows the sharing of information between migratory connectivity and population data. We first assembled an integrated migratory connectivity model and an integrated population model to join the analysis of GPS, live‐reencounter, dead‐recovery, capture–mark–recapture, and population count data within a unified framework. Based on simulated data, we assessed the ability of the resulting integrated connectivity and population model to produce unbiased and precise connectivity and demographic estimates. We then applied the same assessment to real data using the Eurasian Curlew (Numenius arquata) as a case study. On simulated data, the integrated connectivity and population model estimated connectivity and survival parameters with no bias and similar precision to the connectivity model alone. However, it outperformed the population model in estimating fecundity in the absence of explicit productivity data. When applied to the Eurasian Curlew, the integrated connectivity and population model produced overall similar migratory connectivity and more accurate demographic estimates than the connectivity model alone, consistent with previous studies. Additionally, the model was able to estimate fecundity, whereas the data were too sparse for the population model alone to disentangle juvenile survival and fecundity. The sharing of information between migratory connectivity and population data improved the estimation of demographic parameters by the population model and improved connectivity parameter estimates when data were scarce. This flexible framework can be generalised to include diverse data on migration movements, population structure, individual heterogeneity or environmental variables, allowing further investigation of the interaction between migration patterns and population dynamics.

Biased birth sex ratios have been documented in many mammalian populations, but it is often difficult to know whether they result from biases in the sex ratio at conception and/or sex differences in prenatal mortality. It is generally admitted that there is an excess of males at conception and a higher level of mortality during gestation for males because of a positive relationship between size and vulnerability. Here, we challenge this classical prediction in a wild boar (Sus scrofa) population facing highly variable food resources (mast seeding) and in which male fetuses are heavier than females. Using long-term hunting and mast seeding data, we show that sex ratio at conception is balanced and that females suffer from higher embryonic mortality particularly in large litters, whatever the level and the type of food resources. One possible explanation is that a female embryo is ready for implantation later than an identically aged male because of slower development and is more likely to miss the implantation window. To what extent a lower survival of female embryos is a common feature in mammals remains to be carefully explored.

Coastal lagoons are diverse habitats with significant ecological gradients, which provide crucial ecosystem services but face threats from human activities such as invasive species and pollution. Among the species inhabiting the lagoons, the critically endangered European eel (Anguilla anguilla) is an emblematic species strongly impacted by contamination and parasitism. Several indicators were developed to assess the quality of eel at a large geographic scale. Most indicators are based on the concentration of individual pollutant and/or abundance of parasites separately without considering individual variations. This study assessed the quality of 59 eels captured at three different sites inside a Mediterranean lagoon complex (the Camargue, South of France), by integrating multiple degradation factors (POPs, TEs, and A. crassus infestation) and considering individual eel characteristics (length, age, growth rate, and sex). Using multivariate TOPSIS analysis including these degradation factors, this study found that eel quality decreased with age but did not significantly vary between sites. When focusing on each degradation factor, A. crassus infestation rates were lower in older eels, independently to the site; however, the POPs and TEs contaminations were lower in the Grandes Cabanes site compared to the Vaccarès and Fumemorte sites even if smaller and younger eels were more contaminated by POPs. These findings reveal the fine-scale spatial variability in eel quality, with TOPSIS analysis providing a robust method to rank and score scenarios. This approach enhances the understanding of habitat degradation sources affecting eel contamination and parasitic infestation, supporting more effective strategies for sustainable habitat management.

The installation of automatic detection systems (ADSs) on operating wind energy facilities is a mitigation measure to reduce bird collisions. The effectiveness of an ADS depends on a combination of parameters, including the detection distance of the bird, its flight speed, and the time to complete the chosen action (e.g., turbine shutdown). We created a web application, Eoldist, to calculate cautionary detection distances required by an ADS, using bird flight speed and turbine shutdown time as input parameters. We compiled a database of the flight speeds of 168 Western Palearctic birds from a review of scientific literature supplemented by an analysis of unpublished GPS‐tracking datasets. To estimate turbine shutdown time, we conducted 137 field trials of experimental shutdown at seven wind farms and found that the duration to reach residual rotor speeds of 3 or 2 rotations per minute (rpm) was respectively 32.2 or 38.8 s on average. Based on this data, Eoldist allows the user to select a species from the database, wind turbine characteristics, and a residual rotor speed (3 or 2 rpm); it then calculates the time to reach the selected threshold and provides a distribution curve for the cautionary detection distance needed to prevent collision. This article includes examples of cautionary detection distances required for several species to demonstrate the sensitivity of key input parameters. Eoldist is freely available and should help the wind energy industry, ADS suppliers, and environmental agencies to define requirements for ADS bird detection that are compatible with the biology of the target species.

Survival and cause‐specific mortality rates are vital for evidence‐based population forecasting and conservation, particularly for large carnivores, whose populations are often vulnerable to human‐caused mortalities. It is therefore important to know the relationship between anthropogenic and natural mortality causes to evaluate whether they are additive or compensatory. Further, the relation between survival and environmental covariates could reveal whether specific landscape characteristics influence demographic performance. We used telemetry data on 681 Eurasian lynx (Lynx lynx), a model apex predator with large spatial requirements, that were tracked across their European distribution. Through time‐to‐event analyses, we sought to determine the variables associated with differences in their survival. Illegal killing was the main cause of mortality (33.8%), and mortality rates were similar in protected and hunted populations (8.6% and 7.0% per year, respectively). Survival varied greatly across populations (70–95% per year). Across all study sites, higher hunting and anthropogenic mortality rates were partially compensated by lower rates of other mortality causes but not by natural mortality alone. Variation in survival depended on sex (female survival was 1.5 times greater than male survival) and seasonality (highest risk during hunting season and winter), and lower survival rates were correlated with higher human modification of landscapes at both coarse (home range composition) and fine (habitat use within home range) scales. Some variation in survival was driven by unobserved factors, which, given the high rates of human‐caused mortalities, including illegal killing, are of foremost concern. Due to the low natural mortality rates in protected and hunted populations, we conclude that anthropogenic causes of mortality are likely close to additive, such that maintaining or increasing refuge habitat with little human disturbance is critical to lynx conservation.

Fiber is essential for rumen health, microbial fermentation, and the energy supply of herbivores. Even though the study of fecal fiber contents (neutral detergent fiber NDF, acid detergent fiber ADF, and acid detergent lignin ADL) using near-infrared reflectance spectroscopy (NIRS) has allowed investigating nutritional ecology of different herbivore species, NIRS calibrations are species-specific and require a large number of samples for predictions. A multispecies calibration would be an advantage since samples from different herbivores could be used to calibrate a model capable of predicting the fecal fiber content of other herbivores. To date, however, multispecies models have not been developed to predict fiber contents in the feces of herbivores. Here, we fill this gap by calibrating three fiber multispecies models (NDF, ADF and ADL) using fecal samples from domestic and wild herbivore species. We also evaluated the effect of incorporating sodium sulfite in fiber determination protocol. The initial dataset consisting of 445 samples of six herbivore species was used to calibrate (80% of the samples) and validate (20% of the samples) the models. Subsequently, 63 samples of five herbivores not included in the calibration set were used for the external validation of the model. Since sodium sulfite did not significantly improve fecal fiber prediction, our model was developed without this compound. The multispecies models obtained were highly accurate determining NDF, ADF and ADL (R²CAL, coefficient of determination in calibration, ≥ 0.93, R²VAL, coefficient of determination in validation, ≥ 0.91) and independent of external confounders. For external validation, the accuracy in predicting fecal samples in other herbivore species was also satisfactory, with consistently better values for NDF (R²VAL, 0.86–0.94) and ADF (R²VAL, 0.80–0.95) than for ADL (R²VAL, 0.66–0.89). We show that multispecies NIRS calibrations can be used with high accuracy to assess fecal fiber contents across diverse herbivore species. This finding represents a significant advance in the study of the nutritional ecology of herbivores with contrasting foraging patterns. In the future, widening the data range (e.g., species and locations) of the initial dataset could further improve the accuracy of these models.

Carbon pathways in freshwater ecosystems are particularly complex because of the multiple origins, forms, and transformations of carbon by aquatic organisms. In high-altitude lakes, located above the treeline, most of the carbon pool is of indigenous origin. However, little is known about the influence of lake and watershed characteristics on carbon transfer pathways and their variability over an annual cycle. We analyzed simultaneously carbon stable isotopic composition (δ13C) and C/N ratio of organic matter from pelagic (POM, zooplankton) and benthic components (benthic invertebrates, sediments) in eight high-altitude lakes and hypothesized that the origin of the carbon used and the composition of organic matter in the pelagic and benthic compartments vary according to the lake’s characteristics. The results showed that most of the organic matter composing the sediments is of autochthonous origin, regardless of the lake’s characteristics. We observed a common tendency of seasonal shift in the source of carbon used, from a C–CO2 respired or a C–CH4-derived in early summer to a C–CO2 dissolved in late summer. However, the origin of the carbon used and the contribution of pelagic and benthic primary producers to the carbon transfers varied according to the lakes’ depth, lithology, and food web structure. These findings highlight that the complexity of high-altitude lakes and how the balance between benthic and pelagic food webs will be important in future ecological trajectory predictions.

The common bottlenose dolphin (Tursiops truncatus) exhibits significant intraspecific diversity globally, with distinct ecotypes identified in various regions. In the Guadeloupe archipelago, the citizen science NGO OMMAG has been monitoring these dolphins for over a decade, documenting two distinct morphotypes. This study investigates whether these morphotypes represent coastal and oceanic ecotypes, which have not been previously identified in the region. We characterized morphological differences between the two morphotypes, analyzed genetic variation in individuals stranded around Guadeloupe over the past ten years, and modeled their habitats. Results revealed that these morphotypes align with the ecotypes described in the Atlantic Ocean, forming two distinct genetic groups corresponding to Caribbean ecotypes. Habitat modeling showed differences in habitat preferences between the morphotypes. These findings provide strong evidence for the existence of two distinct ecotypes of T. truncatus in Guadeloupe. Considering the varied risks of exposure to maritime traffic, our study suggests that these ecotypes should be managed as separate units within the species to better inform conservation strategies in the region.