Centre d'Écologie Fonctionnelle et Évolutive, French National Centre for Scientific Research

Environmental DNA (eDNA) metabarcoding is changing the way biodiversity is surveyed in many types of ecosystems. eDNA surveys are now commonly performed and integrated into biodiversity monitoring programs and public databases. Although it is widely recognized that eDNA records require interpretation in light of taxonomy and biogeography, there remains a range of perceptions about how thoroughly records should be evaluated and which ones should be reported. Here, we present a modular procedure, available as an R script, that uses a set of five steps to assess the confidence of species‐level eDNA records by assigning them a score from 0 to 5. This procedure includes evaluations of the known geographic distribution of each taxon, the taxonomic resolution of the marker used, the regional completeness of the reference database, the diversification rate, and the range map of each taxon. We tested the procedure on a large‐scale marine fish eDNA dataset (572 samples) covering 15 ecoregions worldwide, from the poles to the tropics, using the teleo marker on the mitochondrial 12S ribosomal gene. Our analysis revealed broad variation in the average confidence score of eDNA records among regions, with the highest scores occurring along the European and Eastern Atlantic coasts. Generalized linear models applied to record covariates highlighted the significant influences of latitude and species richness on low confidence scores (< 2.5). The polar regions notably displayed high proportions of low confidence scores, probably due to the limited completeness of the regional reference databases and the taxonomic resolution of the teleo marker. We conclude that only records with high confidence scores (> 2.5) should be integrated into biodiversity databases. The medium (2.5) to relatively low‐confidence (< 2.5) records correspond to species that require further investigation and may be integrated after inspection to ensure high‐quality species records.

Our understanding of demographic processes is mainly based on the analysis of the adult components of populations. However, juvenile survival is decisive for recruitment, and therefore for the dynamics of populations. Our study aims at understanding the environmental determinants of juvenile survival in the emperor penguin, a species for which this critical phase is poorly known. We used capture-mark-recapture models to leverage 13-years of electronic monitoring of birds tagged as fledglings at Pointe Géologie, Adélie Land. Emperor penguin juvenile survival showed very high interannual variability (0.08 to 0.48), a pattern no longer observed in immatures and adults. Furthermore, we emphasized the importance of body mass on juvenile survival, and which was tightly associated with sea ice extent during the chick rearing period. We also showed that oceanographic conditions (width of the polar front) during the first weeks after fledging are an important predictor of juvenile survival. Our results suggest that the conditions of accessibility and abundance of food resources during this phase of learning to swim and dive play a crucial role in the survival of young penguins. Finally, our study provides new insights into sex-specific differences in survival in this species, which seems to emerge only in adulthood.

The interconnecting links between individuals in an animal social network are often defined by discrete, directed behaviours, but where these are difficult to observe, a network link (edge) may instead be defined by individuals sharing a space at the same time, which can then be used to infer a social association. The method by which these associations are defined should be informed by the biological significance of edges, and therefore often vary between studies. Identifying an appropriate measure of association remains a challenge to behavioural ecologists. Here, we use automatically recorded feeder visit data from four bird systems to compare three methods to identify a social association: (1) strict time-window, (2) co-occurrence in a group, and (3) arrival-time. We tested the similarity of the resulting networks by comparing the repeatability and sensitivity of individuals’ social traits (network degree, strength, betweenness). We found that networks constructed using different methods but applying similar, ecologically relevant definitions of associations based on individuals’ spatio-temporal co-occurrence, showed similar characteristics. Our findings suggest that the different methods to construct animal social networks are comparable, but result in subtle differences driven by species biology and feeder design. We urge researchers to carefully evaluate the ecological context of their study systems when making methodological decisions. Specifically, researchers in ecology and evolution should carefully consider the biological relevance of an edge in animal social networks, and the implications of adopting different definitions.

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.

The Metropolitan Area of São Paulo (MASP) in southern Brazil is impacted by high ozone levels posing significant threats to its urban forests and the Atlantic Forest remnants. These green areas, covering 540 km² and constituting 30% of MASP’s territory, necessitate an urgent assessment of air pollution impacts on their flora. Our study investigates the effects of atmospheric pollution on the morphoanatomical and physiological responses of four native tree species (Alchornea sidifolia, Casearia sylvestris, Guarea macrophylla, and Machaerium nyctitans) across two Atlantic Forest remnants in MASP. We examined visual and morphoanatomical changes in leaves, gas exchange, photosynthetic pigments, and plant volatile organic compounds to identify markers for biomonitoring urban environments. Our results reveal that MASP vegetation is adversely affected by tropospheric ozone. Species with porous mesophyll structures, such as M. nyctitans and G. macrophylla, exhibited greater visual and structural damage. In contrast, species with compact mesophyll, such as A. sidifolia and C. sylvestris, demonstrated higher tolerance. This suggests that anatomical architecture critically influences species’ responses to atmospheric pollutants, such as tropospheric ozone. Additionally, we propose that ozone influx occurs through both stomatal pathways and as a result of direct and indirect injuries to the plant tissues. Additionally, our study identifies non-visual markers, including anatomical and physiological parameters and plant volatile organic compounds (e.g., presence of salicylates), as effective tools for monitoring plant species in urban environments. These insights highlight key anatomical and metabolic markers that help distinguish ozone-tolerant species from sensitive species, providing valuable information for monitoring air pollution in urban forests.

In war and conflict zones, the jamming of Global Navigation Satellite System (GNNS) signals by military forces disrupts the tracking of tagged animals, and has increased in frequency following the recent escalation of conflicts in Eastern Europe and the Middle East. Such disruption to data collection strongly hampers research into the protection and conservation of endangered animals.

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.

Freshwater turtles are one of the most threatened vertebrate groups in the world, mainly due to the degradation of their habitats. Some species, including the European pond turtle ( Emys orbicularis ), have been the subject of long‐term monitoring programmes carried out within large, well‐preserved wetlands and based on robust capture–mark–recapture (CMR) protocols. Yet demographic studies of small isolated populations are very scarce. In this study, a highly isolated population of E. orbicularis was intensively monitored in the Durance River Valley in southeastern France over five consecutive years (2013–2017). In total, 153 adult individuals were used to estimate demographic parameters using two different CMR Robust Design model formulations. These models estimated a relatively constant adult population size, annual survival and seniority probability over time, similar for both sexes, but a highly unbalanced sex ratio in favour of females (0.24 male per female on average). The results showed that this isolated population exhibits atypical and little‐known demographic parameters in this species. The highly unbalanced sex ratio in favour of females could be the result of factors impacting sexual determinism during embryonic development. This imbalance could ultimately reduce the reproductive output and increase the risk of extinction of the population. These results highlight the need for both a better understanding of the mechanisms underlying the origin of such an imbalance, and in identifying the critical thresholds that must not be crossed to guarantee the viability of sex‐biased populations.

Understanding speciation is a fundamental goal in evolutionary biology. Genomic regions of accentuated differentiation among populations often reveal patterns and mechanisms of species formation. While substantial progress has been achieved on this front for genetic variation, the contribution of epigenetic mechanisms to divergence patterns remains unclear. Here, we present evidence that DNA methylation is associated with regions exhibiting accentuated genetic differentiation between populations of Timema cristinae stick insects. We do so by integrating analyses of differentially methylated regions (DMRs) between individuals from different host-plant species with genomic sequencing. Our results reveal that DMRs exhibit accentuated genetic differentiation (FST) between populations. Strikingly, the strength of this association increases with the geographical distance between populations. We present results evaluating the contributions of mutation, reduced recombination, gene flow and selection to these divergence patterns. The overall results are consistent with a role for a balance between selection and gene flow, a finding further supported by evidence for selection in a previously-published survival field experiment. Nevertheless, details of our results suggest that selection on DMRs might be indirect and not strictly host-related. Our results establish associations between methylation and genetic change, but further work is required to clarify the exact causes of this association. Nonetheless, our results provide insight into how the interplay of epigenetic and genetic variation may influence population divergence and potentially contribute to speciation.

Climate change is one of the main drivers of biodiversity decline. Rapidly changing climate in the form of warming, drying, and habitat isolation causes freshwater species to change their spatial extent, as most species have little capacity for in situ responses. However, the relative contribution of these three effects to freshwater species’ changing spatial distributions is actively debated. To shed light on this debate, we explored temperature, hydroperiod, and habitat connectivity effects on alpine pond species occupancy probabilities in the northern French Alps. We studied alpine ponds as ideal test systems because they face climate change effects more rapidly, and in more concentrated areas, than any other freshwater ecosystem. We used multispecies occupancy models with three biological groups (amphibians, macrophytes, and Odonata) to examine contrasting responses to climate change. Contrary to expectations, temperature was not the main driver of species occupancy probabilities. Instead, hydroperiod and connectivity were stronger predictors of species occupancy probabilities. Furthermore, temperature increases had the same effect on occupancy probabilities of non-alpine specialist and alpine specialist species. Nonetheless, temperature disproportionately affected a greater number of specialist species compared with non-alpine specialists. We conclude that climate change mitigation will primarily benefit a greater number of alpine specialist species than non-alpine specialists. Finally, we suggest that enhancing our understanding of freshwater hydroperiods will improve our predictions of climate change effects on freshwater species distributions.

Context Throughout their annual cycle and life stages, animals depend on a variety of habitats to meet their vital needs. However, habitat loss, degradation, and fragmentation are making it increasingly difficult for mobile species such as birds to find suitable habitats. Wetlands are highly productive systems of great importance to many animals, but their continued degradation threatens their capacity to support different species, including waterbirds. In this context, waterbirds are likely to benefit not only from the creation and management of protected wetlands, but also from the existence of anthropogenic wetlands, managed for economic or recreational activities. Objectives We investigated the habitat use of Eurasian spoonbills within an extensive and heterogeneous area in Southern France, and how it varies across the annual cycle and for different age classes. Methods We tracked 91 spoonbills of different ages throughout their annual cycle and tested for overall differences in the use of strongly protected areas in Camargue between periods and age classes. Additionally, we identified the main sites used and their management practices. Results Our study shows that privately managed wetland areas play a complementary role to strongly protected areas: they may provide spoonbills (and other waterbirds) with suitable foraging habitat at certain periods of the year when these are less available in strongly protected areas. Conclusions This study illustrates how the spoonbill, a moderately specialized species, is benefiting from current global changes due to its ability to use suitable habitats, natural and artificial, in fragmented landscapes. Nevertheless, reliance on privately managed wetland areas may have serious consequences for species that are highly dependent on them, and thus, habitat management promoting natural conditions may be crucial to maintain species resilience. It is therefore essential to understand how specific management actions may affect waterbird presence and habitat use, not only to enhance the effectiveness of conservation efforts, but also to promote wetland connectivity and species resilience, particularly in fragmented landscapes.

Great progress in cytotaxonomic research during the last decades indicated an importance of relationships between morphological features, geographical distribution of plants, and chromosome counts. This study is aimed to fill the gaps in our knowledge on Bolboschoenus chromosome numbers related to morphological differentiation of plants and their distribution worldwide. We counted gametophytic chromosome numbers in meiotic phase of plants, collected from localities worldwide during the period 1980–2013, and cultivated in an experimental garden in Průhonice. The chromosome numbers of seven species (Bolboschoenus affinis, B. caldwellii, B.grandispicus, B. medianus, B. novae-angliae, B. robustus and B. schmidii) were counted for the first time. All the studied Bolboschoenus taxa were divided into groups according to chromosome numbers, which were found to correspond to morphotypes formerly described. We have improved the taxonomic classification of some species. The relationship between chromosome counts and morphotypes appeared to be identical within some continents, and may indicate parallel evolution within the genus.

Seasonal migration has evolved as an adaptation for exploiting peaks of resource abundance and avoiding unfavourable climatic conditions. Differential migratory strategies and choices of wintering areas by long‐distance migratory species may impose varying selective pressures and mortality risks with fitness consequences. Recently developed tracking technologies allow wintering movements of migratory species to be studied. However, these technologies typically involve a limited number of tracked individuals, which gives low statistical power for any robust estimate of survival probabilities. Additionally, when utilising geolocators, data become accessible only upon individual recapture, presenting a potential source of bias. We used multievent modelling to include information of 147 identified wintering tracks in the analysis of 1104 long‐term individual capture histories (2000–2022) of migratory seabird Calonectris diomedea and then test if individual preferences for wintering areas may drive heterogeneity in adult survival. We also examined individual fidelity to wintering areas and tested if climatic and oceanographic conditions, as represented by the wNAO and SOI climatic indices, influenced survival and fidelity. The probability of fidelity to a wintering area was ca. 0.79. Annual changes between areas were influenced by environmental variability driven by the wNAO. Survival probability was influenced by the SOI and differed between wintering areas; these differences coupled with high wintering site fidelity, generated individual heterogeneity in adult survival. Our study reveals that, over the last two decades, some individuals wintered in less suitable areas, with nonnegligible consequences on adult survival, the parameter to which the population growth rate is most sensitive in long‐lived species. Winter oceanographic conditions such as stormy weather or the proximity to upwellings probably play a relevant role in driving survival heterogeneity. Further research is needed to enhance our understanding of how the interlinked effects of climate, local selective pressures and individual condition shape population dynamics in migratory species.

Nitrogen (N) availability is crucial to maintaining crop productivity in agroecosystems, driven primarily by soil microbial processes such as nitrification and denitrification. Weeds are an integral part of agroecosystems and are involved in many processes related to the N cycle, but how weed management could shift plant–microbe interactions, and thus, N‐cycling is yet to be determined. Using a network of 15 Mediterranean vineyards, we quantified the effect of 5 years of different weed management practices (chemical weeding, tillage, mowing) on the above‐ground and below‐ground functional properties of weed communities and soil microbial N‐cycling. Specific root length (SRL) of the tilled and mowed weed communities were 30% and 44% lower than in the herbicide‐treated weed communities. Soil pH and texture were the main drivers of soil microbial activity as quantified by substrate‐induced respiration (SIR), potential denitrifying enzyme activities to SIR ratio (PDEA:SIR) and potential nitrifying and denitrifying enzyme activity ratio (PNEA:PDEA). SIR was also impacted by the management: Mowed weed communities had 58% higher SIR compared to herbicide‐treated communities. Weed communities with high SRL were associated with soils with a higher nitrifying enzyme efficiency per unit of respired carbon. Synthesis and applications. Overall, our findings indicate that vineyard weed management influences the potential nitrifying enzyme activities by modifying the root strategies of weed communities. This study highlights that the design of sustainable weed management strategies should incorporate unintended effects on soil microbial communities and N‐cycling.

Following deglaciation, lowland sites in eastern Canada that were covered by proglacial Lake Ojibway recorded direct afforestation with boreal mixedwood taxa, without an initial tundra phase, contrary to sites that were never covered by this lake. Because former islands of proglacial Lake Ojibway were colonized by vegetation before lake drainage around 8200 cal a bp, we hypothesized that these paleo-islands went through a non-arboreal phase which eventually transitioned to boreal mixedwoods, hence providing a source of propagules for rapid and later colonization of the lowlands. We carried out a multi-proxy analysis combining pollen, macro-remains, sedimentary ancient DNA and charcoal to document vegetation composition and dynamics on two paleo-islands. Both study sites recorded progressive vegetation establishment starting with a tundra-like phase with only herbs and shrubs, followed by open forests dominated by either larch or pine, culminating with the establishment of the boreal mixedwoods about 300 years before the final drainage of proglacial Lake Ojibway. Fire regimes seem to have partially driven vegetation dynamics and diversity on the paleo-islands. Paleo-islands were sources of propagules, which helps explain how the former Lake Ojibway lowlands were directly colonized by boreal mixedwoods, without an initial tundra phase.

Aim The Mediterranean Sea is one of the most anthropized seas in the world but also a marine biodiversity hotspot with many fish species under threat. The main goal of the study is to test whether on the heavily fished and anthropized Mediterranean coast, the less impacted Corsica and Balearic Islands, can be considered as refugia for threatened and elasmobranch fishes independently of protection by marine reserves. Location The French Mediterranean coast and three north‐western Mediterranean islands: Corsica and also Mallorca and Minorca from the Balearic archipelago. Methods We performed 187 fish surveys using environmental DNA metabarcoding on three islands and 109 along the continental coast. Of the 78 surveys on islands 22 correspond to no‐take marine reserves and of the 109 continental surveys 26 were carried out within reserves. After eDNA filtration, extraction, amplification, and sequencing we estimated the number of fish species but also the number commercial, threatened and elasmobranch fish species on each sample. We then performed an ANOVA by permutation to test the effect of insularity and protection on these four biodiversity metrics. We also modelled these four biodiversity metrics as a function of protection and human pressure but also environmental, habitat and sampling conditions. We also built species accumulation curves to obtain asymptotes representing the potential regional pools for each species category on both island and continental coasts. Results We obtained a total of 175,982,610 reads over the 187 eDNA samples that were assigned to 153 fish species including 17 elasmobranch species among which 7 were only detected on islands. We observed a higher total fish richness on continental than island surveys regardless of protection but a higher threatened and elasmobranch fish richness on the island than on continental surveys. We obtained a significant, negative and predominant human gravity impact on the diversity of elasmobranch species. The modelled asymptote reached 148 teleostean fish species on islands and 196 on the continental coastline with a very similar rate of diversity increase with sampling effort but the shape of the species accumulation curves differed markedly for elasmobranchs with a stronger increase in diversity with sampling effort on islands. Main Conclusions Our findings highlight that Mediterranean islands can be refugia for sharks and rays but also threatened fishes in this overexploited region. Our results also suggest that reducing or banning trawling activities may play a key role for conserving vulnerable fishes, beyond the benefits of no‐take marine reserves, which appear limited on these large home‐range species.

Spontaneous plant communities have undergone considerable constraints due to human‐mediated changes. Understanding how plant communities are shifting in response to land management and climate changes is necessary to predict future ecosystem functioning and improve the resilience of managed ecosystems, such as agroecosystems. Using Mediterranean weed communities as models of managed plant communities in a climate change hotspot, we quantified the extent to which they have shifted from the 1980s to the 2020s in response to climate and management changes in vineyards. The weed communities of the same 40 vineyards in the Montpellier region were surveyed using the same protocol in spring, summer, and autumn, for two years, with a 40‐year interval (1978–1979 vs. 2020–2021). In four decades, the annual range of temperatures (i.e., the difference between the warmest month's and the coldest month's mean temperatures) increased by 1.2°C and the summer temperatures by 2°C. Weed management diversified over time with the adoption of mowing that replaced the chemical weeding of interrows. Chemical weeding is now mostly limited to the area under the row. Current weed communities were 41% more abundant, 24% more diverse, and with a less even distribution of abundance across species than the 1980s communities at the vineyard level. Modern communities were composed of more annual species (57% of annual species in the 1980s vs. 80% in the 2020s) with lower community‐weighted seed mass and were composed of fewer C4 species. They had higher community‐weighted specific leaf area, higher leaf dry matter content, and lower leaf area than the 1980s weed communities. At the community level, the onset of flowering was earlier and the duration of flowering was longer in the 2020s. Climate change induced more stress‐tolerant communities in the 2020s while the diversification of weed management practices favored less ruderal communities. This study shows that plant communities are shifting in response to climate change and that land management is a strong lever for action to model more diverse and eventually more desirable weed communities in the future.

Understanding how ecological assemblages vary in space and time is essential for advancing our knowledge of biodiversity dynamics and ecosystem functioning. Metabarcoding of environmental DNA (eDNA) is an efficient method for documenting biodiversity changes in both marine and terrestrial ecosystems. However, current methods fail to detect and display the biodiversity structure within and between eDNA samples limiting ecological and biogeographical interpretations. We present a spatial matrix factorization method that identifies optimal eDNA sample assemblages—called pools—assuming that taxonomic unit composition is based on a fixed number of unknown sources. These sources, in turn, represent taxonomic units sharing similar habitat properties or characteristics. The method aims to reduce the multi‐taxa composition structure into a low number of dimensions defined by these sources. This method is inspired by admixture analysis in population genetics. Using a marine fish eDNA survey on 263 sampling stations detecting 2888 molecular operational taxonomic units (MOTUs), we apply this method to analyse the biogeography and mixing patterns of fish assemblages at regional and large scales. At large scale, our analysis reveals six primary pools of fish samples characterized by distinct biogeographic patterns, with some mixtures between these pools. We identify pools composed of unique sources, corresponding to distinct and more isolated regions such as the Mediterranean and Scotia Seas. We also identify pools composed of a greater mix of sources, corresponding to geographically connected areas, such as tropical regions. Additionally, we identify the taxa underpinning the formation of each pool. In the regional analysis of Mediterranean eDNA samples, our method successfully identifies different pools, allowing the detection of not only geographic gradients but also human‐induced gradients corresponding to protection levels. Spatial matrix factorization adds a new method in community ecology, where each sample is considered as a mixture of K unobserved sources, to assess the dissimilarity of ecological assemblages revealing environmental and human‐induced gradients. Beyond the study of fish eDNA samples, this method has the potential to shed new light on any biodiversity survey and provide new bioindicators of global change.