Biology subjects

Bretagnolle, V.

Publications and source records attributed to Bretagnolle, V..

15 recordsLinked to original sources

bioRxiv2026

High residual pesticide contamination despite contrasted feeding treatments in semi-captive bred grey partridges

Food security is one of the major ongoing global anthropic challenges, driving the intensification of agricultural systems notably through the widespread use of phyto-pharmaceutical products (PPPs). Although effective for maximizing production yields through pest control, PPP contamination is pervasive across the entire agroecosystem, raising concerns about human and non-target species exposure and health effects. Organic farming has therefore been promoted as a sustainable alternative to ensure human food security and mitigate these impacts. Yet, the pathways of PPP non-target organisms contamination are insufficiently understood. While most research has focused on ingestion as the primary route of exposure, increasing evidence suggests more complex contamination dynamics. In this study, we investigated the role of food intake in shaping PPP contamination profiles in semi-captive grey partridges (Perdix perdix). To do so, 80 birds were housed in open aviaries within an agricultural landscape and fed either conventional or organic grains over a five-month period. After drawing their PPP blood profiles at the end of the exposure period, we assessed their loads and compared the pesticide prevalence and abundance between food treatments. We found similar quantity and diversity of PPP residues in blood from conventionally- and organically-fed partridges, with few differences in specific PPP compounds. Overall, these findings suggest that food intake is not necessarily the only source of contamination for non-target organisms, with alternative pathways (e.g., inhalation, dermal contact, soil and water exposure) likely playing a substantial role. Integrating multi-pathway contamination monitoring across trophic levels within a One Health framework would now be essential to better understand and mitigate PPP contamination risks.

ecology↗

bioRxiv2025

Long-term population monitoring reveals an alarming decline in the endangered endemic Reunion Harrier Circus maillardi

Insular species are disproportionately vulnerable to extinction due to small population sizes, geographic isolation, and high susceptibility to stochastic and anthropogenic pressures. The endemic Reunion Harrier (Circus maillardi), the last breeding raptor on La Reunion (Indian Ocean), is currently listed as "endangered" (EN) on the IUCN Red List. Concerns have recently emerged regarding the demographic impacts of secondary poisoning from anticoagulant rodenticides used for rat control in agricultural landscapes, in addition to other threats such as habitat loss and fragmentation, and reduced genetic diversity. Here, we analysed data from three standardized island-wide breeding censuses (1998-2000, 2009-2010, 2017-2019), encompassing 355 sampling points and totalising > 1,500 h of observations, to quantify overall population trends and spatial variation within those. Using generalized additive mixed models accounting for spatial variation in the different census designs, we estimated a significant decrease of -46% (95% CI: -61% to -28%) in the relative abundance of breeding pairs at the island scale over 21 years (equivalent to three generations), which supports its current endangered (EN) status. Decline was more pronounced in the eastern part of the island (-56%, 95% CI: -69% to -40%) compared to the western part (-29%, 95% CI: -52% to +0.3%). Combined with previous work on inbreeding and mutational load, exposure to anticoagulant rodenticides and ongoing threats (habitat changes), these results suggest this harrier population is undergoing an extinction vortex that requires immediate and targeted, spatially explicit, conservation actions. We also recommend that population size continues to be monitored and that knowledge of demographic parameters be improved to guide adaptive management for the species.

ecology↗

bioRxiv2025

Field-based evidence of sperm quality impairment associated with conventional farming in two passerine birds.

The detrimental effects of conventional farming on bird biodiversity are increasingly documented. Despite this, the specific impacts of both organic and conventional farming practices on bird coloration and sperm quality in natural settings remain unexplored. This study aimed to determine whether these farming practices differentially affect body mass, coloration intensity, and sperm quality in passerine birds inhabiting agricultural landscapes. We captured seven passerine species in hedgerows adjacent to fields farmed organically or conventionally, within a 250-meter radius representative of their breeding home ranges. Body mass was measured across all species, and an index of coloration intensity, based on carotenoid (yellow/orange) and melanin (black) pigments, was assessed in four species. Additionally, we evaluated three sperm quality parameters (sperm density, percentage of abnormal sperm, and intra-individual variance of sperm morphology) using fresh sperm samples collected from four species in the field. We hypothesized that birds living near conventional fields would exhibit lower body mass due to reduced food availability. Additionally, we predicted that the more favourable conditions associated with organic farming, such as greater food abundance and lower exposure to pollutants, would benefit birds, leading to enhanced coloration and improved sperm quality. Our results did not reveal any difference in body mass or coloration. The absence of observable effects might be due to several factors: methodological limitations, cross-contamination between habitats or insufficient exposure to farming practices that may hide any potential difference between the two habitats, or the intrinsic adaptive strategies of the species. However, subgroup analysis of three and four species revealed a decrease in sperm density and a higher proportion of abnormal spermatozoa in the Common Whitethroat and Common Nightingale living in conventional farming, respectively. Although our sample size was limited, we believe these findings highlight the potential negative effects of conventional farming on birds.

ecology↗

bioRxiv2025

Off target: herbicides applied in cereal fields exclude non-competitive species, while replacing them by competitive weeds.

Weed diversity plays an important role in maintaining resilient agroecosystems, yet agricultural practices, such as pesticide applications, significantly shape weed communities. Previous studies have primarily focused on comparing organic and conventional farming, with a particular emphasis on land-use intensification, with less attention on the impact of pesticides. Our study examined the impact of herbicide, fungicide, and insecticide use - both in terms of Treatment Frequency Index (TFI), i.e. intensity of application, and quantity - on weed communities in 96 non-organic cereal fields over 4 years. Interestingly, our results indicate that fungicide application intensity decreased weed abundance by 11.6% and species richness by 14.6% for each one-standard-deviation (1-SD) increase in TFI, whereas the total quantity applied (QA) did not. In contrast, for herbicides, QA had a stronger negative impact on weed communities than TFI, with a 14.3% decrease in weed abundance and a 12.4% decrease in species richness for each 1-SD increase in QA. This suggests that TFI of fungicide, which may reflect low-dose but frequent applications, could exert indirect and long-term effects on weed suppression, potentially by altering symbiotic arbuscular mycorrhizal fungi in the soil. In comparison, QA of herbicide more directly reflects the toxic load delivered to weeds and is therefore a better predictor of their suppression. Based on a combination of multivariate and univariate analyses and the study of underlying mechanisms in community changes, our results reveal that herbicides are the main factor shaping weed communities by decreasing the abundance of non-target/non-competitive species while replacing them by problematic, competitive to crops, weed species. These findings point out the potential ineffectiveness of herbicides application on problematic weeds and emphasize the need to reconsider the use of herbicides to maintain weed diversity in agricultural landscapes.

ecology↗

bioRxiv2023

Environmental variables and species traits as drivers of wild bee pollination in intensive agroecosystems -a metabarcoding approach

Wild bees are known to be efficient pollinators of wild plants and cultivated crops and they are essential ecosystem service providers. However, wild bee populations have been suffering from significant declines in the last decades mainly due to the use of agrochemicals. Within this framework, we aimed to characterize wild bees pollination spectrum (i.e. the community of pollinated flowering plants) in intensive agroecosystems, and describe the environmental variables and wild bee species traits influencing the pollination. To do this, we conducted metabarcoding analyses of pollen loads from wild bees collected in sunflower crops in the French region of Nouvelle-Aquitaine. Our study revealed that wild bees visited flowering plants corresponding to 231 different Operational Taxonomic Units, classified in 38 families of which Asteraceae, Brassicaceae and Apiaceae were the most visited and more than 90% of the visited taxa turned out to be wild flowers. We also analysed the potential effect of environmental variables and wild bee species traits in governing their choice of pollinated plants. The community composition of pollinated plants varied depending on the flowering stages of the sunflower and the farming system. Our results also show that pollination niche breadth (alpha diversity) varied depending on the flowering stages of the sunflower but was not different between organic and conventional farming systems. Regarding wild bee species traits, the community composition of pollinated plants varied in relation to wild bees body sizes and, sociality levels. Our results are consistent with previous studies, suggesting that solitary bees are more specialists when it comes to flower selection than social bees, which are more generalist. The metabarcoding of pollen loads enabled us to draw a global picture of plant-wild bee interactions in an intensive agroecosystem. Our findings support the hypothesis that a higher diversity of weeds may increase wild bee diversity in intensive agroecosystems.

ecology↗

bioRxiv2023

A comparison of live versus kill pitfall traps to assess the diet of carabids through a metabarcoding approach

Metabarcoding approaches are powerful tools to unravel trophic relationships between predators and prey. To apply metabarcoding analyses on invertebrate gut contents, specimens must be well preserved from DNA degradation, thus the trapping method should be selected accordingly. Dry pitfall traps are commonly assumed to provide a better DNA preservation than traps that use a killing agent. However, this assumption has never been specifically tested for gut content analyses. In our study, we compared how two types of pitfall trapping, dry vs. with brine, affect the conservation of prey DNA contained in the digestive tract of predators and subsequent metabarcoding analyses. We placed dry and "classic" pitfall traps in oilseed rape fields within an intensive agricultural area in the French Nouvelle-Aquitaine region. Traps were set up in autumn and compared for carabid trapping efficiency as well as our capacity to retrieve dietary information from the digestive tract of the main carabid species, Nebria salina and Calathus fuscipes. PCR success rate was higher in dry pitfall traps compared to classic ones for N. salina. We hypothesise that this was due to the presence of PCR inhibitors in the gut of this species. The ability to sequence prey DNA did not differ between specimens caught in both trap types. The list of predated species was similar between both trap types. However, sequencing yielded more prey OTUs from specimens caught in dry pitfall traps, leading to difference in prey community composition and a greater ability to reconstruct prey community Our analyses also shed light on the prey spectrum of Calathus fuscipes and Nebria salina in oilseed rape in autumn.

ecology↗

bioRxiv2021

Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits

Substitution rate variation among branches can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Body mass is often assumed to have a major influence on substitution rate, though other factors such as population size, life history traits, and flight demands are also thought to have an influence. Birds of the order Procellariiformes--which encompasses petrels, storm-petrels and albatrosses--show a striking 900-fold difference in body mass between the smallest and largest members, divergent life history traits, and substantial heterogeneity in mitochondrial substitution rates. Here, we used genome-scale nuclear DNA sequence data from 4365 ultraconserved element loci (UCEs) in 51 procellariiform species to examine whether phylogenetic reconstruction using genome-wide datasets is robust to the presence of rate heterogeneity, and to identify predictors of substitution rate variation. Our results provide a backbone phylogeny for procellariiform seabirds and resolve several controversies about the evolutionary history of the order, demonstrating that albatrosses are basal, storm-petrels are paraphyletic and diving petrels nestled within the Procellariidae. We find evidence of rate variation; however, all phylogenetic analyses using both concatenation and multispecies coalescent approaches recovered the same branching topology, including analyses implementing different clock models, and analyses of the most and least clock-like loci. Overall, we find that rate heterogeneity is little impacted by body mass, population size, age at first breeding, and longevity but moderately correlated with hand-wing index, a proxy for wing shape and flight efficiency. Given our results and the context of the broader literature perhaps it is time that we begin to question the prevailing paradigm that one or a few traits largely explain rate variation and accept instead that substitution rate may be the product of weak interactions among many, potentially taxon-specific, variables.

evolutionary biology↗

bioRxiv2021

Functional traits of carabid beetles reveal seasonal variation in community assembly in annual crops

O_LITrait-based community assembly studies have mostly been addressed along spatial gradients, and do not consider explicitly a fundamental dimension governing community assembly, the time. Nevertheless, such consideration seems particularly necessary in systems in which organisms have to face regular disturbances and rapid changes in vegetation phenology, such as in intensively managed farmlands. C_LIO_LIIn this study, we aimed at understanding how the functional diversity of carabid beetle communities varied across the growing season in response to crop type. We tested three alternative hypotheses on mechanisms underlying the community assembly. C_LIO_LIWe used data from a long-term monitoring conducted over nine years in an intensively-managed farmland in central western France, in a total of 625 fields. First, we measured morphological traits related to body size, dispersal mode, and resource acquisition on the 13 dominant carabid species (> 85 % of all trapped individuals) and identified three independent dimensions of functional specialization within our species pool along axes of a PCA and highlighted key traits for community assembly. Second, we evaluated the community assembly temporal dynamics and the impact of habitat filtering and niche differentiation in the different crop types with time, using linear mixed-effects models. C_LIO_LIWe showed that functional species assembly of carabid beetle communities occurring in crop fields varies importantly intra-annually, with strong variations in these dynamics depending on crop type and crop phenology. Each crop acted as a filter on carabid communities for body size and resource-acquisition traits, and functional differentiation between crops increased with time. We did not find any evidence of habitat filtering on traits related to dispersal mode. C_LIO_LIOur results emphasize the major role of crop phenology but also disturbances involved by agricultural practices such as crop harvesting on changes in community assembly, likely due to seasonal and inter-annual redistributions of species in agricultural landscapes in response to such changes. The temporal dimension cannot be ignored to understand the assembly of local carabid communities in farmlands. C_LI

ecology↗

bioRxiv2020

Investigating spatiotemporal variation in the diet of Westland Petrel through metabarcoding, a non-invasive technique

As top predators, seabirds can be indirectly impacted by climate variability and commercial fishing activities through changes in marine communities. However, high mobility and foraging behaviour enables seabirds to exploit prey distributed patchily in time and space. This capacity to adapt to environmental change can be described through the study of their diet. Traditionally, the diet of seabirds is assessed through the morphological identification of prey remains in regurgitates. This sampling method is invasive for the bird and limited in terms of taxonomic resolution. However, the recent progress in DNA-based approaches is now providing a non-invasive means to more comprehensively and accurately characterize animal diets. Here, we used a non-invasive metabarcoding approach to characterize the diet of the Westland petrel (Procellaria westlandica), which is an endangered burrowing species, endemic to the South Island of New Zealand. We collected 99 fresh faecal samples at two different seasons and in two different sub-colonies. Our aims were to describe the diet of the Westland petrel, investigate seasonal and spatial variation in the petrels diet, and assess potential impacts of the New Zealand fishery industry. We found that amphipods were the most common prey, followed by cephalopods and fish. Our results could be the result of natural foraging behaviour, but also suggest a close link between the composition of prey items and New Zealands commercial fishing activities. In particular, the high abundance of amphipods could be the result of Westland petrels feeding on discarded fisheries waste (fish guts). Our results also showed significant differences in diet between seasons (before hatching vs chick-rearing season) and between sampling sites (two sub-colonies 1.5 km apart), indicating plasticity in the foraging strategy of the Westland petrel. Due to its non-invasive nature, metabarcoding of faecal samples can be applied to large numbers of samples to help describe dietary variation in seabirds and indicate their ecological requirements. In our example, dietary DNA (dDNA) provided valuable information regarding the dietary preferences of an iconic species in New Zealands unique biodiversity. dDNA can thus inform the conservation of endangered or at-risk species that have elusive foraging behaviours.

ecology↗

bioRxiv2020

Measuring ontogenetic shifts in central-place foraging insects: a case study with honey bees

O_LIMeasuring time-activity budgets over the complete individual lifespan is now possible for many animals with the recent advances of life-long individual monitoring devices. Although analyses of changes in the patterns of time-activity budgets have revealed ontogenetic shifts in birds or mammals, no such technique has been applied to date on insects. C_LIO_LIWe tested an automated breakpoint-based procedure to detect, assess and quantify shifts in the temporal pattern of the flight activities in honey bees. We assumed that the learning and foraging stages of honey bees will differ in several respects, to detect the age at onset of foraging (AOF). C_LIO_LIUsing an extensive dataset covering the life-long monitoring of 2,100 individuals, we compared the AOF outputs with the more conventional approaches based on arbitrary thresholds. We further evaluated the robustness of the different methods comparing the foraging time-activity budget allocations between the presumed foragers and confirmed foragers. C_LIO_LIWe revealed a clear-cut learning-foraging ontogenetic shift that differs in duration, frequency, and time of occurrence of flights. Although AOF appeared to be highly plastic among bees, the breakpoint-based procedure seems better able to detect it than arbitrary threshold-based methods that are unable to deal with inter-individual variation. C_LIO_LIWe developed the aof R-package including a broad range of examples with both simulated and empirical dataset to illustrate the simplicity of use of the procedure. This simple procedure is generic enough to be derived from any individual life-long monitoring devices recording the time-activity budgets of honey bees, and could propose new ecological applications of bio-logging to detect ontogenetic shifts in the behaviour of central-place foraging insects. C_LI

ecology↗

bioRxiv2019

A Nature-based solution in practice: ecological and economic modelling shows pollinators outperform agrochemicals in oilseed crop production

AO_SCPLOWBSTRATC_SCPLOWNature-based agriculture, reducing dependency on chemical inputs, requires using ecological principles for sustainable agro-ecosystems, balancing ecology, economics and social justice. There is growing evidence that pollinator-dependent crops with high insect pollination service can give higher yields. However, the interacting effects between insect pollination and agricultural inputs on crop yields and farm economics remain to be established to reconcile food production with biodiversity conservation. We investigated the effects of insect pollination and agricultural inputs on oilseed rape (Brassica napus L.). We show that not only yield but also gross margins are 16-40% higher in fields with higher pollinator abundance than in fields with reduced pollinator abundance. This effect is however strongly reduced by pesticides use. Higher yields may be achieved by either increasing agrochemicals (reducing pests) or increasing bee abundance, but crop economic returns was only increased by the latter, because pesticides did not increase yields while their costs reduced gross margins.

ecology↗

bioRxiv2019

A global synthesis reveals biodiversity-mediated benefits for crop production

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by few abundant species or rely on high richness remains unclear. Using a global database from 89 crop systems, we partition the relative importance of abundance and species richness for pollination, biological pest control and final yields in the context of on-going land-use change. Pollinator and enemy richness directly supported ecosystem services independent of abundance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.

ecology↗

bioRxiv2018

Reconciling biodiversity conservation, food production and farmers’ demand

Agricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee the provision of ecosystem services that reaches stakeholders demands, especially considering the observed biodiversity decline and the current global change predictions that may affect food security. Here, we use a model to examine how landscape composition - fraction of semi-natural habitat (SNH) - affects biodiversity and crop production services in intensively-managed agricultural systems. We analyse three groups of stakeholders assumed to value different ecosystem services most - individual farmers (crop yield per area), agricultural unions (landscape production) and conservationists (biodiversity). We find that trade-offs among stakeholders demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder, i.e. function thresholds. Intermediate amounts of SNH can allow for the delivery of relatively high levels of the three ecosystem services. Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, these results suggest ways of managing landscapes to reconcile the demands of several actors and ensure for biodiversity conservation and food production.

ecology↗

bioRxiv2018

Trade-offs in provisioning and stability of multiple ecosystem services in agroecosystems

Changes in land use generate trade-offs in the delivery of ecosystem services in agricultural landscapes. However, we know little about how the stability of ecosystem services responds to landscape composition, and what ecological mechanisms underlie these trade-offs. Here, we develop a model to investigate the dynamics of three ecosystem services in intensively-managed agroecosystems, i.e. pollination-independent crop yield, crop pollination, and biodiversity. Our model reveals trade-offs and synergies imposed by landscape composition that affect not only the magnitude but also the stability of ecosystem service delivery. Trade-offs involving crop pollination are strongly affected by the degree to which crops depend on pollination and by their relative requirement for pollinator densities. We show conditions for crop production to increase with biodiversity and decreasing crop area, reconciling farmers profitability and biodiversity conservation. Our results further suggest that, for pollination-dependent crops, management strategies that focus on maximising yield will often overlook its stability. Given that agriculture has become more pollination-dependent over time, it is essential to understand the mechanisms driving these trade-offs to ensure food security.

ecology↗

bioRxiv2018

DNA metabarcoding diet analysis reveals dynamic feeding behaviour and biological control potential of carabid farmland communities

Maximizing the delivery of key ecosystem services such as biological control through the management of natural enemy communities is one of the major challenges for modern agriculture. The main obstacle lies in our yet limited capacity of identifying the factors that drive the dynamics of trophic interactions within multi-species assemblages. Invertebrate generalist predators like carabid beetles are known for their dynamic feeding behaviour. Yet, at what extent different carabid species contribute to the regulation of animal and plant pests within agroecosystems is currently unknown. Here, we developed a DNA metabarcoding approach for characterizing the full diet spectrum of a community of fourteen very common carabid species inhabiting an intensively managed Western-European agroecosystem. We then investigated how diet and biological control potential within the carabid community varies with the sampling field location and the crop type (wheat vs oilseed rape). DNA metabarcoding diet analysis allowed to detect a wide variety of animal and plant taxa from carabid gut contents thus confirming their generalist feeding behaviour. The most common prey categories detected were arachnids, insects, earthworms and several plant families potentially including many weed species. Our results also show that the field location and the crop type are much stronger determinants then the species regarding carabid dietary choice: significantly more trophic links involving dipteran prey were observed in wheat, whereas more collembolan and plant prey was consumed in oilseed rape by the same carabid community. We speculate that structural differences in the habitats provided by these two crop types drive differences in resource availability cascading up the trophic chain, and we assume that specific carabid taxa could hardly be used to infer levels of ecosystem services (biological control) or disservices (e.g. intraguild predation). However, as this is the first study to report the use of DNA metabarcoding diet analysis in predatory carabid beetles we urge caution over the interpretation of our results. For instance, overall detection rates were rather low (31% of the individuals analysed tested positive for at least one prey category) most likely due to the overwhelming amplification of the carabid host DNA. Therefore, we acknowledge that more studies are required in order to confirm our observations and conclude with few recommendations for further improvements of the community-level DNA metabarcoding analysis of carabid diet.

ecology↗