Biology subjects

Benoit, L.

Publications and source records attributed to Benoit, L..

10 recordsLinked to original sources

bioRxiv2024

The first example of extreme and independent host plant shifts mediated by parasitic plants in insects

Phytophagous insects have specialized on virtually every plant lineage. Parasitic plants, however, are uncommon hosts. Among insects, only a single lineage of weevils, the Smicronychini, has successfully radiated on both parasitic and non-parasitic plants in a large panel of distantly related Asterid families. This unusual pattern suggests that major host plant shifts have occurred over the course of their diversification. Through the analysis of a phylogenomic dataset, we reconstruct for the first time their evolutionary history and ancestral host plant associations. Our results show that independent host plant shifts occurred both from parasitic to non-parasitic hosts and between distinct parasitic lineages. These results suggest that host shift mechanisms can be driven by ecological opportunities provided by plant-plant interactions. This first evidence of extreme insect host plant shifts apparently mediated by parasitic plant-plant interactions emphasizes the core importance of ecological interactions as driving forces behind insect host plant shifts.

evolutionary biology↗

bioRxiv2023

Reproductive tactics, birth timing and the trade-off between risk avoidance and foraging in an income breeder

The behavioural trade-off between foraging and risk avoidance is expected to be particularly acute during gestation and lactation, when the energetic demands of reproduction peak. We investigated how female roe deer, an income breeding ungulate, adjust their management of this trade-off during the birth period in terms of foraging activity and habitat use. We showed that activity levels of reproductive females more than doubled immediately following parturition, when energy demand is highest. Moreover, reproductive females increased their use of open habitat during daytime and ranged closer to roads, but slightly further from refuge woodland, compared to non-reproductive females. However, these post-partum modifications in behaviour were particularly pronounced in late-parturient females who adopted a more risk prone tactic, presumably to compensate for the fitness handicap of their late-born offspring. In income breeders, individuals that give birth late may be forced to trade risk avoidance for resource acquisition during peak allocation to reproduction, likely with significant fitness consequences.

animal behavior and cognition↗

bioRxiv2023

Using accelerometers to infer behaviour of cryptic species in the wild

Accelerometery is revolutionising the field of behavioural ecology through its capacity to detect the fine-scale movements of animals resulting from their behaviour. Because it is often difficult to infer the behaviour of wildlife on a continuous basis, particularly for cryptic species, accelerometers potentially provide powerful tools for remote monitoring of their behavioural responses to the environment. The goal of this study was to provide a detailed, calibrated methodology, including practical guidelines, to infer the behaviour of free-ranging animals from acceleration data. This approach can be employed to reliably infer the time budget of species that are difficult to observe in certain environments or at certain times of the day. To this end, we trained several behavioural classification algorithms with accelerometer data obtained on captive roe deer, then validated these algorithms with data obtained on free-ranging roe deer, and finally predicted the time-budgets of a substantial sample of unobserved free-ranging roe deer in a human-dominated landscape. The best classification algorithm was the Random Forest which predicted five behavioural classes with a high overall level of accuracy ({approx} 90%). Except for grooming (34-38%), we were able to predict the behaviour of free-ranging roe deer over the course of a day with high accuracy, in particular, foraging head down, running, walking and immobile (68-94%). Applied to free-ranging individuals, the classification allowed us to estimate, for example, that roe deer spent about twice as much time foraging head-down, walking or running during dawn and dusk than during daylight or night-time. By integrating step by step calibration and validation of accelerometer data prior to application in the wild, our approach is transferable to other free-ranging animals for predicting key behaviours in cryptic species.

animal behavior and cognition↗

bioRxiv2022

Combining RADseq and contact zone analysis to decipher cryptic diversification in reptiles: insights from Acanthodactylus erythrurus (Reptilia: Lacertidae)

Linnaean and Wallacean shortfalls (Uncertainties on species taxonomy and distribution, respectively) are major factors hampering efficient conservation planning in the current context of biodiversity erosion. These shortfalls concern even widespread and abundant species in relatively well-studied regions such as the Mediterranean biodiversity hotspot which still hosts a large fraction of unrecognised biodiversity, notably in small vertebrates. Species delimitations have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification in this context can be obscured by incomplete lineage sorting, introgression or isolation by distance. Recently, integrative approaches coupling various sets of characters or analyses of contact zones aiming at estimating reproductive isolation (RI) have been advocated instead. Analyses of introgression patterns in contact zone with genomic data represent a powerful way to confirm the existence of independent lineages and estimate the strength of their RI at the same time. The Spiny-footed Lizard Acanthodactylus erythrurus (Schinz, 1833) is widespread in the Iberian Peninsula and the Maghreb and exhibits a large amount of genetic diversity, although the precise number and distribution of its genetic lineages remain poorly understood. We applied a RADseq approach to obtain a genome wide SNPs dataset on a contact zone in central Morocco between the previously described Rif and Middle-Atlas lineages. We show that these two lineages exhibit strong RI across this contact zone, as shown by the limited amount and restricted spatial extant of gene flow. We interpret these results as evidence for species-level divergence of these two lineages. Our study confirms the usefulness of RADseq approaches applied on contact zones for cryptic diversity studies and therefore to resolve Linnaean and Wallacean shortfalls.

genomics↗

bioRxiv2020

Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

AO_SCPLOWBSTRACTC_SCPLOWWith frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may also be involved in or affected by colonization processes, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its microbiota. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the ones from Morocco and North America that are likely the result of recent colonization events. Coalescent-based inferences revealed high levels of gene flow among populations during the colonization but did not allow determining the sequence of colonization of Europe, North America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. We found that D. plantaginea rarely hosts other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play an important role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

evolutionary biology↗

bioRxiv2020

Modelling the flow of nocturnal bird migration with year-round European weather radar network

The movements of migratory birds constitute huge biomass flows that influence ecosystems and human economy, agriculture and health through the transport of energy, nutrients, seeds, and parasites. To better understand the influence on ecosystems and the corresponding services and disservices, we need to characterize and quantify the migratory movements at various spatial and temporal scales. Representing the flow of birds in the air as a fluid, we applied a flow model to interpolated maps of bird density and velocity retrieved from the European weather radar network, covering almost a full year. Using this model, we quantified how many birds take-off, fly, and land across Western Europe, (1) to track waves of bird migration between nights, (2) cumulate the number of bird on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects. Our results show that up to 188 million (M) birds take-off over a single night. Exemplarily, we tracked a migration wave in spring, in which birds crossed the study area in 4 days with nocturnal flights of approximately 300 km. Over the course of a season, we estimated that 494 million (M) birds entered through the southern transects and, at the same time, 251 M left in the northern transects, creating a surplus of 243 M birds within the study area. Similarly, in autumn, 544 M more birds departed than arrived: 314 M birds entered through the northern transects while 858 M left through the southern transects. Our study show-cases the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to seasonal and yearly time-scales and from regional to continental spatial scales.

ecology↗

bioRxiv2020

How bank vole-PUUV interactions influence the eco-evolutionary processes driving nephropathia epidemica epidemiology: An experimental and genomic approach.

In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of haemorrhagic fever with renal syndrome (HFSR). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas, and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. We showed that the serological response and the presence of PUUV in excretory organs were more important in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs was higher than in other non-excretory organs for the NE endemic cross-infection, but not for the NE non-endemic cross-infection. Altogether, our results showed that genetically different PUUV strains, and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans, and in turn at least partly shape NE epidemiology in France.

evolutionary biology↗

bioRxiv2019

A geostatistical approach to estimate high resolution nocturnal bird migration densities from a weather radar network.

O_LIQuantifying nocturnal bird migration at high resolution is essential for (1) understanding the phenology of migration and its drivers, (2) identifying critical spatio-temporal protection zones for migratory birds, and (3) assessing the risk of collision with man-made structures.\nC_LIO_LIWe propose a tailored geostatistical model to interpolate migration intensity monitored by a network of weather radars. The model is applied to data collected in autumn 2016 from 69 European weather radars. To cross-validate the model, we compared our results with independent measurements of two bird radars.\nC_LIO_LIOur model estimated bird densities at high resolution (0.2{degrees}latitude-longitude, 15min) and assessed the associated uncertainty. Within the area covered by the radar network, we estimated that around 120 million birds were simultaneously in flight [10-90 quantiles: 107-134]. Local estimations can be easily visualized and retrieved from a dedicated interactive website: birdmigrationmap.vogelwarte.ch.\nC_LIO_LIThis proof-of-concept study demonstrates that a network of weather radar is able to quantify bird migration at high resolution and accuracy. The model presented has the ability to monitor population of migratory birds at scales ranging from regional to continental in space and daily to yearly in time. Near-real-time estimation should soon be possible with an update of the infrastructure and processing software.\nC_LI

ecology↗

bioRxiv2018

Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping

History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries--a time of agricultural intensification well before the Inka and Spanish conquests--and then between the 13th century and today--a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.

ecology↗

bioRxiv2017

Bank Vole Immunoheterogeneity May Limit Nephropatia Epidemica Emergence In A French Non-Endemic Region

Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole, Myodes glareolus. Despite the continuous distribution of the reservoir in Europe, PUUV occurence is highly fragmented. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions using serological and virological surveys. We used bank vole population genetics to demonstrate the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to establish, circulate and persist in the NE-free region. Immune responsiveness was phenotyped both in the wild and during experimental infections, using serological, virological and immune related gene expression assays. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. In natural populations, antiviral gene expression (Tnf and Mx2 genes) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE endemic region. Altogether, our results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, what might limit PUUV circulation and persistence, and in turn, the risk of NE.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC=\"FIGDIR/small/130252_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@f90a69org.highwire.dtl.DTLVardef@1a9e0dorg.highwire.dtl.DTLVardef@17e96b8org.highwire.dtl.DTLVardef@1d936e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗