Biology subjects

Calcagno, V.

Publications and source records attributed to Calcagno, V..

13 recordsLinked to original sources

bioRxiv2025

An annotated chromosome-level genome assembly ofthe Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae)

The genus Ostrinia (Lepidoptera: Crambidae) comprises two of the most important maize pests worldwide, the Asian and the European corn borers. Here, we present an annotated, chromosome-level genome assembly for the most closely related species, the Adzuki bean borer Ostrinia scapulalis, which feeds on various dicotyledon plants. The previous reference genome assembly for this species was generated from short-read sequencing data, resulting in high fragmentation and low completeness. Combining PacBio long read and Hi-C sequencing, we generated a 476 Mb genome with 48 contigs organised into 31 chromosomes (30 autosomes and one Z sex chromosome), with a contig N50 of 16.1 Mbp and BUSCO completeness exceeding 98%. We further combined published and novel RNA-seq data encompassing multiple life stages, tissues, and sexes to annotate 14,261 gene models, reaching a proteome BUSCO completeness of 95%. This highly contiguous reference genome assembly provides a much-improved resource for carrying comparative genomic approaches and better understanding speciation and host plant adaptation in the Ostrinia genus.

evolutionary biology↗

bioRxiv2023

Taking fear back into the Marginal Value Theorem: the risk-MVT and optimal boldness

Foragers exploiting heterogeneous habitats must make strategic movement decisions in order to maximize fitness. Foraging theory has produced very general formalizations of the optimal patch-leaving decisions rational individuals should make. One is Charnovs Marginal Value Theorem (MVT), which models the sequential visit of habitat patches and their spatial distribution. The MVT has a simple intuitive graphical interpretation in terms of gain functions and travel times. However, it considers only energy gains, and the effect of predation risk on the time allocation strategy is notoriously lacking. An important development that includes predation risk was Browns economic treatment of optimal patch leaving decisions, the basis of giving-up density (GUD) theory, often cited as an extension of the MVT. However, it is a more abstract result that does not have the specificities or graphical appeal of the MVT. Although both successful, the two theories are cited by distinct communities and are seldom connected in texbooks. Here we formally introduce the risk-MVT (rMVT), a generalization of the MVT that can incorporate most types of predation risks. We show that Browns GUD-theory is equivalent to a rMVT, but applies for one type of predation risk only. The rMVT retains the structure and graphical simplicity of the MVT, but implies a shift from residence time to expected dose of risk (micromort units, as used in decision analysis) as the domain over which rates of gain are computed and maximized. Applications of the rMVT show that different types of risk can yield opposite responses of optimal strategies to an increase in the risk level, and predict differential responses of behaviours observed in experimental versus natural conditions. The risk-MVT can also be used to predict the optimal level of risk taking, or "optimal boldness", and suggests that individuals should generally be bolder in riskier habitats.

evolutionary biology↗

bioRxiv2022

Coevolution of species colonization rates controls food-chain length in spatially structured food webs

The complexity of food webs and how it depends on environmental variables is a long-standing question in ecology. Food-chain length depends on many factors, such as productive space, disturbance and spatial processes. It is not clear though how food-chain length should vary with adaptive evolutionary changes of the constitutive species. Assuming that each trophic level is subject to a competition-colonization trade-off, we model the adaptive evolution of their colonization rates and its consequences on equilibrium occupancies and food-chain length. When colonization rates are allowed to evolve, longer food chains can persist. Extinction, perturbation and habitat loss all affect the evolutionary-stable colonization rates, but trade-off strength (costs of dispersal) has a major role: weaker trade-offs yield longer chains. Our results suggest a strong link between within-trophic level competition, spatial occupancies and food-chain length. Although these eco-evo dynamics partly alleviate the constraint on food-chain length in metacommunities, we show it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. Our model generates qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.

ecology↗

bioRxiv2022

When complex movement yields simple dispersal: behavioural heterogeneity, spatial spread and parasitism in groups of micro-wasps

O_LIUnderstanding how behavioural dynamics, inter-individual variability and individual interactions scale-up to shape the spatial spread and dispersal of animal populations is a major challenge in ecology. For biocontrol agents, such as the microscopic Trichogramma parasitic wasps, an understanding of movement strategies is also critical to predict pest-suppression performance in the field. C_LIO_LIWe experimentally studied the spatial propagation of groups of parasitoids and their patterns of parasitism. We investigated whether population spread is density-dependent, how it is affected by the presence of hosts, and whether the spatial distribution of parasitism (dispersal kernel) can be predicted from the observed spread of individuals. C_LIO_LIUsing a novel experimental device and high-throughput imaging techniques, we continuously tracked the spatial spread of groups of parasitoids over large temporal and spatial scales (eight hours; and six metres, ca. 12,000 body lengths). We could thus study how population density, the presence of hosts and their spatial distribution impacted the rate of population spread, the spatial distribution of individuals during population expansion, the overall rate of parasitism and the dispersal kernel (position of parasitism events). C_LIO_LIHigher population density accelerated population spread, but only transiently: the rate of spread reverted to low values after four hours, in a "tortoise-hare" effect. Interestingly, the presence of hosts suppressed this transiency and permitted a sustained high rate of population spread. Importantly, we found that population spread did not obey classical diffusion, but involved dynamical switches between resident and explorer movement modes. Population distribution was therefore not Gaussian, though surprisingly the distribution of parasitism (dispersal kernel) was. C_LIO_LIEven homogenous asexual groups of animals were shown to develop behavioral heterogeneties over a few hours. Explorer individuals were responsible for most parasitism and dispersal, and determined spatial spread and density-dependent dispersal. We showed that simple Gaussian dispersal did not emerge from simple diffusion, but rather from the interplay of several non-linearities at individual level. This suggests expectations from classical diffusion theory may not hold generally to active dispersers. These results highlight the need to take into account behaviour and inter-individual heterogeneity to understand population spread in animals. C_LI

ecology↗

bioRxiv2022

A double-spiral maze and hi-resolution tracking pipeline to study dispersal by groups of minute insects

Minute insects such as parasitic micro-wasps have high basic and applied importance, for their widespread use as biocontrol agents. Their dispersal is a phenotype of particular interest. Classically, it is evaluated using field releases, but those are time consuming, costly, and their results highly variable, preventing high-throughput and repeatability. Alternatively, dispersal can be studied using small-scale assays, but those neglect important higher-scale processes. Consequently, proper evaluation of dispersal is often complicated or lacking in academic studies and biocontrol breeding programs. Here we introduce a new method, the double-spiral maze, that allows the study of spatial propagation at relevant scales (several hours and meters), retaining high throughput and experimental power. The method records the location of every individual at every time, enabling accurate precise estimates of diffusion coefficients or other dispersal metrics. We describe this affordable, scalable, and easy-to-implement method, and illustrate its application with a species of agricultural interest.

ecology↗

bioRxiv2022

Non-target effects of ten essential oils on the egg-parasitoid Trichogramma evanescens

Essential oils (EOs) are increasingly used as biopesticides due to their insecticidal potential. This study addresses their non-target effects on a biological control agent: the egg parasitoid Trichogramma evanescens. In particular, we tested whether EOs affected parasitoid fitness either directly, by decreasing pre-imaginal survival, or indirectly, by disrupting parasitoids orientation abilities. The effect of Anise, Fennel, Sweet orange, Basil, Coriander, Oregano, Peppermint, Mugwort, Rosemary and Thyme EOs were studied on five strains of T. evanescens. Specific experimental setups were developed, and data obtained from image analysis were interpreted with phenomenological models fitted with Bayesian inference. Results highlight the fumigant toxicity of EOs on parasitoid development. Anise, Fennel, Basil, Coriander, Oregano, Peppermint and Thyme EOs are particularly toxic and drastically reduce the emergence rate of T. evanescens. Most EOs also affect parasitoid behavior: (i) Basil, Coriander, Oregano, Peppermint, Mugwort and Thyme EOs are highly repellent for naive female parasitoids; (ii) Anise and Fennel EOs can have repellent or attractive effects depending on strains; and (iii) Sweet orange, Oregano and Rosemary EOs have no detectable impact on orientation behavior. This study shows that EOs fumigation have non-target effects on egg parasitoids. This highlights the need to cautiously precise the deployment framework of biopesticides in an agroecological perspective.

ecology↗

bioRxiv2021

Migration pulsedness alters patterns of allele fixation and local adaptation in a mainland-island model

Geneflow across populations is a critical determinant of population genetic structure, divergence and local adaptation. While evolutionary theory typically envisions geneflow as a continuous connection among populations, many processes make it fluctuating and intermittent. We analyze a mainland-island model in which migration occurs as recurrent "pulses". We derive mathematical predictions regarding how the level of migration pulsedness affects the effective migration rate, for neutral and selected mainland alleles. We find that migration pulsedness can either decrease or increase geneflow, depending on the selection regime. Migration increases gene-flow for sufficiently (counter)selected alleles (s < s1), but reduces it otherwise. We provide a mathematical approximation of the threshold selection s1, which is verified in stochastic simulations. Migration pulsedness thus affects the fixation rate at different loci in opposite ways, in a way that cannot be described as a change in effective population size. We show that migration pulsedness would generally reduce the level of local adaptation, and introduce an additional genetic load: the "pulsedness load". Our results indicate that migration pulsedness can be detrimental to the adaptation and persistence of small peripheral populations, with implications in management and conservation. Our results highlight temporally variable migration as an important process for evolutionary and population genetics.

evolutionary biology↗

bioRxiv2021

Metacommunity dynamics and the spurious detection of species associations in co-occurrence analyses: patch disturbance matters

O_LI1: Many statistical methods attempt to detect species associations - and so infer inter-specific interactions - from species co-occurrence patterns. Habitat heterogeneity and out-of-equilibrium colonization histories are well recognized as potentially causing species associations, even when interactions are absent. The potential for patch disturbance, a classical component of metacommunity dynamics, to also drive spurious species associations has however been over-looked. C_LIO_LI2: Using a new general metacommunity model, we derive mathematical predictions regarding how patch disturbance would affect the patterns of species associations detected in "null" co-occurrence matrices. We also conduct numerical simulations to test our predictions and to compare the performance of several widespread statistical methods, including direct tests of pairwise independence, matrix permutation approaches and joint species distribution modelling. C_LIO_LI3: We show how classical metacommunity dynamics can produce statistical associations, both positive and negative, even when species do not interact, when there is no habitat heterogeneity, and at equilibrium. This occurs as soon as there is some rate of patch disturbance (i.e. simultaneous extinction of several species in a patch) and/or a finite life-span of patches, a common feature of a broad range of plant, animal or microbial systems. C_LIO_LI4: Patch disturbance can compromise species co-occurrence analyses and cause the artefactual detection of species associations if not taken into account. Including patch age (i.e. the time since the last patch disturbance event) as a covariate in a joint species distribution model can resolve the artefact. However, this requires additional data that often are not available in practice. We argue that the consequences of patch disturbance should not be underestimated when analysing species distribution patterns in metacommunity-like systems. C_LI

ecology↗

bioRxiv2021

Landscape connectivity alters the evolution of density-dependent dispersal during pushed range expansions

AO_SCPLOWBSTRACTC_SCPLOWAs human influence reshapes communities worldwide, many species expand or shift their ranges as a result, with extensive consequences across levels of biological organization. Range expansions can be ranked on a continuum going from pulled dynamics, in which low-density edge populations provide the "fuel" for the advance, to pushed dynamics in which high-density rear populations "push" the expansion forward. While theory suggests that evolution during range expansions could lead pushed expansions to become pulled with time, empirical comparisons of phenotypic divergence in pushed vs. pulled contexts are lacking. In a previous experiment using Trichogramma brassicae wasps as a model, we showed that expansions were more pushed when connectivity was lower. Here we used descendants from these experimental landscapes to look at how the range expansion process and connectivity interact to shape phenotypic evolution. Interestingly, we found no clear and consistent phenotypic shifts, whether along expansion gradients or between reference and low connectivity replicates, when we focused on low-density trait expression. However, we found evidence of changes in density-dependence, in particular regarding dispersal: populations went from positive to negative density-dependent dispersal at the expansion edge, but only when connectivity was high. As positive density-dependent dispersal leads to pushed expansions, our results confirm predictions that evolution during range expansions may lead pushed expansions to become pulled, but add nuance by showing landscape conditions may slow down or cancel this process. This shows we need to jointly consider evolution and landscape context to accurately predict range expansion dynamics and their consequences.

ecology↗

bioRxiv2020

Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens

Improvements in the biological control of agricultural pests require improvements in the phenotyping methods used by practitioners to select efficient biological control agent (BCA) populations in industrial rearing or field conditions. Consistent inter-individual variations in behaviour (i.e. animal personality) probably affect BCA efficiency, but have never been taken into account in the development of phenotyping methods, despite having characteristics useful for phenotyping: repeatable (by definition), often heritable, etc. We developed a video-tracking method targeting animal personality traits and evaluated the feasibility of its use for genetic improvement in the BCA Trichogramma evanescens, by phenotyping 1,049 individuals from 24 isogenic lines. We found consistent individual variations in boldness, activity and exploration. Personality differences between the 24 isogenic lines suggested a genetic origin of the variations in activity and exploration (broad-sense heritability estimates of 0.06 to 0.11) and revealed a trade-off between exploration and fecundity.

ecology↗

bioRxiv2020

Shifts from pulled to pushed range expansions caused by reductions in connectedness

AO_SCPLOWBSTRACTC_SCPLOWRange expansions are key processes shaping the distribution of species; their ecological and evolutionary dynamics have become especially relevant today, as human influence reshapes ecosystems worldwide. Many attempts to explain and predict range expansions assume, explicitly or implicitly, so-called "pulled" expansion dynamics, in which the low-density edge populations provide most of the "fuel" for the species advance. Some expansions, however, exhibit very different dynamics, with high-density populations behind the front "pushing" the expansion forward. These two types of expansions are predicted to have different effects on e.g. genetic diversity and habitat quality sensitivity. However, empirical studies are lacking due to the challenge of generating reliably pushed vs. pulled expansions in the laboratory, or discriminating them in the field. We here propose that manipulating the degree of connectivity among populations may prove a more generalizable way to create pushed expansions. We demonstrate this with individual-based simulations as well as replicated experimental range expansions (using the parasitoid wasp Trichogramma brassicae as model). By analyzing expansion velocities and neutral genetic diversity, we showed that reducing connectivity led to pushed dynamics. Low connectivity alone, i.e. without density-dependent dispersal, can only lead to "weakly pushed" expansions, where invasion speed conforms to pushed expectations, but the decline in genetic diversity does not. In empirical expansions however, low connectivity may in some cases also lead to adjustments to the dispersal-density function, recreating "classical" pushed expansions. In the current context of habitat loss and fragmentation, we need to better account for this relationship between connectivity and expansion regimes to successfully predict the ecological and evolutionary consequences of range expansions.

ecology↗

bioRxiv2019

How community adaptation affects biodiversity-ecosystem-functioning relationships

Evidence is growing that evolutionary dynamics can impact biodiversity-ecosystem functioning (BEF) relationships. However the nature of such impacts remains poorly understood. Here we use a modelling approach to compare random communities, with no trait evolutionary fine-tuning, and co-adapted communities, where traits have co-evolved, in terms of emerging biodiversity-productivity, biodiversitystability, and biodiversity-invasion relationships. Community adaptation impacted most BEF relationships, sometimes inverting the slope of the relationship compared to random communities. Biodiversity-productivity relationships were generally less positive among co-adapted communities, with reduced contribution of sampling effects. The effect of community-adaptation, though modest regarding invasion resistance, was striking regarding invasion tolerance: co-adapted communities could remain very tolerant to invasions even at high diversity. BEF relationships are thus contingent on the history of ecosystems and their degree of community adaptation. Short-term experiments and observations following recent changes may not be safely extrapolated into the future, once eco-evolutionary feedbacks have taken place.

evolutionary biology↗

bioRxiv2019

A multi-seasonal model of plant-nematode interactions and its use to identify optimal plant resistance deployment strategies

O_LIRoot-knot nematodes (RKNs) are soil-borne polyphagous pests with major impact on crop yield worlwide. Resistant crops efficiently control avirulent RKNs, but favour the emergence of virulent forms. Virulence being associated with fitness costs, susceptible crops counter-select virulent RKNs. In this study we identify optimal rotation strategies between susceptible and resistant crops to control RKNs and maximize crop yield.\nC_LIO_LIWe developed an epidemiological model describing the within-season dynamics of avirulent and virulent RKNs on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic and genetic parameters.\nC_LIO_LICrop rotations were found to be efficient under realistic parameter ranges. They were characterised by low ratios of resistant plants, and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts.\nC_LIO_LISwitching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available to us.\nC_LI

ecology↗