Biology subjects

Bocedi, G.

Publications and source records attributed to Bocedi, G..

13 recordsLinked to original sources

bioRxiv2026

Pest evolution amplifies projected crop losses under climate change

Climate change influences the physiology and population dynamics of ectothermic pests, with major repercussions for global crop production. Yet, how evolution modulates these outcomes remains unclear. We exposed the widespread beetle pest Callosobruchus maculatus to 10 years of experimental evolution at different temperatures and quantified thermal responses of life-history traits. Hot- and cold-adapted populations evolved differences in thermal sensitivity, but these were modest relative to evolved differences in trait averages. By leveraging high-resolution temperature time-series we show that the observed evolution translates into cold-adapted genotypes having highest fitness in cold climates and hot-adapted genotypes in warm climates. Hot-adapted beetles maximize fitness in warm climates by increased larval growth, resulting in larger body sizes and higher fecundity. This evolutionary strategy compounds projected crop losses under warming by increasing both intrinsic population growth and per-capita host consumption rates. By year 2100 under intermediate-to-high warming (SSP3-7.0), pest evolution is projected to increase global crop damage potential by +113% from present--twice that expected from warming alone (not accounting for evolution). In major crop-producing areas, where temperatures and the beetles host consumption rates are already high, warming increases average crop damage potential by +29%, but evolution amplifies this three-fold to +87%. Evolution also expands C. maculatus projected colonizable range and in some regions even flips forecasted crop damage reductions into increases. These results identify climate-driven evolution of pest life-histories as an amplifier of agricultural losses and suggest that current projections may significantly understate the threat warming poses to future food security.

ecology↗

bioRxiv2026

The flaws of fitness functions in changing environments

When predicting species responses to changing environments, one can use mathematical functions that describe how individual fitness components depend on the environment, or a single "composite" function that directly links fitness to the environmental state. The former approach is a cornerstone of process-based modelling, but the latter remains standard for developing fundamental theory and making ecological predictions. Yet, fitness is not a single instantaneous trait, but an integrated outcome of multiple underlying processes accruing throughout an organisms life. We show that by ignoring the distinct environmental dependence of the underlying processes, predictions from composite fitness functions become inherently flawed in variable environments. We explore the magnitude of this error by leveraging empirical thermal reaction norms for four important life-history processes in an insect pest, the seed beetle Callosobruchus maculatus. We parameterize two fitness functions: one explicitly modelling the temperature-dependence of the four life-history traits independently (the "ground truth") and one composite function, which treats fitness as a single, instantaneous outcome of the environment. By combining these two functions with hourly temperature data, we projected demographic responses under different warming scenarios across 300 sites over three beetle population origins (California, USA; Yemen; Brazil). We show that the composite function over- or underestimates fitness depending on subtle climatic differences and whether fitness is assumed to accumulate additively or multiplicatively, highlighting the problems of applying composite fitness functions to variable conditions. We conclude that explicitly modeling trait-specific processes will become increasingly important for accurate eco-evolutionary forecasting under future environmental change.

ecology↗

bioRxiv2025

Landscape context drives within-species variation in dispersal kernels and limits transferability

Dispersal is a key ecological trait that ensures connectivity, gene flow, and range dynamics, yet empirical information about the dispersal process remains scarce. While interspecific differences have been synthesized, intraspecific variation driven by individual movement and landscape context remains poorly understood. Here, we use the individual-based modelling platform RangeShifter to simulate movement trajectories of four animal species, from insects to mammals, across neutral landscapes varying in habitat amount and fragmentation. From these simulations we derived dispersal kernels using five probability density functions and analysed their response to landscape context. Across species, log-normal (fat-tailed) kernels consistently best described dispersal, but both median and long-distance dispersal varied strongly with habitat configuration. Habitat loss consistently reduced abundances, whereas fragmentation per se more strongly shaped dispersal kernels, providing mechanistic insight into a central debate in landscape ecology. Our results highlight that dispersal kernels do not transfer reliably across environments and should be treated as emergent, context-dependent properties. Progress in predicting species responses to global change will require empirical studies explicitly integrated with mechanistic modelling to uncover generalizable links between dispersal, traits, and landscape context.

ecology↗

bioRxiv2024

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation. Significance statementPlant species in the genus Silene (campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genus Silene and the family Caryophyllaceae more generally.

evolutionary biology↗

bioRxiv2023

A general time-in, time-out model for the evolution of nuptial gift-giving

Nuptial gift-giving occurs in several taxonomic groups including insects, snails, birds, squid, arachnids and humans. Although this trait has evolved many times independently, no general framework has been developed to predict the conditions necessary for nuptial gift-giving to evolve. We use a time-in time-out model to derive analytical results describing the requirements necessary for selection to favour nuptial gift-giving. Specifically, selection will favour nuptial gift-giving if the fitness increase caused by gift-giving exceeds the product of expected gift search time and encounter rate of the opposite sex. Selection will favour choosiness in the opposite sex if the value of a nuptial gift exceeds the inverse of the time taken to produce offspring multiplied by the rate at which mates with nuptial gifts are encountered. Selection can differ between the sexes, potentially causing sexual conflict. We further investigate these results using an individual-based model inspired by a system of nuptial gift-giving spiders, Pisaura mirabilis, by estimating the fitness benefit of nuptial gift-giving using experimental data from several studies. Our results provide a general framework for understanding when the evolution of nuptial gift-giving can occur and provide novel insight into the evolution of worthless nuptial gifts, occurring in multiple taxonomic groups with implications for understanding parental investment.

evolutionary biology↗

bioRxiv2022

Inferring the distributions of fitness effects and proportions of strongly deleterious mutations

The distribution of fitness effects is a key property in evolutionary genetics as it has implications for several evolutionary phenomena including the evolution of sex and mating systems, the rate of adaptive evolution, and the prevalence of deleterious mutations. Despite the distribution of fitness effects being extensively studied, the effects of strongly deleterious mutations are difficult to infer since such mutations are unlikely to be present in samples of haplotypes, so genetic data may contain very little information about them. Recent work has attempted to correct for this issue by expanding the classic gamma-distributed model to explicitly account for strongly deleterious mutations. Here, we use simulations to investigate one such method, adding a parameter (plth) to capture the proportion of strongly deleterious mutations. We show that plth can improve the model fit when applied to individual species but can underestimate the true proportion of strongly deleterious mutations. The parameter can also artificially maximize the likelihood when used to jointly infer a distribution of fitness effects from multiple species. As plth and related parameters are used in current inference algorithms, our results are relevant with respect to avoiding model artifacts and improving future tools for inferring the distribution of fitness effects.

bioinformatics↗

bioRxiv2021

Evolution of reduced dormancy during range expansions

There is increasing evidence that life-history traits can evolve rapidly during range expansion and that this evolution can impact the ecological dynamics of population spread. While dispersal evolution during range expansion has received substantial attention, dormancy (dispersal in time) has not. Here, we use an individual-based model to investigate the evolution of seed dormancy during range expansion. When a population is at spatial equilibrium our model produces results that are consistent with previous theoretical studies: seed dormancy evolves due to kin competition and the degree of dormancy increases as temporal environmental variation increases. During range expansions we consistently observe evolution towards reduced rates of dormancy at the front. Behind the front there is selection for higher rates of dormancy. Notably, the decreased dormancy towards the expanding margin reduces the regional resilience of recently expanded populations to a series of harsh years. We discuss how dormancy evolution during range expansion, and its consequences for spatial population dynamics, may impact other evolutionary responses to environmental change. We end with suggestions for future theoretical and empirical work.

evolutionary biology↗

bioRxiv2021

Inbreeding depression drives evolution of dispersal and polyandry

Understanding evolution of complex life-histories requires explicitly considering their multiple interactions, feedbacks, and shared drivers. Inbreeding depression is hypothesized to drive evolution of two life-histories which have far-reaching ecological and evolutionary consequence: dispersal and polyandry. Yet, the role of inbreeding depression in the separate evolution of these key life-histories is still debated, while the possibility for their joint evolution and consequent covariation has not been considered. I propose that dispersal and polyandry might be competing means of inbreeding avoidance which negatively feedback on each others evolution. Using a genetically explicit individual-based model, I first demonstrate that inbreeding depression can drive the separate evolution of dispersal and polyandry. Although this is largely known for dispersal, it is not as well established for polyandry evolution, which generally remains an evolutionary puzzle. Here, I show that polyandry can indeed evolve as means of indirect inbreeding avoidance in spatially structured populations. Second, when dispersal and polyandry can evolve jointly, a negative feedback emerges, such that they evolve as alternative inbreeding avoidance strategies across replicate systems, especially if there are fitness costs associated. Finally, although both dispersal and polyandry might be expected to shape the level of inbreeding depression, this is mainly affected by dispersal, while polyandry has a much more limited effect. These results emphasize the need to consider the potential joint evolution of dispersal and mating system in general, together with their genetic effects, to further our understanding of life-history evolution in spatially structured systems, and provide theoretical expectations for new empirical testing.

evolutionary biology↗

bioRxiv2021

Strong spatial population structure shapes the temporal coevolutionary dynamics of costly female preference and male display

Female mating preferences for exaggerated male display traits are commonplace. Yet, comprehensive understanding of the evolution and persistence of costly female preference through indirect (Fisherian) selection in finite populations requires some explanation for the persistence of additive genetic variance (Va) underlying sexual traits, given that directional preference is expected to deplete Va in display and hence halt preference evolution. However, the degree to which Va, and hence preference-display coevolution, may be prolonged by spatially variable sexual selection arising solely from limited gene flow and genetic drift within spatially structured populations has not been examined. Our genetically and spatially explicit model shows that spatial population structure arising in an ecologically homogeneous environment can facilitate evolution and long-term persistence of costly preference given small subpopulations and low dispersal probabilities. Here, genetic drift initially creates spatial variation in female preference, leading to persistence of Va in display through "migration-bias" of genotypes maladapted to emerging local sexual selection, thus fuelling coevolution of costly preference and display. However, costs of sexual selection increased the probability of subpopulation extinction, limiting persistence of high preference-display genotypes. Understanding long-term dynamics of sexual selection systems therefore requires joint consideration of coevolution of sexual traits and metapopulation dynamics.

evolutionary biology↗

bioRxiv2021

Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography

Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within- and between-species spatial structure of real datasets and implement it in a new R package - fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.

ecology↗

bioRxiv2020

RangeShifter 2.0: An extended and enhanced platform for modelling spatial eco-evolutionary dynamics and species' responses to environmental changes.

O_LIProcess-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability of species across complex landscapes. C_LIO_LIHere we introduce a new version, RangeShifter 2.0, which incorporates important new functionality. It is now possible to simulate dynamics over user-specified, temporally changing landscapes. Additionally, the genetic and evolutionary capabilities have been strengthened, notably by introducing an explicit genetic modelling architecture, which allows for simulation of neutral and adaptive genetic processes. Furthermore, emigration, transfer and settlement rules can now all evolve, allowing for sophisticated simulation of the evolution of dispersal. We illustrate the potential application of RangeShifter 2.0s new functionality by two examples. The first illustrates the range expansion of a virtual species across a dynamically changing UK landscape. The second demonstrates how the software can be used to explore the concept of evolving connectivity in response to land-use modification, by examining how movement rules come under selection over landscapes of different structure and composition. C_LIO_LIRangeShifter 2.0 is built using object-oriented C++ providing computationally efficient simulation of complex individual-based, eco-evolutionary models. The code has been redeveloped to enable use across operating systems, including on high performance computing clusters, and the Windows GUI has been enhanced. Furthermore, the recoding of the package has supported the development of a new version running under the R platform, RangeShiftR. C_LIO_LIRangeShifter 2.0 will facilitate the development of in-silico assessments of how species will respond to environmental changes and to potential management options for conserving or controlling them. By making the code available open source, we hope to inspire further collaborations and extensions by the ecological community. C_LI

ecology↗

bioRxiv2020

RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species' responses to environmental change

O_LIReliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses. C_LIO_LIWe present RangeShiftR, an R package that provides flexible and fast simulations of spatial eco-evolutionary dynamics and species responses to environmental changes. It implements the individual-based simulation software RangeShifter for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the packages functionality, describe the underlying model structure with its main components and present a short example. C_LIO_LIRangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with comprehensive documentation and elaborate tutorials to provide a low entry level. Thanks to the implementation of the core code in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. C_LIO_LIThe RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification, and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. C_LI

ecology↗

bioRxiv2017

Evolution Of Pre-Copulatory And Post-Copulatory Strategies Of Inbreeding Avoidance And Associated Polyandry

Inbreeding depression is widely hypothesised to drive adaptive evolution of pre-copulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesised to affect evolution of polyandry (i.e., female multiple mating). However, surprisingly little theory or modelling critically examines selection for pre-copulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for pre-copulatory inbreeding avoidance, requires polyandry, while interactions between pre-copulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e., degeneracy) potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting pre-copulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry, and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower cost alternative strategy. Further, fixed pre-copulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of pre-copulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry are therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of pre-copulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry.

evolutionary biology↗