Biology subjects

Billiard, S.

Publications and source records attributed to Billiard, S..

18 recordsLinked to original sources

bioRxiv2026

Breakdown of sporophytic self-incompatibility: Diploids versus tetraploids

Many angiosperm species possess self-incompatibility (SI) systems that prevent self-fertilization. Because empirical studies often report higher selfing rates in tetraploids than in diploids, we investigate whether sporophytic self-incompatibility (SSI) is more likely to break down after the introduction of a self-compatible (SC) allele in tetraploid populations. To address this question, we use analytical models and individual-based simulations to compare diploid and tetraploid populations under two main scenarios: (1) all SI alleles are codominant, and (2) SI alleles are structured into dominance classes. Overall, our results indicate that SSI is more difficult to maintain in tetraploids than in diploids, with dominance relationships playing a key role in the invasion success of an SC allele. When SI alleles are organized into dominance classes, increasing the dominance of the SC allele generally favors SSI breakdown in tetraploids, while diploids show weaker sensitivity to dominance, with SSI maintained across all dominance scenarios for the SC allele under sufficiently high inbreeding depression. However, when the SC allele is dominant over all SI alleles, SSI is more readily maintained in both the codominant and dominance-class models.

plant biology↗

bioRxiv2026

The fate of mutations on Y chromosomes andautosomes: a unified Wright-Fisher frameworkaccounting for segregation time

Understanding how mutations evolve on Y chromosomes is central to explaining the origin, diversity and persistence of sex chromosomes. Mutations occurring on the Y chromosome in sexual populations experience selective dynamics that differ markedly from those on autosomes, due to a reduced effective population size and the presence of large non-recombining regions containing alleles maintained in a permanently heterozygous state. These specific features alter gene transmission in the Y chromosome population compared to autosomes, even within the same pedigree. Here, we provide a two-sex diploid Wright-Fisher model that explicitly incorporates both sex chromosomes and autosomes within a unified population framework, in order to capture the influence of these specificities on the fate of mutations, not only considering fixation probabilities but also segregation times. We use diffusion approximations and provide analytical and numerical tools to compute these quantities across a wide range of parameters and selection regimes. We recover classical results on fixation probabilities in various scenarios, including purely beneficial, deleterious or overdominant mutations, and extend them in the light of mean segregation time, a key but often overlooked determinant of evolutionary outcomes over finite timescales. In particular, our analyses show that overdominant mutations are overall more likely to fix in observable time windows on the Y chromosome than on autosomes. Individual-based simulations corroborate our approximations and highlight parameter regimes where the theoretical approach is particularly useful, especially for parameter values inducing long segregation times or small fixation probabilities, for which simulations are impractical. Our results provide a comprehensive and tractable framework for clarifying how chromosome-specific features shape evolutionary dynamics beyond fixation probabilities alone.

evolutionary biology↗

bioRxiv2025

Disentangling the sources of variation in functional responses: between-individuals variability, measurements errors and inherent stochasticity of the prey-predator interaction process

The consumption rate of prey by predators, or functional responses, are known to be highly variable even within a single population. Identifying and estimating the different sources of variation of functional responses is a long-standing challenge. We develop here a statistical framework derived from a mechanistic stochastic process model that explicitly accounts for different sources of variation. We apply it to disentangle and estimate in particular 1) residual variance due to measurement errors and model misspecification, 2) between-predator variability, and 3) the interaction stochasticity, i.e. the intrinsic and mechanistic variability due to interactions processes between prey and predators. We show that it is possible to estimate these sources of variation under realistic experimental conditions. Our results also show that model fitting can compensate by overestimating residual source of variation, leading to biased parameter estimates when interaction stochasticity is misspecified. Applied to empirical data, the model reveals that standard assumptions, such as prey renewal and lack of spatial structure, fail to capture observed variability. We also show how experimental design affects parameter identifiability, highlighting the trade-off between the number of individuals and repeated observations.

ecology↗

bioRxiv2024

Stochastic foraging paths primarily drives within-species variations of prey consumption rates

The speed at which individuals interact, in particular prey and predators, affects ecological processes at all scales, including how fast matter and energy flow through ecosystems, and how stable communities are. Environmental heterogeneity and individual variabilities are generally believed to be the main factors underlying the variation of consumption rates of prey by predators. We challenge this view by comparing predicted variability from a stochastic model to experimental data. We first analyze a stochastic model of a simple random walk with elementary ecological processes involved in prey consumption, including prey depletion, predator movements and prey handling. We provide sharp approximations of the distribution of the consumption rate and a quantitative prediction of the coefficient of variation when stochastic foraging is the only source of variability. Predictions are then compared to the coefficients of variation estimated from data from dozens of various species and experimental contexts. We show that the predictions only accounting for intrinsic stochasticity in foraging are compatible with the range of observed values, in particular in 1 or 2 dimensional space. After evaluating the robustness of our models predictions through stochastic computer simulations, we conclude that the main driver of the variation of the consumption rate is the foraging process itself rather than environmental or between-individual variabilities. Our approach lays the foundations for unifying foraging theory and population ecology, and as such has many empirical and theoretical implications for both fields.

ecology↗

bioRxiv2024

Traits related to pollination and mating result in diverse reproductive strategies in angiosperms

O_LIFlowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes are associated with floral and life-history traits that have evolved together, making it difficult to interpret correlations between traits. C_LIO_LIWe analysed variation in 21 traits related to flowers, pollination, mating, sexual systems and life history from 361 species representative of flowering plant diversity. C_LIO_LIOutcrossing was mainly found among long-lived, large-stature plants, but hermaphroditic outcrossers and dioecious species appeared as largely non-overlapping strategies in the trait space. Level of floral investment was the main difference between these strategies, with dioecious species having generally smaller, less rewarding flowers, a pattern that also occurred in biotically pollinated species. C_LIO_LIThis multi-trait study shows that pollination can be achieved in many, often contrasting, ways. Despite extensive variation in reproductive traits, dioecy stands out as being linked to floral traits primarily, while correlations with lifespan and dispersal traits appear spurious. We provide a conceptual framework based on lifespan, floral investment, and sexual separation that can be used to integrate pollination, reproduction and plant growth in future research on plant evolution and ecology. C_LI

evolutionary biology↗

bioRxiv2023

The diallelic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene

Sexual reproduction in flowering plants is commonly controlled by self-incompatibility (SI) systems that are either homomorphic (and typically governed by large numbers of distinct allelic specificities), or heteromorphic (and then typically governed by only two allelic specificities). The SI system of the Oleaceae family is a striking exception to this rule and represents an evolutionary conundrum, with the long-term maintenance of only two allelic specificities, but often in the complete absence of morphological differentiation between them. To elucidate the genomic architecture and molecular bases of this highly unusual SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals belonging to the two SI specificities and connected them to a genetic map. Comparison of the S-locus region revealed a segregating 543-kb indel specific to one of the two specificities, suggesting a hemizygous genetic architecture. Only one of the predicted genes in this indel is conserved with the olive tree Olea europaea, where we also confirmed the existence of a segregating hemizygous indel. We demonstrated full association between presence/absence of this gene and the SI groups phenotypically assessed across six distantly related Oleaceae species. This gene is predicted to be involved in catabolism of the Gibberellic Acid (GA) hormone, and experimental manipulation of GA levels in developing buds modified the male and female SI responses in an S-allele-specific manner. Thus, our results provide a unique example of a reproductive system where a single conserved gibberellin-related gene in a 500-700kb hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility.

evolutionary biology↗

bioRxiv2022

The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing

Large regions of suppressed recombination having extended over time occur in many organisms around genes involved in mating compatibility (sex-determining or mating-type genes). The sheltering of deleterious alleles has been proposed to be involved in such expansions. However, the dynamics of deleterious mutations partially linked to genes involved in mating compatibility are not well understood, especially in finite populations. In particular, under what conditions deleterious mutations are likely to be maintained for long enough near mating-compatibility genes remains to be evaluated, especially under selfing, which generally increases the purging rate of deleterious mutations. Using a branching process approximation, we studied the fate of a new deleterious or overdominant mutation in a diploid population, considering a locus carrying two permanently heterozygous mating-type alleles, and a partially linked locus at which the mutation appears. We obtained analytical and numerical results on the probability and purging time of the new mutation. We investigated the impact of recombination between the two loci and of the mating system (outcrossing, intra and inter-tetrad selfing) on the maintenance of the mutation. We found that the presence of a fungal-like mating-type locus (i.e. not preventing diploid selfing) always sheltered the mutation under selfing, i.e. it decreased the purging probability and increased the purging time of the mutations. The sheltering effect was higher in case of automixis (intra-tetrad selfing). This may contribute to explain why evolutionary strata of recombination suppression near the mating-type locus are found mostly in automictic (pseudo-homothallic) fungi. We also showed that rare events of deleterious mutation maintenance during strikingly long evolutionary times could occur, suggesting that deleterious mutations can indeed accumulate near the mating-type locus over evolutionary time scales. In conclusion, our results show that, although selfing purges deleterious mutations, these mutations can be maintained for very long times near a mating-type locus, which may contribute to promote the evolution of recombination suppression in sex-related chromosomes.

evolutionary biology↗

bioRxiv2022

Human-environment feedback and the consistency of proenvironmental behaviour

Addressing global environmental crises such as anthropogenic climate change requires the consistent adoption of proenvironmental behavior by a large part of a population. Here, we develop a mathematical model of a simple behavior-environment feedback loop to ask how the individual assessment of the environmental state combines with social interactions to influence the consistent adoption of proenvironmental behavior, and how this feeds back to the perceived environmental state. In this stochastic individual-based model, individuals can switch between two behaviors, active (or actively proenvironmental) and baseline, differing in their perceived cost (higher for the active behavior) and environmental impact (lower for the active behavior). We show that the deterministic dynamics and the stochastic fluctuations of the system can be approximated by ordinary differential equations and a Ornstein-Uhlenbeck type process. By definition, the proenvironmental behavior is adopted consistently when, at population stationary state, its frequency is high and random fluctuations in frequency are small. We find that the combination of social and environmental feedbacks can promote the spread of costly proenvironmental behavior when neither, operating in isolation, would. To be adopted consistently, strong social pressure for proenvironmental action is necessary but not sufficient - social interactions must occur on a faster timescale compared to individual assessment, and the difference in perceived environmental impact must be small. This simple model suggests a scenario to achieve large reductions in environmental impact, which involves incrementally more active and potentially more costly behavior being consistently adopted under increasing social pressure for proenvironmentalism.

ecology↗

bioRxiv2022

How does the host community structure affect the epidemiological dynamics of emerging infectious diseases?

Many pathogens, especially those responsible for emerging infectious diseases, are transmitted in a host community. How the host community structure affects an epidemic is still debated, particularly whether increasing the host community complexity would tend to amplify or dilute the incidence of an epidemic in a target population, e.g. humans or cattle. In this paper, we build a stochastic SIR model and compare epidemiological dynamics in a target population between three simple host community structures with an increasing complexity. Globally, our results show two possible main outcomes. First, an intermediate host can have a diluting effect by preventing the direct transmission from hosts to the target population, thus reducing the prevalence of infection. Second, when two sources of infection are considered, the effects of the epidemic are generally amplified. By highlighting that the structure of the ecological hosts network can dramatically affect epidemics, our results may have implications for the control of emerging infectious diseases.

ecology↗

bioRxiv2021

Revisiting the number of self-incompatibility alleles in finite populations: from old models to new results

Under gametophytic self-incompatibility (GSI), plants are heterozygous at the self-incompatibility locus (S-locus) and can only be fertilized by pollen with a different allele at that locus. The last century has seen a heated debate about the correct way of modeling the allele diversity in a GSI population that was never formally resolved. Starting from an individual-based model, we derive the deterministic dynamics as proposed by Fisher (1958), and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (1964) is close to our theoretical prediction, in line with earlier numerical confirmation. Additionally, we approximate the invasion probability of a new S-allele, which scales inversely with the number of resident S-alleles. Lastly, we use the stationary allele frequency distribution to estimate the population size of a plant population from an empirically obtained allele frequency spectrum, which complements the existing estimator of the number of S-alleles. Our expression of the stationary distribution resolves the long-standing debate about the correct approximation of the number of S-alleles and paves the way to new statistical developments for the estimation of the plant population size based on S-allele frequencies.

evolutionary biology↗

bioRxiv2021

Balancing selection and the crossing of fitness valleys in structured populations: diversification in the gametophytic self-incompatibility system

The self-incompatibility locus (S-locus) of flowering plants displays a striking allelic diversity. How such a diversity has emerged remains unclear. In this paper, we performed numerical simulations in a finite island population genetics model to investigate how population subdivision affects the diversification process at a S-locus, given that the two-genes architecture typical of S-loci involves the crossing of a fitness valley. We show that population structure slightly reduces the parameter range allowing for the diversification of self-incompatibility haplotypes (S-haplotypes), but at the same time also increases the number of these haplotypes maintained in the whole metapopulation. This increase is partly due to a higher rate of diversification and replacement of S-haplotypes within and among demes. We also show that the two-genes architecture leads to a higher diversity in structured populations compared with a simpler genetic architecture where new S-haplotypes appear in a single mutation step. Overall, our results suggest that population subdivision can act in two opposite directions: it renders S-haplotypes diversification easier, although it also increases the risk that the self-incompatibility system is lost.

evolutionary biology↗

bioRxiv2020

Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae)

The breakdown of self-incompatibility (SI) in angiosperms is one of the most commonly observed evolutionary transitions. While multiple examples of SI breakdown have been documented in natural populations, there is strikingly little evidence of stable within-population polymorphism with both inbreeding (self-compatible) and outcrossing (self-incompatible) individuals. This absence of mating system polymorphism corroborates theoretical expectations that predict that in/outbreeding polymorphism is possible only under very restricted conditions. However, theory also predicts that a diallelic sporophytic SI system facilitates the maintenance of such polymorphism. We tested this prediction by studying the mating system of Ligustrum vulgare L., an entomophilous hermaphroditic species of the Oleaceae family. Using stigma tests with controlled pollination and paternity assignment of open-pollinated progenies, we confirmed the existence of two self-incompatibility groups in this species. We also demonstrated the existence of self-compatible individuals in different populations of Western Europe arising from a mutation affecting the expression of the pollen component of SI. We then estimated the selfing rate in a garden experiment. Our results finally show that the observed low frequency of self-compatible individuals in natural populations is compatible with theoretical predictions only if inbreeding depression is very high.

evolutionary biology↗

bioRxiv2019

On deleterious mutations in perennials: inbreeding depression, mutation load and life-history evolution

In Angiosperms, perennials typically present much higher levels of inbreeding depression than annuals. One hypothesis to explain this pattern stems from the observation that inbreeding depression is expressed across multiple life stages in Angiosperms. It posits that increased inbreeding depression in more long-lived species could be explained by differences in the way mutations affect fitness in these species, through the life stages at which they are expressed. In this study, we investigate this hypothesis. We combine a physiological growth model and multilocus population genetics approaches to describe a full genotype-to-phenotype-to-fitness map. We study the behaviour of mutations affecting growth or survival, and explore their consequences in terms of inbreeding depression and mutation load. Although our results only agree with empirical data within a narrow range of conditions, we argue that they may point us towards the type of traits susceptible to underlie inbreeding depression in long-lived species, that is traits under sufficiently strong selection, on which selection decreases sharply as life expectancy increases. Then, we study the role deleterious mutations maintained at mutation-selection balance may play in the coevolution between growth and survival strategies. Description of the manuscriptThe main text of the manuscript, excluding captions and headers, is 5712 words long. There are 4 figures in the main text, numbered from 1 to 4. In the present file, pages 1 to 33 correspond to the main text (including title page, abstract and litterature cited), while the remaining pages (33 to 72) correspond to appendices. There are 5 sections in Appendices, which are all available at the end of the manuscript file. There are 12 figures in Appendices, numbered from S1 to S12.

evolutionary biology↗

bioRxiv2019

Inference with selection, varying population size and evolving population structure: Application of ABC to a forward-backward coalescent process with interactions

Genetic data are often used to infer history, demographic changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed a priori known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interaction to describe an asexual population, and we develop an inferential procedure for ecological, demographic and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated and real data. We show that the procedure give accurate estimate of the parameters of the model. We finally carry an illustration on real data and analyze the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia populations in order to test whether different social organizations show significantly different fertility.

genetics↗

bioRxiv2019

Identifying conversion efficiency as a key mechanism underlying food webs evolution: A step forward, or backward?

Body size or mass is generally seen as one of the main factors which structure food webs. A large number of evolutionary models have shown that indeed, the evolution of body size (or mass) can give rise to hierarchically organized trophic levels with complex between and within trophic interactions. However, because these models have often very different assumptions, sometimes arbitrary, it is difficult to evaluate what are the real key factors that determine food webs evolution, and whether these models results are robust or not. In this paper, we first review the different adaptive dynamics models, especially highlighting when their assumptions strongly differ. Second, we propose a general model which encompasses all previous models. We show that our model recovers all previous models results under identical assumptions. However, most importantly, we also show that, when relaxing some of their hypotheses, previous models give rise to degenerate food webs. Third, we show that the assumptions made regarding the form of biomass conversion efficiency are key for food webs evolution, a parameter which was neglected in previous models. We conclude by discussing the implication of biomass conversion efficiency, and by questioning the relevance of such models to study the evolution of food webs.

ecology↗

bioRxiv2018

Breakdown of gametophytic self-incompatibility in subdivided populations

Many hermaphroditic flowering plants species possess a genetic self-incompatibility (SI) system that prevents self-fertilization and is typically controlled by a single multiallelic locus, the S-locus. The conditions under which SI can be stably maintained in single isolated populations are well known and depend chiefly on the level of inbreeding depression and the number of SI alleles segregating at the S-locus. However, while both the number of SI alleles and the level of inbreeding depression are potentially affected by population subdivision, the conditions for the maintenance of SI in subdivided populations remain to be studied. In this paper, we combine analytical predictions and two different individual-based simulation models to show that population subdivision can severely compromise the maintenance of SI. Under the conditions we explored, this effect is mainly driven by the decrease of the local diversity of SI alleles rather than by a change in the dynamics of inbreeding depression. We discuss the implications of our results for the interpretation of empirical data on the loss of SI in natural populations.\n\nData accessibility statementNo data to be archived

evolutionary biology↗

bioRxiv2018

The joint evolution of lifespan and self-fertilisation

In Angiosperms, there exists a strong association between mating system and lifespan. Most self-fertilising species are short-lived and most predominant or obligate outcrossers are long-lived. This association is generally explained by the influence of lifespan on the evolution of the mating system, considering lifespan as fixed. Yet, lifespan can itself evolve, and the mating system may as well influence the evolution of lifespan, as is suggested by joint evolutionary shifts of lifespan and mating system between sister species. In this paper, we build modifier models to study the joint evolution of self-fertilisation and lifespan, including both juvenile and adult inbreeding depression. We show that self-fertilisation is expected to promote evolution towards shorter lifespan, and that the range of conditions under which selfing can evolve rapidly shrinks as lifespan increases. We study the effects of inbreeding depression affecting various steps in the life cycle, and discuss how extrinsic mortality conditions are expected to affect evolutionary associations. In particular, we show that selfers may sometimes remain short-lived even in a very stable habitat, as a strategy to avoid the deleterious effects of inbreeding.

evolutionary biology↗

bioRxiv2017

Stochastic dynamics of an epidemics with recurrent spillovers from an endemic reservoir

Most emerging human infectious diseases have an animal origin. Yet, while zoonotic diseases originate from a primary reservoir, most theoretical studies have principally focused on single-host processes, either exclusively humans or exclusively animals, without considering the importance of animal to human transmission for understanding the dynamics of emerging infectious diseases. Here we aim to investigate the importance of spillover transmission for explaining the number and the size of outbreaks. We propose a simple stochastic Susceptible-Infected-Recovered model with a recurrent infection of an incidental host from a reservoir (e.g. humans by a zoonotic species), considering two modes of transmission, (1) animal-to-human and (2) human-to-human. The model assumes that (i) epidemiological processes are faster than other processes such as demographics or pathogen evolution and (ii) that an epidemic occurs until there are no susceptible individuals left. The results show that during an epidemic, even when the pathogens are barely contagious, multiple outbreaks are observed due to spillover transmission. Overall, the findings demonstrate that the only consideration of direct transmission between individuals is not sufficient to explain the dynamics of zoonotic pathogens in an incidental host.

epidemiology↗