Biology subjects

Mullon, C.

Publications and source records attributed to Mullon, C..

At least 19 recordsLinked to original sources

bioRxiv2026

The evolutionary interplay between self-fertilisation and sex allocation in flowering plants

Flowering plants vary in sex allocation (resource division between male and female function) and in selfing rate. These traits should evolve together: selfing changes fitness returns from pollen and ovules, whereas sex allocation changes the pollen available for selfing and export. Yet most models allow only one trait to evolve, leaving their evolutionary feedback unresolved. Here we model the joint evolution of sex allocation, pollen export and maternal control of competition between self- and cross-pollen. We show that selfing and sex allocation strongly influence one another, as selection favours associations between sex allocation and mating-system traits. When maternal control is fixed to recover classical mass-action, evolution can lead to the stable coexistence of selfing hermaphrodites and males specialised in pollen export. This androdioecy persists because hermaphrodites cannot prevent fertilisation by males. When maternal control of pollen competition also evolves, we find that where a mixed-mating equilibrium exists, selection again favours the emergence of androdioecy. As hermaphrodites evolve to favour their own pollen, however, they progressively exclude pollen from males, driving them extinct. The population may then return to mixed mating and repeat the process, or evolve complete selfing. We discuss these results with reference to known variation in the mating and sexual systems of plants.

evolutionary biology↗

bioRxiv2026

The effects of supergene evolution on the structure and stability of the G-matrix

The additive genetic variances and covariances of traits, collected in the G-matrix, summarise heritable variation within populations and are commonly used to predict the rate and direction of short-term multivariate evolution. These (co)variances are shaped by pleiotropy and genetic linkage, two features often associated with supergenes formed by chromosomal inversions. Yet how supergene evolution affects the structure and temporal stability of the G-matrix remains unclear. Here, we use mathematical analysis and individual-based simulations to investigate the evolution and genetic consequences of inversions capturing multiple pleiotropic loci underlying two traits subject to disruptive and correlational selection (selection favouring particular combinations of trait values). We show that inversions evolve under disruptive selection and are maintained by balancing selection because they preserve associations among alleles that together generate discrete phenotypic morphs. The genetic architecture reflects how selection acts on the traits: selection favouring diversification along a joint trait combination generally produces a single multi-trait supergene, whereas selection favouring independent diversification of each trait produces multiple independently segregating inversions. By suppressing recombination, these inversions increase additive genetic variance and narrow-sense heritability, and stabilise the overall amount of additive genetic variation through time. When dominance is allowed to evolve, dominance relationships become coordinated across linked loci within supergenes, although most genetic variance remains additive at the population level. Together, these results link the form of multivariate selection to the evolution of supergenes and to their consequences for the structure and temporal stability of the G-matrix.

evolutionary biology↗

bioRxiv2026

The evolution of family reputation extends indirect reciprocity

Reputation plays a major role in supporting cooperation among unrelated individuals through indirect reciprocity. By helping others, individuals build a good personal reputation and receive greater benefits from future partners. Most models of indirect reciprocity assume that a person's reputation reflects only their own behaviour. Yet in many societies, people are also judged by their family's reputation. How family reputation affects the evolution of cooperation, and whether reliance on it can itself evolve, remain unclear. Here we show that reputation inheritance expands the conditions under which indirect reciprocity favours cooperation, increasing helping and favouring greater reciprocity. Greater reciprocity in turn favours stronger reliance on inherited reputation, creating a positive feedback that stabilises cooperation, especially when interactions are infrequent or personal behaviour is difficult to observe. This feedback arises because cooperation generates future benefits both for the individual, through their personal reputation, and for their descendants, through inherited reputation. Reputation inheritance thereby provides a route via which kin selection and reciprocity, often treated as alternative explanations for cooperation, can reinforce one another. Our model helps explain why family-based reputation occurs across diverse human societies and provides an evolutionary framework for studying phenomena organised around family standing, including kin-based institutions, feuds between families and honour-based violence within them.

evolutionary biology↗

bioRxiv2026

The evolution of condition-dependent self-fertilisation

Self-fertilisation is common in cosexuals, but selfing rates vary among species, among populations and among individuals within populations. Most evolutionary theory seeking to explain this variation assumes genetically determined selfing rates. Here we study the evolution and consequences of condition-dependent selfing, where individuals adjust their selfing rate in response to their deleterious mutation load. We analyse a two-locus population-genetic model in which one locus determines condition and the other is a modifier locus that determines condition-dependent selfing rates, and then extend the analysis to a polygenic background in which condition is determined by many loci. Our results show that selection favours positive condition dependence: high-condition individuals self-fertilise whereas low-condition individuals outcross. The resulting reaction norm generates stable within-population variation in realised selfing rates at evolutionary equilibrium and reduces the mutation load. We further show that it persists under environmental heterogeneity, and that pollen discounting favours a gradual increase in selfing with condition, leading to a continuum of selfing phenotypes. Altogether, our results indicate that condition-dependent selfing can generate substantial within-population variation in selfing rates. It may therefore contribute to mating-system diversity, and in particular to the maintenance of mixed mating.

evolutionary biology↗

bioRxiv2025

Directional and disruptive selection in populations structured by class and continuous ontogeny under incomplete plasticity

Many organisms undergo ontogeny, whereby individuals change in state (e.g. in size, morphology, or condition) as they age. Understanding the evolution of traits influencing ontogeny is challenging because their fitness effects unfold across an individuals lifetime and may differ between classes such as sexes. Here, we analyse selection on non-plastic traits (e.g., fixed resource allocation strategies) that determine the development of dynamical states throughout life (e.g., body size), with consequences for fecundity and survival in age- and class-structured populations. Using invasion analysis, we derive expressions for directional and quadratic selection that decompose into age- and class-specific components. This allows us to identify convergence stable trait values, assess whether they are uninvadable or potentially experience evolutionary branching, and pinpoint the age and class pathways through which correlational and disruptive selection act. Applying our results to a model of growth under size-mediated sexual selection, we show how selection on growth rates distributes across ages and sexes, and how its relative strength depends on genetic correlations, individual ploidy and life-history. We also show how sex-specific developmental trade-offs and constraints can generate disruptive selection on male growth and favour the evolution of alternative male life histories. More broadly, our results highlight how adaptation is mediated by the interaction of development and demography, and provide tools to investigate how conflicts across ages and classes may influence senescence, sexual dimorphism, and the diversification of ontogenetic strategies. Author SummaryHow does natural selection shape traits that influence how organisms develop through their lifetime? This question is difficult because the effects of such traits unfold dynamically as individuals change in states such as size or condition, which in turn influence survival and reproduction throughout life. We formulate a mathematical model that follows these causal links and characterises the gradual evolution of non-plastic traits affecting development. Our results apply to populations with different classes, such as males and females, that follow distinct developmental and demographic paths. Our model reveals when selection is stabilizing, holding populations fixed for an optimal trait value, and when it is disruptive, favouring trait diversification and the emergence of alternative life-history strategies. As an illustration, we analyse the evolution of sex-specific growth under size-based sexual selection. We show how the evolution of male and female growth rates depends on genetics, such as individual ploidy or genetic correlation between traits, but also on life history, which determines the relative strength of selection acting on trait expression at different ages. We further show how developmental trade-offs and demographic differences can generate disruptive selection on male growth, leading to the coexistence of fast-growing short-lived males and slow-growing long-lived ones. More broadly, our results link development, demography, and adaptation, and show how their interplay shapes biological diversity both within and between populations.

evolutionary biology↗

bioRxiv2025

Plastic germination, temporal niche partitioning, and emergent assortative mating in annual plants

Temporal fluctuations in environmental conditions can promote coexistence via the storage effect, which requires a mechanism buffering different variants during adverse periods. This mechanism readily occurs in annual plants whose seeds do not necessarily germinate each year but instead remain dormant in a seed bank. Yet, how plasticity in germination timing affects genetic diversification and ecological speciation under temporally varying conditions remains poorly understood. Here, we use mathematical modeling and individual-based simulations to investigate the joint evolution of a combination of traits controlling plastic seed germination and plant fecundity under interannual environmental fluctuations. We show that adaptive plasticity in germination readily evolves via a genetic association between seed and plant traits, allowing seeds to germinate preferentially in years favorable for their subsequent growth and reproduction. Such adaptive plasticity enhances the storage effect and promotes genetic divergence among different morphs specialized to distinct yearly conditions. Because these morphs germinate preferentially in different years, plastic germination indirectly generates temporal assortative mating, thereby maintaining genetic associations among seed and plant traits despite the absence of physical linkage between loci controlling these traits. This temporal assortative mating ultimately leads to reproductive isolation between morphs, thus laying the foundation for ecological speciation. Our findings show that adaptive plasticity and genetic diversification are not mutually exclusive but can interact synergistically to enhance biodiversity.

evolutionary biology↗

bioRxiv2025

The evolution of tandem repeat sequences under partial selfing and different modes of selection

Tandem repeat sequences (TRs) occur when short DNA motifs are repeated head-to-tail along chromosomes and are a major source of genetic variation. Population genetics models of TR evolution have focused on large, randomly mating, haploid populations. Yet many organisms reproduce partially through self-fertilisation ("selfing"), which increases homozygosity and thus may alter the evolutionary processes shaping TRs. Here we use mathematical modelling and simulations to study the evolution of homologous TRs in partially selfing, diploid populations under four different selective regimes that may be relevant to TRs: (i) additive purifying selection, (ii) truncation-like purifying selection, (iii) selection against heterozygotes due to misalignment costs, and (iv) stabilising selection favouring an intermediate TR length. We show that selfing influences TR evolution primarily by increasing homozygosity, with two main consequences: (1) it enhances the variation produced by unequal recombination within individuals, and (2) it increases variation between individuals. Consequently, selection against TR expansions becomes more effective under partial selfing across all modes of selection considered, resulting in shorter TRs and lower genetic load, despite higher genetic drift. Overall, our results suggest that mating systems and inbreeding are important factors shaping variation in TRs.

evolutionary biology↗

bioRxiv2025

Ecological inheritance facilitates the coexistence of environmental helpers and free-riders

Variation in social traits and behaviours is widespread in nature and can be maintained by selection. Many social traits influence fitness indirectly by modifying shared environments that are transmitted across generations, a process known as ecological inheritance. Here, we investigate how variation in environmentally mediated social behaviour, such as helping to improve shared resources, can emerge and persist in spatially subdivided populations where locally modified environments are transmitted across generations. Using mathematical and computational modelling, we show that ecological inheritance, when combined with limited dispersal, readily leads to the stable coexistence of two types with opposite environmental legacies: helpers, who improve the local environment for the future at a personal cost, and environmental free-riders, who benefit without contributing to the detriment of future generations. In turn, this polymorphism generates lasting spatial heterogeneity in environmental quality and, consequently, in survival and reproduction--particularly under isolation-by-distance, creating stable clusters of high- and low-quality habitats across an otherwise homogeneous landscape. These findings reveal how ecological inheritance and spatial structure interact to stabilise polymorphism, potentially driving long-term behavioural, ecological, and fitness variation across diverse biological systems.

evolutionary biology↗

bioRxiv2025

Evolution of quantitative traits: exploring the ecological, social and genetic bases of adaptive polymorphism

Adaptive polymorphisms in quantitative traits are characterised by the coexistence of distinct genetically encoded phenotypes maintained by selection. Such intraspecific genetic and phenotypic variation make a substantial contribution to biological diversity. Building on established results from invasion analysis, we analyse conditions under which adaptive polymorphism can emerge under long-term gradual evolution. We first note that, in general, fully characterising an adaptive polymorphism, including its number of morphs, trait values and frequencies, is a computationally hard problem. Nevertheless, standard invasion results reveal a unifying necessary condition for the gradual emergence of polymorphism: negative trait-dependent selection (NTDS), whereby the marginal fitness effect of increasing trait expression in a mutant depends negatively on the population-level trait expression, reflecting a negative interaction between mutant and population trait changes. We use NTDS as an organising principle to structure the pathways through which polymorphism can evolve. This is based on a decomposition of fitness that distinguishes production factors, the inputs to survival and reproduction that are endogenous to individuals, from regulating factors, the ecological, social or genetic inputs to fitness that are influenced in part by conspecifics. This decomposition allows us to clarify how NTDS arises across three broad classes of interactions: ecological, social and genetic; and to identify previously unrecognised adaptive polymorphisms in well-studied scenarios, including life-history, social preferences, and class-structured populations. More broadly, by integrating perspectives from population genetics, evolutionary ecology, adaptive dynamics, game theory and inclusive fitness theory, we aim to provide a common thread among the pathways through which selection favours intraspecific variation.

evolutionary biology↗

bioRxiv2025

Sexual antagonism, mating systems, and recombination suppression on sex chromosomes

The suppression of recombination between sex chromosomes is a widespread feature of genetic sex determination systems. Competing explanations for this evolution fall into two broad categories: recombination arrest driven by the capture of sexually antagonistic variation versus arrest driven without sex-specific selection. Using population-genetic models, we compare the substitution rates of full recombination suppressors (such as inversions) driven by sexually antagonistic selection to those expected under neutrality. We consider both XY and ZW systems, mating ecologies ranging from random mating to polygyny with high male reproductive variance, suppressors arising on heterogametic (Y or W) versus homogametic (X or Z) chromosomes, and the effects of deleterious alleles segregating at other loci on the chromosome. We find that even very weak sexual antagonism is sufficient to expedite suppressor substitution by orders of magnitude relative to neutrality. This acceleration is robust to the presence of deleterious variation, although high variance in male reproductive success can diminish substitution rates of Y-linked suppressors in XY systems. By contrast, in ZW systems, elevated male reproductive variance tends to favour faster recombination arrest via W-linked suppressors, leading to higher overall rates of suppression than in comparable XY systems. Despite stronger selection on Y/W-linked suppressors, recombination arrest driven by sexual antagonism is often expected to arise from homogametic (X/Z-linked) suppressors, because their mutational input is higher and they can experience weaker drift. Together, these results yield testable predictions for the genomic distribution of sex-chromosome inversions across taxa differing in mating system and sex-determination system.

evolutionary biology↗

bioRxiv2024

The evolution of local adaptation in long-lived species

Many species experience heterogeneous environments and adapt genetically to local conditions. The extent of such local adaptation has been shown to depend on a balance between divergent selection and gene flow, but also on other factors such as phenotypic plasticity or the genetic architecture of traits. Here, we explore the role of life history in this process. We develop a quantitative genetics model and run individual-based simulations to contrast the evolution of local adaptation between short- and long-lived species. We show that life history does not have a unidirectional effect on local adaptation. Instead, local adaptation varies with a species life cycle and how this cycle modulates the scheduling of selection and dispersal among stage classes. When a longer generation time is associated with more frequent events of selection than dispersal, local adaptation is more pronounced in long-lived than in short-lived species. If otherwise dispersal occurs more frequently than selection, long-lived species evolve weaker local adaptation. Our simulations confirm these findings and further highlight how the scheduling of selection and dispersal shape additive genetic variance, effective dispersal between patches, and the genetic response at quantitative trait loci. Taken together, our results suggest that the effect of longevity on local adaptation depends on the specifics of a species life cycle, potentially explaining why current meta-analyses have not consistently detected this effect.

evolutionary biology↗

bioRxiv2024

The coevolution of learning schedules and teaching enhances cumulative knowledge and drives a teacher-innovator syndrome

Natural selection shapes how individuals learn and acquire knowledge from their environment. Under the right conditions, this can lead to the evolution of learning schedules--how individuals allocate resources to acquire knowledge throughout their lifespan--that promote the accumulation of knowledge across generations ("cumulative knowledge" or "cumulative culture"). In spite of having been observed across multiple taxa, the role of parental teaching in this evolutionary process remains understudied. Using mathematical modelling, we show that learning schedules and parental teaching coevolve, resulting in greater time spent learning individually and innovating, as well as greater inter-generational transfer of knowledge from parent to offspring. These outcomes together enhance cumulative knowledge. Our analyses further reveal that within populations, selection typically favours an association between teaching and individual learning whereby some individuals innovate and teach within the family ("knowledge producers" with extensive knowledge), while others teach less and learn socially outside of the family ("knowledge scroungers" with less knowledge). Overall, our findings indicate that the coevolution of learning schedules and teaching promotes knowledge accumulation within and between generations, and favours diversity within and between populations in knowledge acquisition, possession and transmission.

evolutionary biology↗

bioRxiv2024

The joint evolution of separate sexes and sexual dimorphism

Dioecious plants are frequently sexually dimorphic. Such dimorphism, which reflects responses to selection acting in opposite directions for male and female components of fitness, is commonly thought to emerge after separate sexes evolved from hermaphroditism. But associations between allocation to male and female function and traits under sexual conflict may well also develop in hermaphroditic ancestors. Here, we show that variation in sex allocation and a trait under sexual conflict inevitably generates an advantage to sexual specialisation, fueling the transition to dioecy. In the absence of constraints, this leads to the joint evolution of separate sexes and sexual dimorphism through the build-up of an association between sex allocation and the conflict trait, such that eventually the population consists of unisexuals expressing their sex-specific optima. We then investigate how such association might materialise genetically, either via recombination suppression or via sex-dependent expression, and show that the genetic architecture of sex allocation and the conflict trait readily evolves to produce the association favoured by selection. Finally and in agreement with previous theory, we demonstrate that limited dispersal and self-fertilisation, which are pervasive ecological characteristics of flowering plants, can offset the advantage of sexual specialisation generated by sexual conflict and thus maintain hermaphroditism. Taken together, our results indicate that advantages to sexual specialisation are inevitable when there is conflict between sexual functions in hermaphrodites, but these advantages can be counterbalanced by ecological benefits of hermaphroditism.

evolutionary biology↗

bioRxiv2023

The maintenance of genetic polymorphism in sexually antagonistic traits

AbstractSelection often favours different trait values in males and females, leading to genetic conflicts between the sexes when traits have a shared genetic basis. Such sexual antagonism has been proposed to maintain genetic polymorphism. However, this notion is based on insights from population genetic models of single loci with fixed fitness effects. It is thus unclear how readily polymorphism emerges from sex-specific selection acting on continuous traits, where fitness effects arise from the genotype-phenotype map and the fitness landscape. Here we model the evolution of a continuous trait that has a shared genetic basis but different optima in males and females, considering a wide variety of genetic architectures and fitness landscapes. For autosomal loci, the long-term maintenance of polymorphism requires strong conflict between males and females that generates uncharacteristic sex-specific fitness patterns. Instead, more plausible sex-specific fitness landscapes typically generate stabilising selection leading to an evolutionarily stable state that consists of a single homozygous genotype. Except for sites tightly linked to the sex determining region, our results indicate that genetic variation due to sexual antagonism should arise only rarely and often be transient, making these signatures challenging to detect in genomic data.

evolutionary biology↗

bioRxiv2023

Evolution of environmentally mediated social interactions under isolation by distance

Many social interactions happen indirectly via modifications of the environment, e.g. through the secretion of functional compounds or the depletion of renewable resources. Here, we derive the selection gradient on a quantitative trait affecting dynamical environmental variables that feed back on reproduction and survival in a finite patch-structured population subject to isolation by distance. Our analysis shows that the selection gradient depends on how a focal individual influences the fitness of all future individuals in the population through modifications of the environmental variables they experience, weighted by the neutral relatedness between recipients and the focal. The evolutionarily relevant trait-driven environmental modifications are formalized as the extended phenotypic effects of an individual, quantifying how a trait change in an individual in the present affects the environmental variables in all patches at all future times. When the trait affects reproduction and survival through a payoff function, the selection gradient can be expressed in terms of extended phenotypic effects weighted by scaled-relatedness. We show how to compute extended phenotypic effects, relatedness, and scaled-relatedness using Fourier analysis, which allow us to investigate a broad class of environmentally mediated social interactions in a tractable way. We use our approach to study the evolution of a trait controlling the costly production of some lasting commons (e.g. a common-pool resource or a toxic compound) that can diffuse in space and persist in time. We show that indiscriminate posthumous spite readily evolves in this scenario. More generally whether selection favours environmentally mediated altruism or spite is determined by the spatial correlation between an individuals lineage and the commons originating from its patch. The sign of this correlation depends on interactions between dispersal patterns and the commons renewal dynamics. More broadly, we suggest that selection can favour a wide range of social behaviours when these have carry-over effects in space and time.

evolutionary biology↗

bioRxiv2023

Tempo of hard and soft sweeps in subdivided populations

The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficial de novo mutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs from de novo recessive mutations, and dispersal is not too limited (such that approximately FST < 0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of meta-population dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, while de novo mutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.

evolutionary biology↗

bioRxiv2023

On the origins of Y and W chromosomes as an outcome of sex allocation evolution

In plants with separate sexes, the development of an individual as male or female is controlled by a dominant allele at a sex-determining locus - the fundamental basis of XY and ZW systems. The many independent transitions from hermaphroditism to dioecy that have taken place in flowering plants must therefore often have entailed the emergence of such a locus. One proposition is that this evolution occurs in two steps, with the initial invasion of a male-sterility mutation at one locus followed by mutations causing female sterility at a second closely linked locus. Here, we show how dioecy with heterogametic sex determination can also emerge in a gradual adaptive process, involving the co-evolution of resource allocation to different sexual functions jointly with its genetic architecture. Our model reveals that whether an XY or a ZW system evolves depends on the mating system of the ancestral hermaphrodites as well as the trade-off they face between allocation to male and female functions. In particular, the evolution of dioecy in response to selection to avoid selfing and inbreeding depression favours the emergence of XY systems, which characterise the vast majority of dioecious flowering plants. Selection favouring female specialisation also favours XY over ZW sex determination. Taken together, our results throw new light on the possible origins of dioecy from hermaphroditism by revealing a hitherto unrecognised link between the ecology and economics of sex allocation and the genetic basis of sex determination.

evolutionary biology↗

bioRxiv2021

RCaN: a software for Chance and Necessity modelling

Uncertainty is a challenge in modelling ecological systems and has been a source of misunderstandings between modelers and non-modelers. The "Chance and Necessity" (CaN) modelling approach has been proposed to address this issue, in the case of trophic network modelling. CaN modelling focuses exploring food-web trajectories that can satisfy fundamental physical and biological laws, while being compatible with observations and domain knowledge. This type of approach can facilitate discussion among actors as it promotes sharing of information and does not presuppose any knowledge of modelling practices. It is therefore suitable for participatory modelling, i.e. a modelling approach in which different actors can confront their knowledge and understanding of the marine system and of the associated uncertainties. One important ingredient to achieve participatory modelling is the availability of a modelling platform that is efficient, fast and transparent, so that all actors can understand and follow the modelling steps and choices, and can rapidly visualize and discuss the results. But, until now, there existed no software to easily perform CaN modelling. Here, we present RCaN and RCaNconstructor. Combined, these provide the first tool to build CaN models in an intuitive way that is 1) suitable within participatory frameworks, 2) transparent, 4) computationally efficient, 5) fully documented through the provision of meta-information and 6) supportive of exploratory analyses through predefined graphical functions.

ecology↗