Highly clustered mating networks in naturally fragmented riparian tree populations.

Understanding how spatial patterns of mating and gene flow respond to habitat loss and geographical isolation is a crucial aspect of forest fragmentation genetics. Naturally fragmented riparian tree populations exhibit unique characteristics that significantly influence these patterns. In this study, we investigate mating patterns, pollen-mediated gene flow, and genetic diversity in relict populations of Frangula alnus in southern Spain by testing specific hypotheses related to the riparian habitat. We employ a novel approach that combines paternity analysis, particularly suited for small and isolated populations, with complex network theory and Bayesian models to predict mating likelihood among tree pairs. Our findings reveal a prevalence of short-distance pollination, resulting in spatially driven local mating clusters with a distinct subset of trees being highly connected in the mating network. Additionally, we observe numerous pollination events over distances of hundreds of metres and considerable pollen immigration. Local neighbourhood density is the primary factor influencing within-population mating patterns and pollen dispersal; moreover, mating network properties reflect the population's size and spatial configuration. Conversely, among-population pollen dispersal is mainly determined by tree size, which influences floral display. Our results do not support a major role of directional pollen dispersal in longitudinal trends of genetic diversity. We provide evidence that long-term fragmented tree populations persist in unique environments that shape mating patterns and impose constraints to pollen-mediated gene flow. Nevertheless, even seemingly strongly isolated populations can maintain functional connectivity over extended periods, especially when animal-mediated mating networks promote genetic diversity, as in this riparian tree species.

Seed predation-induced Allee effects, seed dispersal and masting jointly drive the diversity of seed sources during population expansion.

The environmental factors affecting plant reproduction and effective dispersal, in particular biotic interactions, have a strong influence on plant expansion dynamics, but their demographic and genetic consequences remain an understudied body of theory. Here, we use a mathematical model in a one-dimensional space and on a single reproductive period to describe the joint effects of predispersal seed insect predators foraging strategy and plant reproduction strategy (masting) on the spatio-temporal dynamics of seed sources diversity in the colonisation front of expanding plant populations. We show that certain foraging strategies can result in a higher seed predation rate at the colonisation front compared to the core of the population, leading to an Allee effect. This effect promotes the contribution of seed sources from the core to the colonisation front, with long-distance dispersal further increasing this contribution. As a consequence, our study reveals a novel impact of the predispersal seed predation-induced Allee effect, which mitigates the erosion of diversity in expanding populations. We use rearrangement inequalities to show that masting has a buffering role: it mitigates this seed predation-induced Allee effect. This study shows that predispersal seed predation, plant reproductive strategies and seed dispersal patterns can be intermingled drivers of the diversity of seed sources in expanding plant populations, and opens new perspectives concerning the analysis of more complex models such as integro-difference or reaction-diffusion equations.

Sexual interference revealed by joint study of male and female pollination success in chestnut.

Most seed plants produce both pollen and ovules. In principle, pollen export could interfere with pollen import through self-pollination, resulting in ovule usurpation and reduced fruit set. Evidence for such interference exists under experimental settings but its importance under natural conditions is unknown. To test for sexual interference in nature, it is necessary to study together mating system, through paternity analyses, and fruit set, the proportion of flowers giving seeds or fruits. We developed a new model combining both processes, using chestnut (Castanea) as case study. We carried out a paternity analysis in an intensively studied plot of 273 trees belonging to three interfertile chestnut species and including a range of individuals with more or less functional stamens, resulting in a large data set of 1924 mating events. We then measured fruit set on 216 of these trees. Fruit set of male-fertile trees was much lower than that of male-sterile trees. Our process-based model shows that pollen is not limiting in the study site and hence cannot account for reduced fruit set. It also indicates that self-pollination is high (74%) but selfing rate is low (4%). Self-pollen is less competitive than cross-pollen, reducing sexual interference, but not sufficiently, as many ovules end up being self-fertilized, 95% of which abort before fruit formation, resulting in the loss of 46% of the fruit crop. These results suggest that the main cause of reduced reproductive potential in chestnut is sexual interference by self-pollen, raising questions on its evolutionary origins.

Sex-specific spatial variation in fitness in the highly dimorphic Leucadendron rubrum.

Sexual dimorphism in plants may emerge as a result of sex-specific selection on traits enhancing access to nutritive resources and/or to sexual partners. Here we investigated sex-specific differences in selection of sexually dimorphic traits and in the spatial distribution of effective fecundity (our fitness proxy) in a highly dimorphic dioecious wind-pollinated shrub, Leucadendron rubrum. In particular, we tested for the effect of density on male and female effective fecundity. We used spatial and genotypic data of parent and offspring cohorts to jointly estimate individual male and female effective fecundity on the one hand and pollen and seed dispersal kernels on the other hand. This methodology was adapted to the case of dioecious species. Explicitly modelling dispersal avoids the confounding effects of heterogeneous spatial distribution of mates and sampled seedlings on the estimation of effective fecundity. We also estimated selection gradients on plant traits while modelling sex-specific spatial autocorrelation in fecundity. Males exhibited spatial autocorrelation in effective fecundity at a smaller scale than females. A higher local density of plants was associated with lower effective fecundity in males but was not related to female effective fecundity. These results suggest sex-specific sensitivities to environmental heterogeneity in L. rubrum. Despite these sexual differences, we found directional selection for wider canopies and smaller leaves in both sexes, and no sexually antagonistic selection on strongly dimorphic traits in L. rubrum. Many empirical studies in animals similarly failed to detect sexually antagonistic selection in species expressing strong sexual dimorphism, and we discuss reasons explaining this common pattern.

Weak founder effects but significant spatial genetic imprint of recent contraction and expansion of European beech populations.

Understanding the ecological and evolutionary processes occurring during species range shifts is important in the current context of global change. Here, we investigate the interplay between recent expansion, gene flow and genetic drift, and their consequences for genetic diversity and structure at landscape and local scales in European beech (Fagus sylvatica L.) On Mont Ventoux, South-Eastern France, we located beech forest refugia at the time of the most recent population minimum, ~150 years ago, and sampled 71 populations (2042 trees) in both refugia and expanding populations over an area of 15,000 ha. We inferred patterns of gene flow and genetic structure using 12 microsatellite markers. We identified six plots as originating from planting, rather than natural establishment, mostly from local genetic material. Comparing genetic diversity and structure in refugia versus recent populations did not support the existence of founder effects: heterozygosity (He = 0.667) and allelic richness (Ar = 4.298) were similar, and FST was low (0.031 overall). Still, significant spatial evidence of colonization was detected, with He increasing along the expansion front, while genetic differentiation from the entire pool (ßWT) decreased. Isolation by distance was found in refugia but not in recently expanding populations. Our study indicates that beech capacities for colonization and gene flow were sufficient to preserve genetic diversity despite recent forest contraction and expansion. Because beech has long distance pollen and seed dispersal, these results illustrate a 'best case scenario' for the maintenance of high genetic diversity and adaptive potential under climate-change-related range change.

Impact of Lockdown on the Epidemic Dynamics of COVID-19 in France.

The COVID-19 epidemic was reported in the Hubei province in China in December 2019 and then spread around the world reaching the pandemic stage at the beginning of March 2020. Since then, several countries went into lockdown. Using a mechanistic-statistical formalism, we estimate the effect of the lockdown in France on the contact rate and the effective reproduction number R e of the COVID-19. We obtain a reduction by a factor 7 (R e = 0.47, 95%-CI: 0.45-0.50), compared to the estimates carried out in France at the early stage of the epidemic. We also estimate the fraction of the population that would be infected by the beginning of May, at the official date at which the lockdown should be relaxed. We find a fraction of 3.7% (95%-CI: 3.0-4.8%) of the total French population, without taking into account the number of recovered individuals before April 1st, which is not known. This proportion is seemingly too low to reach herd immunity. Thus, even if the lockdown strongly mitigated the first epidemic wave, keeping a low value of R e is crucial to avoid an uncontrolled second wave (initiated with much more infectious cases than the first wave) and to hence avoid the saturation of hospital facilities.

Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.

The number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work is to estimate the actual number of people infected with COVID-19 and to deduce the IFR during the observation window in France. We develop a `mechanistic-statistical' approach coupling a SIR epidemiological model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The actual number of infected cases in France is probably higher than the observations: we find here a factor ×8 (95%-CI: 5-12) which leads to an IFR in France of 0.5% (95%-CI: 0.3-0.8) based on hospital death counting data. Adjusting for the number of deaths in nursing homes, we obtain an IFR of 0.8% (95%-CI: 0.45-1.25). This IFR is consistent with previous findings in China (0.66%) and in the UK (0.9%) and lower than the value previously computed on the Diamond Princess cruse ship data (1.3%).

Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species.

In species with long-distance dispersal capacities and inhabiting a large ecological niche, local selection and gene flow are expected to be major evolutionary forces affecting the genetic adaptation of natural populations. Yet, in species such as trees, evidence of microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited. Here, we used extensive genetic and phenotypic data from European beech seedlings collected along an elevation gradient, and grown in a common garden, to study the signature of selection on the divergence of eleven potentially adaptive traits, and to assess the role of gene flow in resupplying adaptive genetic variation. We found a significant signal of adaptive differentiation among plots separated by < 1 km, with selection acting on growth and phenological traits. Consistent with theoretical expectations, our results suggest that pollen dispersal contributes to increase genetic diversity for these locally differentiated traits. Our results thus highlight that local selection is an important evolutionary force in natural tree populations and suggest that management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and enhance their adaptive potential to rapidly changing environments.

Sex-specific selection on plant architecture through "budget" and "direct" effects in experimental populations of the wind-pollinated herb, Mercurialis annua.

Sexual selection may contribute to the evolution of plant sexual dimorphism by favoring architectural traits in males that improve pollen dispersal to mates. In both sexes, larger individuals may be favored by allowing the allocation of more resources to gamete production (a "budget" effect of size). In wind-pollinated plants, large size may also benefit males by allowing the liberation of pollen from a greater height, fostering its dispersal (a "direct" effect of size). To assess these effects and their implications for trait selection, we measured selection on plant morphology in both males and females of the wind-pollinated dioecious herb Mercurialis annua in two separate experimental common gardens at contrasting density. In both gardens, selection strongly favored males that disperse their pollen further. Selection for pollen production was observed in the high-density garden only, and was weak. In addition, male morphologies associated with increased mean pollen dispersal differed between the two gardens, as elongated branches were favored in the high-density garden, whereas shorter plants with longer inflorescence stalks were favored in the low-density garden. Larger females were selected in both gardens. Our results point to the importance of both a direct effect of selection on male traits that affect pollen dispersal, and, to a lesser extent, a budget effect of selection on pollen production.

Tree, sex and size: Ecological determinants of male vs. female fecundity in three Fagus sylvatica stands.

Interindividual variation in fecundities has major consequences on population evolutionary potential, through genetic drift and selection. Using two spatially explicit mating models that analyse the genotypes of seeds and seedlings, we investigated the variation of male and female fecundities within and among three European beech (Fagus sylvatica) stands situated along an altitudinal gradient. Female and male individual fecundity distributions were both skewed in this monoecious species, and we found a higher variance in female as compared to male fecundities. Both female and male fecundities increased with tree size and decreased with density and competition in the neighbourhood, the details of these effects suggesting sex-specific strategies to deal with the impact of limited resource on fecundity. The studied populations were functionally male-biased. Among-individual variations in functional gender were not driven by tree size but by density and competition in the neighbourhood. Femaleness decreased under limited resource availability, an expected consequence of the higher cost of female reproduction. Considering the variation of gene flow and genetic drift across elevation, our results suggest that the adaptive potential could be enhanced by low genetic drift at low elevation, and by high pollen-mediated gene flow at high elevation. Finally, this study predicts a more efficient response to selection for traits related to male vs. female fitness, for a given selection intensity.

Genetic signatures of a range expansion in natura: when clones play leapfrog.

The genetic consequences of range expansions have generally been investigated at wide geographical and temporal scales, long after the colonization event. A unique ecological system enabled us to both monitor the colonization dynamics and decipher the genetic footprints of expansion over a very short time period. Each year an epidemic of the poplar rust (Melampsora larici-populina) expands clonally and linearly along the Durance River, in the Alps. The colonization dynamics observed in 2004 showed two phases with different genetic outcomes. Upstream, fast colonization maintained high genetic diversity. Downstream, the colonization wave progressively faltered, diversity eroded, and differentiation increased, as expected under recurrent founder events. In line with the high dispersal abilities of rust pathogens, we provide evidence for leapfrog dispersal of clones. Our results thus emphasize the importance of colonization dynamics in shaping spatial genetic structure in the face of high gene flow.

Long-distance wind-dispersal of spores in a fungal plant pathogen: estimation of anisotropic dispersal kernels from an extensive field experiment.

Given its biological significance, determining the dispersal kernel (i.e., the distribution of dispersal distances) of spore-producing pathogens is essential. Here, we report two field experiments designed to measure disease gradients caused by sexually- and asexually-produced spores of the wind-dispersed banana plant fungus Mycosphaerella fijiensis. Gradients were measured during a single generation and over 272 traps installed up to 1000 m along eight directions radiating from a traceable source of inoculum composed of fungicide-resistant strains. We adjusted several kernels differing in the shape of their tail and tested for two types of anisotropy. Contrasting dispersal kernels were observed between the two types of spores. For sexual spores (ascospores), we characterized both a steep gradient in the first few metres in all directions and rare long-distance dispersal (LDD) events up to 1000 m from the source in two directions. A heavy-tailed kernel best fitted the disease gradient. Although ascospores distributed evenly in all directions, average dispersal distance was greater in two different directions without obvious correlation with wind patterns. For asexual spores (conidia), few dispersal events occurred outside of the source plot. A gradient up to 12.5 m from the source was observed in one direction only. Accordingly, a thin-tailed kernel best fitted the disease gradient, and anisotropy in both density and distance was correlated with averaged daily wind gust. We discuss the validity of our results as well as their implications in terms of disease diffusion and management strategy.

Distinct male reproductive strategies in two closely related oak species.

Reproductive strategies of closely related species distributed along successional gradients should differ as a consequence of the trade-off between competition and colonization abilities. We compared male reproductive strategies of Quercus robur and Q. petraea, two partly interfertile European oak species with different successional status. In the studied even-aged stand, trees of the late-successional species (Q. petraea) grew faster and suffered less from intertree competition than trees of the early-successional species (Q. robur). A large-scale paternity study and a spatially explicit individual-based mating model were used to estimate parameters of pollen production and dispersal as well as sexual barriers between species. Male fecundity was found to be dependent both on a tree's circumference and on its environment, particularly so for Q. petraea. Pollen dispersal was greater and more isotropic in Q. robur than in Q. petraea. Premating barriers to hybridization were strong in both species, but more so in Q. petraea than in Q. robur. Hence, predictions based on the competition-colonization trade-off are well supported, whereas the sexual barriers themselves seem to be shaped by colonization dynamics.

Space, time and complexity in plant dispersal ecology.

Dispersal of pollen and seeds are essential functions of plant species, with far-reaching demographic, ecological and evolutionary consequences. Interest in plant dispersal has increased with concerns about the persistence of populations and species under global change. We argue here that advances in plant dispersal ecology research will be determined by our ability to surmount challenges of spatiotemporal scales and heterogeneities and ecosystem complexity. Based on this framework, we propose a selected set of research questions, for which we suggest some specific objectives and methodological approaches. Reviewed topics include multiple vector contributions to plant dispersal, landscape-dependent dispersal patterns, long-distance dispersal events, spatiotemporal variation in dispersal, and the consequences of dispersal for plant communities, populations under climate change, and anthropogenic landscapes.

Reconstruction of a windborne insect invasion using a particle dispersal model, historical wind data, and Bayesian analysis of genetic data.

Understanding how invasive species establish and spread is vital for developing effective management strategies for invaded areas and identifying new areas where the risk of invasion is highest. We investigated the explanatory power of dispersal histories reconstructed based on local-scale wind data and a regional-scale wind-dispersed particle trajectory model for the invasive seed chalcid wasp Megastigmus schimitscheki (Hymenoptera: Torymidae) in France. The explanatory power was tested by: (1) survival analysis of empirical data on M. schimitscheki presence, absence and year of arrival at 52 stands of the wasp's obligate hosts, Cedrus (true cedar trees); and (2) Approximate Bayesian analysis of M. schimitscheki genetic data using a coalescence model. The Bayesian demographic modeling and traditional population genetic analysis suggested that initial invasion across the range was the result of long-distance dispersal from the longest established sites. The survival analyses of the windborne expansion patterns derived from a particle dispersal model indicated that there was an informative correlation between the M. schimitscheki presence/absence data from the annual surveys and the scenarios based on regional-scale wind data. These three very different analyses produced highly congruent results supporting our proposal that wind is the most probable vector for passive long-distance dispersal of this invasive seed wasp. This result confirms that long-distance dispersal from introduction areas is a likely driver of secondary expansion of alien invasive species. Based on our results, management programs for this and other windborne invasive species may consider (1) focusing effort at the longest established sites and (2) monitoring outlying populations remains critically important due to their influence on rates of spread. We also suggest that there is a distinct need for new analysis methods that have the capacity to combine empirical spatiotemporal field data, genetic data, and environmental data to investigate dispersal and invasion.

Ecological determinants of mating system within and between three Fagus sylvatica populations along an elevational gradient.

Studies addressing the variation of mating system between plant populations rarely account for the variability of these parameters between individuals within populations, although this variability is often non-negligible. Here, we propose a new direct method based on paternity analyses (Mixed Effect Mating Model) to estimate individual migration (mi ) and selfing rates (si ) together with the pollen dispersal kernel. Using this method and the KINDIST approach, we investigated the variation of mating system parameters within and between three populations of Fagus sylvatica along an elevational gradient. Among the mother trees, si varied from 0% to 48%, mi varied from 12% to 86% and the effective number of pollen donors (Nepi ) varied from 2 to 364. The mating patterns differed along the gradient, the top population showing higher m and lower s, and a trend to higher Nep than the bottom populations. The phenological lag shaped long-distance pollen flow both within population (by increasing mi at mother-tree level) and between populations (by increasing m at high elevation). Rather than the mate density, the canopy density was detected as a major mating system determinant within population; it acted as a barrier to pollen flow, decreasing the proportion of long-distance pollen flow and increasing si . Overall, the effects of ecological factors on mating system were not the same within vs. between populations across the gradient, and these factors also differed from those traditionally found to shape variation at range-wide scale, highlighting the interest of multiscale approaches.

Approximate Bayesian computation with functional statistics.

Functional statistics are commonly used to characterize spatial patterns in general and spatial genetic structures in population genetics in particular. Such functional statistics also enable the estimation of parameters of spatially explicit (and genetic) models. Recently, Approximate Bayesian Computation (ABC) has been proposed to estimate model parameters from functional statistics. However, applying ABC with functional statistics may be cumbersome because of the high dimension of the set of statistics and the dependences among them. To tackle this difficulty, we propose an ABC procedure which relies on an optimized weighted distance between observed and simulated functional statistics. We applied this procedure to a simple step model, a spatial point process characterized by its pair correlation function and a pollen dispersal model characterized by genetic differentiation as a function of distance. These applications showed how the optimized weighted distance improved estimation accuracy. In the discussion, we consider the application of the proposed ABC procedure to functional statistics characterizing non-spatial processes.

Fine-scale environmental control of hybridization in oaks.

Natural hybridization is attracting much interest in modern speciation and conservation biology studies, but the underlying mechanisms remain poorly understood. In particular, it is unclear why environmental changes often increase hybridization rates. To study this question, we surveyed mating events in a mixed oak stand and developed a spatially explicit individual-based hybridization model. This model, where hybridization is frequency-dependent, pollen is nonlimiting and which allows immigrant pollen to compete with local pollen, takes into account species-specific pollen dispersal and sexual barriers to hybridization. The consequences of pollen limitation on hybridization were studied using another simple model. The results indicate that environmental changes could increase hybridization rates through two distinct mechanisms. First, by disrupting the spatial organization of communities, they should decrease the proportion of conspecific pollen available for mating, thus increasing hybridization rates. Second, by decreasing the density of conspecifics, they should increase pollen limitation and thus hybridization rates, as a consequence of chance pollination predominating over deterministic pollen competition. Altogether, our results point to a need for considering hybridization events at the appropriate level of organization and provide new insights into why hybridization rates generally increase in disturbed environments.

Variability of individual genetic load: consequences for the detection of inbreeding depression.

Inbreeding depression is a key factor affecting the persistence of natural populations, particularly when they are fragmented. In species with mixed mating systems, inbreeding depression can be estimated at the population level by regressing the average progeny fitness by the selfing rate of their mothers. We applied this method using simulated populations to investigate how population genetic parameters can affect the detection power of inbreeding depression. We simulated individual selfing rates and genetic loads from which we computed fitness values. The regression method yielded high statistical power, inbreeding depression being detected as significant (5 % level) in 92 % of the simulations. High individual variation in selfing rate and high mean genetic load led to better detection of inbreeding depression while high among-individual variation in genetic load made it more difficult to detect inbreeding depression. For a constant sampling effort, increasing the number of progenies while decreasing the number of individuals per progeny enhanced the detection power of inbreeding depression. We discuss the implication of among-mother variability of genetic load and selfing rate on inbreeding depression studies.

Allee effect promotes diversity in traveling waves of colonization.

Most mathematical studies on expanding populations have focused on the rate of range expansion of a population. However, the genetic consequences of population expansion remain an understudied body of theory. Describing an expanding population as a traveling wave solution derived from a classical reaction-diffusion model, we analyze the spatio-temporal evolution of its genetic structure. We show that the presence of an Allee effect (i.e., a lower per capita growth rate at low densities) drastically modifies genetic diversity, both in the colonization front and behind it. With an Allee effect (i.e., pushed colonization waves), all of the genetic diversity of a population is conserved in the colonization front. In the absence of an Allee effect (i.e., pulled waves), only the furthest forward members of the initial population persist in the colonization front, indicating a strong erosion of the diversity in this population. These results counteract commonly held notions that the Allee effect generally has adverse consequences. Our study contributes new knowledge to the surfing phenomenon in continuous models without random genetic drift. It also provides insight into the dynamics of traveling wave solutions and leads to a new interpretation of the mathematical notions of pulled and pushed waves.