107 results on '"Billiard, S."'
Search Results
2. Rejuvenating functional responses with renewal theory
- Author
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Billiard, S., Bansaye, V., and Chazottes, J. -R.
- Subjects
Quantitative Biology - Populations and Evolution - Abstract
Functional responses are widely used to describe interactions and resources exchange between individuals in ecology. The form given to functional responses dramatically affects the dynamics and stability of populations and communities. Despite their importance, functional responses are generally considered with a phenomenological approach, without clear mechanistic justifications from individual traits and behaviors. Here, we develop a bottom-up stochastic framework grounded in Renewal Theory showing how functional responses emerge from the level of the individuals through the decomposition of interactions into different activities. Our framework has many applications for conceptual, theoretical and empirical purposes. First, we show how the mean and variance of classical functional responses are obtained with explicit ecological assumptions, for instance regarding foraging behaviors. Second, we give examples in specific ecological contexts, such as in nuptial-feeding species or size dependent handling times. Finally, we demonstrate how to analyze data with our framework, especially highlighting that observed variability in the number of interactions can be used to infer parameters and compare functional response models., Comment: 37 pages, 7 figures, to appear in the Journal of the Royal Society Interface
- Published
- 2017
3. Molecular mechanisms of dominance evolution in Müllerian mimicry
- Author
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Llaurens, V., Joron, M., and Billiard, S.
- Published
- 2015
4. Parasites of Winter Flounder (Pleuronectes americanus) as an Additional Bioindicator of Stress-Related Exposure to Untreated Pulp and Paper Mill Effluent: A 5-Year Field Study
- Author
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Khan, R. A. and Billiard, S. M.
- Published
- 2007
- Full Text
- View/download PDF
5. Lack of p53 induction in fish cells by model chemotherapeutics
- Author
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Rau Embry, M, Billiard, S M, and Di Giulio, R T
- Published
- 2006
- Full Text
- View/download PDF
6. A one-locus model of androdioecy with two homomorphic self-incompatibility groups: expected vs. observed male frequencies
- Author
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Husse, L., Billiard, S., Lepart, J., Vernet, P., and Saumitou-Laprade, P.
- Published
- 2013
- Full Text
- View/download PDF
7. Sex, outcrossing and mating types: unsolved questions in fungi and beyond
- Author
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BILLIARD, S., LÓPEZ-VILLAVICENCIO, M., HOOD, M. E., and GIRAUD, T.
- Published
- 2012
- Full Text
- View/download PDF
8. Lack of p53 induction in fish cells by model chemotherapeutics
- Author
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Embry, M Rau, Billiard, S M, and Di Giulio, R T
- Published
- 2006
9. The double edged sword: the demographic consequences of the evolution of self-fertilisation
- Author
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Abu Awad, Diala and Billiard, S.
- Subjects
amélioration génétique ,évolution ,extinction ,inbreeding ,mating systems ,models/simulations ,mutations ,population genetics ,Sciences agricoles ,Agricultural sciences ,écologie végétale ,fertilisation - Abstract
Phylogenies indicate that the transition from outcrossing to selfing is frequent, with selfing populations being more prone to extinction. The rates of transition to selfing and extinction, acting on different timescales, could explain the observed distributions of extant selfing species among taxa. However, phylogenetic and theoretical studies consider these mechanisms independently, i.e. transitions do not cause extinction. Here, we theoretically explore the demographic consequences of the evolution of self-fertilization. Deleterious mutations and mutations modifying the selfing rate are recurrently introduced and the number of offspring depends on individual fitness, allowing for a demographic feedback. We show that mutational meltdowns can be triggered in populations evolving near strict selfing. Populations having survived the demographic crash are more stable than ancestral outcrossing populations once deleterious mutations are purged. The relatively rapid time-scales in which extinctions occur indicate that during evolutionary transitions the accumulation of deleterious mutations may not be the cause of extinctions observed on longer time scales, which in turn could lead to the underestimation of transition rates from outcrossing to selfing.
- Published
- 2017
10. Erratum: Lack of p53 induction in fish cells by model chemotherapeutics
- Author
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Rau Embry, M, Billiard, S M, and Di Giulio, R T
- Published
- 2009
- Full Text
- View/download PDF
11. Perenniality induces high inbreeding depression in self-fertilising species
- Author
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Abu Awad, D., primary, Billiard, S., additional, and Tran, V.C., additional
- Published
- 2016
- Full Text
- View/download PDF
12. Evolution of uni- and bifactorial sexual compatibility systems in fungi
- Author
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Nieuwenhuis, B. P. S., Billiard, S., Vuilleumier, Séverine, Petit, E., Hood, M. E., Giraud, T., Nieuwenhuis, B. P. S., Billiard, S., Vuilleumier, Séverine, Petit, E., Hood, M. E., and Giraud, T.
- Abstract
Mating systems, that is, whether organisms give rise to progeny by selfing, inbreeding or outcrossing, strongly affect important ecological and evolutionary processes. Large variations in mating systems exist in fungi, allowing the study of their origin and consequences. In fungi, sexual incompatibility is determined by molecular recognition mechanisms, controlled by a single mating-type locus in most unifactorial fungi. In Basidiomycete fungi, however, which include rusts, smuts and mushrooms, a system has evolved in which incompatibility is controlled by two unlinked loci. This bifactorial system probably evolved from a unifactorial system. Multiple independent transitions back to a unifactorial system occurred. It is still unclear what force drove evolution and maintenance of these contrasting inheritance patterns that determine mating compatibility. Here, we give an overview of the evolutionary factors that might have driven the evolution of bifactoriality from a unifactorial system and the transitions back to unifactoriality. Bifactoriality most likely evolved for selfing avoidance. Subsequently, multiallelism at mating-type loci evolved through negative frequency-dependent selection by increasing the chance to find a compatible mate. Unifactoriality then evolved back in some species, possibly because either selfing was favoured or for increasing the chance to find a compatible mate in species with few alleles. Owing to the existence of closely related unifactorial and bifactorial species and the increasing knowledge of the genetic systems of the different mechanisms, Basidiomycetes provide an excellent model for studying the different forces that shape breeding systems
- Published
- 2016
- Full Text
- View/download PDF
13. Evidence for Fisher's dominance theory: just a 'special case'?
- Author
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Billiard, S., Castric, Vincent, Génétique et évolution des populations végétales (GEPV), and Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] - Abstract
International audience; Dominance, its genetic basis and evolution has been at the heart of one of the most intense controversies in the history of genetics. For more than eighty years the existence of dominance modifiers, genetic elements controlling dominance-recessivity interactions, has been suggested as a theoretical possibility, but the modifier elements themselves have remained elusive. A recent study of the self-incompatibility locus in flowering plants provided the first empirical evidence for such genetic elements: small non-coding RNAs that control dominance-recessivity by mediating methylation of the promoter of the recessive allele. Theory has shown that several biological situations are favorable for the evolution of dominance modifiers. We argue that the elucidation of this mechanism of dominance opens up new research avenues that could lead to uncovering dominance modifiers in other genetic systems, such as genes controlling Batesian and Mu¨ llerian mimicry or host-parasite interactions, thereby shedding light on the generality of the proposed mechanism.
- Published
- 2011
14. An experimental study of the S-Allee effect in the self-incompatible Bisctuella neustriaca (Brassicaceae)
- Author
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Leducq, J.-B., Gosset, C.C., Poiret, M., Hendoux, F., Vekemans, X., Billiard, S., Génétique et évolution des populations végétales (GEPV), and Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,food and beverages - Abstract
International audience; Homomorphic self-incompatibility (SI) evolved in many plant families to enforce selfing avoidance, and is controlled by a single multiallelic locus (the S-locus). In a fragmented landscape, strong variation in population size and in local density is expected to cause strong variation in allelic diversity at the S-locus, which could generate an Allee effect on female reproductive success by constraining compatible pollen availability. In this experimental study, we aimed at detecting this SI-specific Allee effect (or S-Allee effect) in the endangered species Biscutella neustriaca. We demonstrated the occurrence of a SI mating system in the species and determined compatibility relationships among genotypes through a large set of controlled pollinations. For the experiment, we chose three different pollen receptor genotypes, each compatible with respectively 100, 75 and 25% of four other genotypes, which constituted the pollen sources. We placed different ramets of each receptor at different distances from the pollen sources to control for pollen limitation due to low local density, and we measured the seed set on each receptor plant three times consecutively. Analyses performed with generalized linear mixed models showed that both the distance to the pollen sources and the mate availability due to SI had a significant effect on seed set, with a strong reduction observed when mate availability was limited to 25%. Our results suggest that pollen limitation due to a restriction in compatible mate availability could occur in small or scattered populations exhibiting low allelic diversity at the S-locus.
- Published
- 2010
15. volution of dominance in sporophytic self-incompatibility systems: I. Genetic load and coevolution of levels of dominance in pollen and pistil
- Author
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Llaurens, V., Billiard, S., Castric, Vincent, Vekemans, X., Génétique et évolution des populations végétales (GEPV), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), and Duputié, Anne-gestion labo
- Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,[SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,food and beverages - Abstract
International audience; Recent theoretical advances have suggested that various forms of balancing selection may promote the evolution of dominance through an increase of the proportion of heterozygote genotypes. We test whether dominance can evolve in the sporophytic selfincompatibility (SSI) system in plants. SSI prevents mating between individuals expressing identical SI phenotypes by recognition of pollen by pistils, which avoids selfing and inbreeding depression. SI phenotypes depend on a complex network of dominance relationships between alleles at the self-incompatibility locus (S-locus). Empirical studies suggest that these relationships are not random, but the exact evolutionary processes shaping these relationships remain unclear.We investigate the expected patterns of dominance under the hypothesis that dominance is a direct target of natural selection.We follow the fate of a mutant allele at the S-locus whose dominance relationships are changed but whose specificity remains unaltered. We show that strict codominance is not evolutionarily stable in SSI, and that inbreeding depression due to deleterious mutations linked or unlinked to the S-locus exerts strong constraints on changes in relative levels of dominance in pollen and pistil. Our results provide a general adaptive explanation for most patterns of dominance relationships empirically observed in natural plant populations.
- Published
- 2009
16. Evolution of uni- and bifactorial sexual compatibility systems in fungi
- Author
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Nieuwenhuis, Bart P. S., Billiard, S., Vuilleumier, S., Petit, E., Hood, M. E., Giraud, T., Nieuwenhuis, Bart P. S., Billiard, S., Vuilleumier, S., Petit, E., Hood, M. E., and Giraud, T.
- Abstract
Mating systems, that is, whether organisms give rise to progeny by selfing, inbreeding or outcrossing, strongly affect important ecological and evolutionary processes. Large variations in mating systems exist in fungi, allowing the study of their origin and consequences. In fungi, sexual incompatibility is determined by molecular recognition mechanisms, controlled by a single mating-type locus in most unifactorial fungi. In Basidiomycete fungi, however, which include rusts, smuts and mushrooms, a system has evolved in which incompatibility is controlled by two unlinked loci. This bifactorial system probably evolved from a unifactorial system. Multiple independent transitions back to a unifactorial system occurred. It is still unclear what force drove evolution and maintenance of these contrasting inheritance patterns that determine mating compatibility. Here, we give an overview of the evolutionary factors that might have driven the evolution of bifactoriality from a unifactorial system and the transitions back to unifactoriality. Bifactoriality most likely evolved for selfing avoidance. Subsequently, multiallelism at mating-type loci evolved through negative frequency-dependent selection by increasing the chance to find a compatible mate. Unifactoriality then evolved back in some species, possibly because either selfing was favoured or for increasing the chance to find a compatible mate in species with few alleles. Owing to the existence of closely related unifactorial and bifactorial species and the increasing knowledge of the genetic systems of the different mechanisms, Basidiomycetes provide an excellent model for studying the different forces that shape breeding systems.
- Published
- 2013
- Full Text
- View/download PDF
17. The effect of dominance on polymorphism in Müllerian mimicry
- Author
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Llaurens, V., primary, Billiard, S., additional, and Joron, M., additional
- Published
- 2013
- Full Text
- View/download PDF
18. Evolution of uni- and bifactorial sexual compatibility systems in fungi
- Author
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Nieuwenhuis, B P S, primary, Billiard, S, additional, Vuilleumier, S, additional, Petit, E, additional, Hood, M E, additional, and Giraud, T, additional
- Published
- 2013
- Full Text
- View/download PDF
19. COMPUTER PROGRAMS: nessi: a program for numerical estimations in sporophytic self‐incompatibility genetic systems
- Author
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BILLIARD, S., primary
- Published
- 2008
- Full Text
- View/download PDF
20. Parasites of Winter Flounder (Pleuronectes americanus) as an Additional Bioindicator of Stress-Related Exposure to Untreated Pulp and Paper Mill Effluent: A 5-Year Field Study
- Author
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Khan, R. A., primary and Billiard, S. M., additional
- Published
- 2006
- Full Text
- View/download PDF
21. EVOLUTION OF MIGRATION UNDER KIN SELECTION AND LOCAL ADAPTATION
- Author
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Billiard, S. and Thomas Lenormand
- Subjects
Competitive Behavior ,Stochastic Processes ,Models, Genetic ,Adaptation, Biological ,Genetics ,Animal Migration ,Environment ,General Agricultural and Biological Sciences ,Biological Evolution ,Linkage Disequilibrium ,Ecology, Evolution, Behavior and Systematics - Abstract
We present here a stochastic two-locus, two-habitat model for the evolution of migration with local adaptation and kin selection. One locus determines the migration rate while the other causes local adaptation. We show that the opposing forces of kin competition and local adaptation can lead to the existence of one or two convergence stable migration rates, notably depending on the recombination rate between the two loci. We show that linkage between migration and local adaptation loci has two antagonist effects: when linkage is tight, cost of local adaptation increases, leading to smaller equilibrium migration rates. However, when linkage is tighter, the population structure at the migration locus tends to be very high because of the indirect selection, and thus equilibrium migration rates increases. This result, qualitatively different from results obtained with other models of migration evolution, indicates that ignoring drift or the detail of the genetic architecture may lead to incorrect conclusions.
- Published
- 2005
22. nessi: a program for numerical estimations in sporophytic self-incompatibility genetic systems.
- Author
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Billiard, S.
- Subjects
- *
COMPUTER software , *POPULATION genetics , *EQUILIBRIUM , *FORECASTING , *ANIMAL sexual behavior - Abstract
nessi is a computer program generating predictions about allelic and genotypic frequencies at the S-locus in sporophytic self-incompatibility systems under finite and infinite populations. For any pattern of dominance relationships among self-incompatibility alleles,nessi computes deterministic equilibrium frequencies and estimates distributions in samples from finite populations of the number of alleles at equilibrium, allelic and genotypic frequencies at equilibrium and allelic and genotypic frequency changes in a single generation. These predictions can be used to rigorously test the impact of negative frequency-dependent selection on diversity patterns in natural populations. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
23. Identifying conversion efficiency as a key mechanism underlying food webs evolution:a step forward, or backward ?
- Author
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Fritsch, C. (Coralie), Billiard, S. (Sylvain), Champagnat, N. (Nicolas), Institut Élie Cartan de Lorraine [IECL], TO Simulate and CAlibrate stochastic models [TOSCA], and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
- Subjects
food webs models ,trophic interactions ,networks ,community ecology ,ecosystem ,adaptive dynamics ,biomass conversion efficiency ,energy conversion efficiency ,reproduction efficiency
24. Lack of p53 induction in fish cells by model chemotherapeutics.
- Author
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Rau Embry, M., Billiard, S. M., and Di Giulio, R. T.
- Subjects
- *
CATALOGS - Abstract
A correction to the article "Lack of p53 induction in fish cells by model chemotherapeutics," that was published online on January 23, 2006 is presented.
- Published
- 2009
- Full Text
- View/download PDF
25. Toxicity of retene to early life stages of two freshwater fish species
- Author
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Querbach, K., Billiard, S. M., and Hodson, P. V.
- Subjects
- *
POLLUTION , *CYTOCHROME P-450 CYP1A1 , *POLYCYCLIC aromatic hydrocarbons , *DIOXINS , *ENZYME activation , *TOXICITY testing - Abstract
Larval zebrafish (Danio rerio) were exposed for 14 d to graded nominal concentrations of waterborne retene (7-isopropyl-1-methylphenanthrene) from 5 to 336 h postfertilization. Reduced growth, yolk sac edema, and mortality were observed before swim up at nominal concentrations of 320 mug/L and higher in a concentration-dependent manner. Similarly, exposures of rainbow trout (Oncorhynchus mykiss) to retene (32-320 mug/L) for 42 d from the eyed egg stage to hatch and from hatch to the onset of swim up behavior caused exposure-related increases in blue sac disease posthatch. Symptoms included increased activity of cytochrome P4501A (CYP1A) enzymes, yolk sac edema, subcutaneous hemorrhaging, reduced growth, and craniofacial malformations. Chronic exposure to retene resulted in mortality before swim up. Blue sac symptomswere observed in fish exposed to nominal concentrations as low as 32mug/L, the lowest concentration tested, and fin erosion and opercular sloughing were evident in 100% of retene-exposed swim up larvae. Nosymptoms were observed in control fish or in fish exposed to acetone, the solvent carrier. The observed pathology resembles the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin toxicity to developing stages of fish, and our results suggest that chronic exposure to polycyclic aromatic hydrocarbons may be responsible for recruitment failure associated with pulp mill effluents and oil spills. [ABSTRACT FROM AUTHOR]
- Published
- 1999
26. The homomorphic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene.
- Author
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Castric V, Batista RA, Carré A, Mousavi S, Mazoyer C, Godé C, Gallina S, Ponitzki C, Theron A, Bellec A, Marande W, Santoni S, Mariotti R, Rubini A, Legrand S, Billiard S, Vekemans X, Vernet P, and Saumitou-Laprade P
- Subjects
- Oleaceae genetics, Oleaceae metabolism, Oleaceae growth & development, Self-Incompatibility in Flowering Plants genetics, Genome, Plant, Flowers genetics, Flowers growth & development, Plant Proteins genetics, Plant Proteins metabolism, Gibberellins metabolism
- Abstract
In flowering plants, outcrossing is commonly ensured by self-incompatibility (SI) systems. These can be homomorphic (typically with many different allelic specificities) or can accompany flower heteromorphism (mostly with just two specificities and corresponding floral types). The SI system of the Oleaceae family is unusual, with the long-term maintenance of only two specificities but often without flower morphology differences. To elucidate the genomic architecture and molecular basis of this SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals and related them to a genetic map. The S-locus region proved to have a segregating 543-kb indel unique to one specificity, suggesting a hemizygous region, as observed in all distylous systems so far studied at the genomic level. Only one of the predicted genes in this indel region is found in the olive tree, Olea europaea, genome, also within a segregating indel. We describe complete association between the presence/absence of this gene and the SI types determined for individuals of seven 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 of the two specificities in different ways. Our results provide a unique example of a homomorphic SI system, where a single conserved gibberellin-related gene in a hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
27. Human-environment feedback and the consistency of proenvironmental behavior.
- Author
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Ecotière C, Billiard S, André JB, Collet P, Ferrière R, and Méléard S
- Subjects
- Humans, Feedback, Interpersonal Relations, Social Interaction, Environment, Models, Theoretical
- Abstract
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 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., Competing Interests: None of the authors have a competing interests that could be perceived to bias this work., (Copyright: © 2023 Ecotière et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
- Full Text
- View/download PDF
28. Opposing effects of plant traits on diversification.
- Author
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Anderson B, Pannell J, Billiard S, Burgarella C, de Boer H, Dufay M, Helmstetter AJ, Méndez M, Otto SP, Roze D, Sauquet H, Schoen D, Schönenberger J, Vallejo-Marin M, Zenil-Ferguson R, Käfer J, and Glémin S
- Abstract
Species diversity can vary dramatically across lineages due to differences in speciation and extinction rates. Here, we explore the effects of several plant traits on diversification, finding that most traits have opposing effects on diversification. For example, outcrossing may increase the efficacy of selection and adaptation but also decrease mate availability, two processes with contrasting effects on lineage persistence. Such opposing trait effects can manifest as differences in diversification rates that depend on ecological context, spatiotemporal scale, and associations with other traits. The complexity of pathways linking traits to diversification suggests that the mechanistic underpinnings behind their correlations may be difficult to interpret with any certainty, and context dependence means that the effects of specific traits on diversification are likely to differ across multiple lineages and timescales. This calls for taxonomically and context-controlled approaches to studies that correlate traits and diversification., Competing Interests: The authors declare no competing interests., (© 2023.)
- Published
- 2023
- Full Text
- View/download PDF
29. Balancing selection and the crossing of fitness valleys in structured populations: diversification in the gametophytic self-incompatibility system.
- Author
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Stetsenko R, Brom T, Castric V, and Billiard S
- Subjects
- Haplotypes, Mutation, Germ Cells, Plant, Alleles, Models, Genetic, Genetics, Population
- Abstract
The self-incompatibility locus (S-locus) of flowering plants displays a striking allelic diversity. How such a diversity has emerged remains unclear. In this article, 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-gene 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-gene 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., (© The Author(s) 2022. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2023
- Full Text
- View/download PDF
30. Revisiting the number of self-incompatibility alleles in finite populations: From old models to new results.
- Author
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Czuppon P and Billiard S
- Subjects
- Alleles, Gene Frequency, Humans, Plants genetics, Pollen genetics, Selection, Genetic
- Abstract
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 modelling 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 (The genetical theory of natural selection - A complete, Variorum edition, Oxford University Press, 1958) and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (Evolution, 18, 609, 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 for new statistical developments for the estimation of the plant population size based on S-allele frequencies., (© 2022 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.)
- Published
- 2022
- Full Text
- View/download PDF
31. The integrative biology of genetic dominance.
- Author
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Billiard S, Castric V, and Llaurens V
- Subjects
- Genes, Dominant, Genotype, Phenotype, Genetics, Population, Models, Genetic
- Abstract
Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype-to-phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross-talk among research fields in the integrative study of dominance evolution., (© 2021 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)
- Published
- 2021
- Full Text
- View/download PDF
32. Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae).
- Author
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De Cauwer I, Vernet P, Billiard S, Godé C, Bourceaux A, Ponitzki C, and Saumitou-Laprade P
- Subjects
- Humans, Phenotype, Plant Breeding, Pollination, Ligustrum, Oleaceae, Self-Incompatibility in Flowering Plants genetics
- Abstract
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 breeding 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 should facilitate the maintenance of such polymorphism. We tested this prediction by studying the breeding system of Ligustrum vulgare L., an insect-pollinated 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 occurrence of self-compatible individuals in different populations of Western Europe arising from a mutation affecting the functioning of the pollen component of SI. Our results 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., (© 2021. The Author(s), under exclusive licence to The Genetics Society.)
- Published
- 2021
- Full Text
- View/download PDF
33. On Deleterious Mutations in Perennials: Inbreeding Depression, Mutation Load, and Life-History Evolution.
- Author
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Lesaffre T and Billiard S
- Subjects
- Genetics, Population, Biological Evolution, Inbreeding Depression, Magnoliopsida classification, Magnoliopsida genetics, Mutation
- Abstract
AbstractIn 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, 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 behavior of mutations affecting growth or survival and explore their consequences in terms of inbreeding depression and mutation load. Although our results agree with empirical data only within a narrow range of conditions, we argue that they may point us toward the type of traits capable of generating high 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 joint evolution of growth and survival strategies.
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- 2021
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34. Inference with selection, varying population size, and evolving population structure: application of ABC to a forward-backward coalescent process with interactions.
- Author
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Lepers C, Billiard S, Porte M, Méléard S, and Tran VC
- Subjects
- Bayes Theorem, Humans, Population Density, Microsatellite Repeats, Models, Genetic
- Abstract
Genetic data are often used to infer demographic history and 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 interactions and asexual reproduction. 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 data from a toy model, and to real data by analyzing the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia human populations in order to test whether different social organizations show significantly different fertilities.
- Published
- 2021
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35. Evolution of self-incompatibility in the Brassicaceae: Lessons from a textbook example of natural selection.
- Author
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Durand E, Chantreau M, Le Veve A, Stetsenko R, Dubin M, Genete M, Llaurens V, Poux C, Roux C, Billiard S, Vekemans X, and Castric V
- Abstract
Self-incompatibility (SI) is a self-recognition genetic system enforcing outcrossing in hermaphroditic flowering plants and results in one of the arguably best understood forms of natural (balancing) selection maintaining genetic variation over long evolutionary times. A rich theoretical and empirical population genetics literature has considerably clarified how the distribution of SI phenotypes translates into fitness differences among individuals by a combination of inbreeding avoidance and rare-allele advantage. At the same time, the molecular mechanisms by which self-pollen is specifically recognized and rejected have been described in exquisite details in several model organisms, such that the genotype-to-phenotype map is also pretty well understood, notably in the Brassicaceae. Here, we review recent advances in these two fronts and illustrate how the joint availability of detailed characterization of genotype-to-phenotype and phenotype-to-fitness maps on a single genetic system (plant self-incompatibility) provides the opportunity to understand the evolutionary process in a unique perspective, bringing novel insight on general questions about the emergence, maintenance, and diversification of a complex genetic system., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)
- Published
- 2020
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36. Stochastic Dynamics of Three Competing Clones: Conditions and Times for Invasion, Coexistence, and Fixation.
- Author
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Billiard S and Smadi C
- Subjects
- Animals, Genotype, Models, Biological, Population Dynamics, Stochastic Processes, Bacterial Physiological Phenomena, Invertebrates physiology, Plant Physiological Phenomena
- Abstract
In large clonal populations, several clones generally compete, resulting in complex evolutionary and ecological dynamics: experiments show successive selective sweeps of favorable mutations as well as long-term coexistence of multiple clonal strains. The mechanisms underlying either coexistence or fixation of several competing strains have rarely been studied altogether. Conditions for coexistence have mostly been studied by population and community ecology, while rates of invasion and fixation have mostly been studied by population genetics. To provide a global understanding of the complexity of the dynamics observed in large clonal populations, we develop a stochastic model where three clones compete. Competitive interactions can be intransitive, and we suppose that strains enter the population via mutations or rare immigrations. We first describe all possible final states of the population, including stable coexistence of two or three strains or the fixation of a single strain. Second, we estimate the invasion and fixation times of a favorable mutant (or immigrant) entering the population in a single copy. We show that invasion and fixation can be slower or faster when considering complex competitive interactions. Third, we explore the parameter space assuming prior distributions of reproduction, death, and competition rates, and we estimate the likelihood of the possible dynamics. We show that when mutations can affect competitive interactions even slightly, stable coexistence is likely. We discuss our results in the context of the evolutionary dynamics of large clonal populations.
- Published
- 2020
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37. Breakdown of gametophytic self-incompatibility in subdivided populations.
- Author
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Brom T, Castric V, and Billiard S
- Subjects
- Alleles, Magnoliopsida genetics, Models, Genetic, Germ Cells, Plant physiology, Inbreeding Depression, Magnoliopsida physiology, Self-Incompatibility in Flowering Plants genetics
- Abstract
In many hermaphroditic flowering plants, self-fertilization is prevented by self-incompatibility (SI), often controlled by a single locus, the S-locus. In single isolated populations, the maintenance of SI depends chiefly on inbreeding depression and the number of SI alleles at the S-locus. In subdivided populations, however, population subdivision has complicated effects on both the number of SI alleles and the level of inbreeding depression, rendering the maintenance of SI difficult to predict. Here, we explore the conditions for the invasion of a self-compatible mutant in a structured population. We find that the maintenance of SI is strongly compromised when a population becomes subdivided. We show that this effect is mainly caused by the decrease in the local diversity of SI alleles rather than by a change in the dynamics of inbreeding depression. Strikingly, we also find that the diversity of SI alleles at the whole population level is a poor predictor of the maintenance of SI. We discuss the implications of our results for the interpretation of empirical data on the loss of SI in natural populations., (© 2019 The Authors. Evolution © 2019 The Society for the Study of Evolution.)
- Published
- 2020
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- View/download PDF
38. The joint evolution of lifespan and self-fertilization.
- Author
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Lesaffre T and Billiard S
- Subjects
- Ecosystem, Magnoliopsida classification, Biological Evolution, Longevity physiology, Magnoliopsida physiology, Self-Fertilization physiology
- Abstract
In Angiosperms, there exists a strong association between mating system and lifespan. Most self-fertilizing 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-fertilization and lifespan, including both juvenile and adult inbreeding depression. We show that provided that inbreeding depression affects adult survival, self-fertilization 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., (© 2019 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2019 European Society For Evolutionary Biology.)
- Published
- 2020
- Full Text
- View/download PDF
39. Stochastic dynamics of an epidemic with recurrent spillovers from an endemic reservoir.
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Voinson M, Alvergne A, Billiard S, and Smadi C
- Subjects
- Animals, Humans, Communicable Diseases, Emerging epidemiology, Communicable Diseases, Emerging transmission, Epidemics, Models, Biological, Zoonoses epidemiology, Zoonoses transmission
- Abstract
Most emerging human infectious diseases have an animal origin. While zoonotic diseases originate from a 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 (i.e. spillover 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 continuous time 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 that (ii) 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., (Copyright © 2018 Elsevier Ltd. All rights reserved.)
- Published
- 2018
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40. Rejuvenating functional responses with renewal theory.
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Billiard S, Bansaye V, and Chazottes JR
- Subjects
- Animals, Appetitive Behavior, Female, Male, Sexual Behavior, Animal, Species Specificity, Stochastic Processes, Ecology, Models, Biological
- Abstract
Functional responses are widely used to describe interactions and resource exchange between individuals in ecology. The form given to functional responses dramatically affects the dynamics and stability of populations and communities. Despite their importance, functional responses are generally considered with a phenomenological approach, without clear mechanistic justifications from individual traits and behaviours. Here, we develop a bottom-up stochastic framework grounded in renewal theory that shows how functional responses emerge from the level of the individuals through the decomposition of interactions into different activities. Our framework has many applications for conceptual, theoretical and empirical purposes. First, we show how the mean and variance of classical functional responses are obtained with explicit ecological assumptions, for instance regarding foraging behaviours. Second, we give examples in specific ecological contexts, such as in nuptial-feeding species or size-dependent handling times. Finally, we demonstrate how to analyse data with our framework, especially highlighting that observed variability in the number of interactions can be used to infer parameters and compare functional response models., (© 2018 The Author(s).)
- Published
- 2018
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41. Polygamy or subdioecy? The impact of diallelic self-incompatibility on the sexual system in Fraxinus excelsior (Oleaceae).
- Author
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Saumitou-Laprade P, Vernet P, Dowkiw A, Bertrand S, Billiard S, Albert B, Gouyon PH, and Dufay M
- Subjects
- Reproduction, Fraxinus physiology, Phenotype, Self-Incompatibility in Flowering Plants
- Abstract
How flowering plants have recurrently evolved from hermaphroditism to separate sexes (dioecy) is a central question in evolutionary biology. Here, we investigate whether diallelic self-incompatibility (DSI) is associated with sexual specialization in the polygamous common ash ( Fraxinus excelsior ), which would ultimately facilitate the evolution towards dioecy. Using interspecific crosses, we provide evidence of strong relationships between the DSI system and sexual phenotype. The reproductive system in F. excelsior that was previously viewed as polygamy (co-occurrence of unisexuals and hermaphrodites with varying degrees of allocation to the male and female functions) and thus appears to actually behave as a subdioecious system. Hermaphrodites and females belong to one SI group and functionally reproduce as females, whereas males and male-biased hermaphrodites belong to the other SI group and are functionally males. Our results offer an alternative mechanism for the evolution of sexual specialization in flowering plants., (© 2018 The Author(s).)
- Published
- 2018
- Full Text
- View/download PDF
42. Stochasticity in cultural evolution: a revolution yet to happen.
- Author
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Billiard S and Alvergne A
- Subjects
- Humans, Models, Theoretical, Anthropology methods, Archaeology methods, Cultural Evolution, Ecology methods, Genetics, Population methods, Stochastic Processes
- Abstract
Over the last 40 years or so, there has been an explosion of cultural evolution research in anthropology and archaeology. In each discipline, cultural evolutionists investigate how interactions between individuals translate into group level patterns, with the aim of explaining the diachronic dynamics and diversity of cultural traits. However, while much attention has been given to deterministic processes (e.g. cultural transmission biases), we contend that current evolutionary accounts of cultural change are limited because they do not adopt a systematic stochastic approach (i.e. accounting for the role of chance). First, we show that, in contrast with the intense debates in ecology and population genetics, the importance of stochasticity in evolutionary processes has generated little discussion in the sciences of cultural evolution to date. Second, we speculate on the reasons, both ideological and methodological, why that should be so. Third, we highlight the inadequacy of genetically-inspired stochastic models in the context of cultural evolution modelling, and ask which fundamental stochastic processes might be more relevant to take up. We conclude that the field of cultural evolution would benefit from a stochastic revolution. For that to occur, stochastic models ought to be developed specifically for cultural data and not through a copy-pasting of neutral models from population genetics or ecology.
- Published
- 2017
- Full Text
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43. Elucidation of the genetic architecture of self-incompatibility in olive: Evolutionary consequences and perspectives for orchard management.
- Author
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Saumitou-Laprade P, Vernet P, Vekemans X, Billiard S, Gallina S, Essalouh L, Mhaïs A, Moukhli A, El Bakkali A, Barcaccia G, Alagna F, Mariotti R, Cultrera NGM, Pandolfi S, Rossi M, Khadari B, and Baldoni L
- Abstract
The olive ( Olea europaea L.) is a typical important perennial crop species for which the genetic determination and even functionality of self-incompatibility (SI) are still largely unresolved. It is still not known whether SI is under gametophytic or sporophytic genetic control, yet fruit production in orchards depends critically on successful ovule fertilization. We studied the genetic determination of SI in olive in light of recent discoveries in other genera of the Oleaceae family. Using intra- and interspecific stigma tests on 89 genotypes representative of species-wide olive diversity and the compatibility/incompatibility reactions of progeny plants from controlled crosses, we confirmed that O. europaea shares the same homomorphic diallelic self-incompatibility (DSI) system as the one recently identified in Phillyrea angustifolia and Fraxinus ornus . SI is sporophytic in olive. The incompatibility response differs between the two SI groups in terms of how far pollen tubes grow before growth is arrested within stigma tissues. As a consequence of this DSI system, the chance of cross-incompatibility between pairs of varieties in an orchard is high (50%) and fruit production may be limited by the availability of compatible pollen. The discovery of the DSI system in O. europaea will undoubtedly offer opportunities to optimize fruit production.
- Published
- 2017
- Full Text
- View/download PDF
44. The double edged sword: The demographic consequences of the evolution of self-fertilization.
- Author
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Abu Awad D and Billiard S
- Subjects
- Consanguinity, Demography, Mutation, Biological Evolution, Phylogeny, Self-Fertilization
- Abstract
Phylogenies indicate that the transition from outcrossing to selfing is frequent, with selfing populations being more prone to extinction. The rates of transition to selfing and extinction, acting on different timescales, could explain the observed distributions of extant selfing species among taxa. However, phylogenetic and theoretical studies consider these mechanisms independently, that is transitions do not cause extinction. Here, we theoretically explore the demographic consequences of the evolution of self-fertilization. Deleterious mutations and mutations modifying the selfing rate are recurrently introduced and the number of offspring depends on individual fitness, allowing for a demographic feedback. We show that mutational meltdowns can be triggered in populations evolving near strict selfing. Populations having survived a demographic crash are more stable than ancestral outcrossing populations once deleterious mutations are purged. The relatively rapid time-scales at which extinctions occur indicate that during evolutionary transitions the accumulation of deleterious mutations may not be the cause of extinctions observed on longer time scales, but could lead to the underestimation of transition rates from outcrossing to selfing., (© 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.)
- Published
- 2017
- Full Text
- View/download PDF
45. The effect of competition and horizontal trait inheritance on invasion, fixation, and polymorphism.
- Author
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Billiard S, Collet P, Ferrière R, Méléard S, and Tran VC
- Subjects
- Adaptation, Physiological genetics, Animals, Competitive Behavior, Ecosystem, Evolution, Molecular, Genetics, Population, Phenotype, Population Density, Population Dynamics, Probability, Stochastic Processes, Time Factors, Algorithms, Gene Transfer, Horizontal genetics, Models, Genetic, Polymorphism, Genetic genetics
- Abstract
Horizontal transfer (HT) of heritable information or 'traits' (carried by genetic elements, plasmids, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is scant. We present a modeling framework for the dynamics of two populations that compete for resources and horizontally exchange (transfer) an otherwise vertically inherited trait. Competition influences individual demographics, thereby affecting population size, which feeds back on the dynamics of transfer. This feedback is captured in a stochastic individual-based model, from which we derive a general model for the contact rate, with frequency-dependent (FD) and density-dependent (DD) rates as special cases. Taking a large-population limit on the stochastic individual-level model yields a deterministic Lotka-Volterra competition system with additional terms accounting for HT. The stability analysis of this system shows that HT can revert the direction of selection: HT can drive invasion of a deleterious trait, or prevent invasion of an advantageous trait. Due to HT, invasion does not necessarily imply fixation. Two trait values may coexist in a stable polymorphism even if their invasion fitnesses have opposite signs, or both are negative. Addressing the question of how the stochasticity of individual processes influences population fluctuations, we identify conditions on competition and mode of transfer (FD versus DD) under which the stochasticity of transfer events overwhelms demographic stochasticity. Assuming that one trait is initially rare, we derive invasion and fixation probabilities and time. In the case of costly plasmids, which are transfered unilaterally, invasion is always possible if the transfer rate is large enough; under DD and for intermediate values of the transfer rate, maintenance of the plasmid in a polymorphic population is possible. In conclusion, HT interacts with ecology (competition) in non-trivial ways. Our model provides a basis to model the influence of HT on evolutionary adaptation., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2016
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46. Correction: Beyond Rational Decision-Making: Modelling the Influence of Cognitive Biases on the Dynamics of Vaccination Coverage.
- Author
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Voinson M, Billiard S, and Alvergne A
- Abstract
[This corrects the article DOI: 10.1371/journal.pone.0142990.].
- Published
- 2016
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47. Evidence for the long-term maintenance of a rare self-incompatibility system in Oleaceae.
- Author
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Vernet P, Lepercq P, Billiard S, Bourceaux A, Lepart J, Dommée B, and Saumitou-Laprade P
- Subjects
- Biological Evolution, Flowers genetics, Flowers physiology, Fraxinus genetics, Fraxinus physiology, Oleaceae genetics, Reproduction, Self-Incompatibility in Flowering Plants, Oleaceae physiology
- Abstract
A rare homomorphic diallelic self-incompatibility (DSI) system discovered in Phillyrea angustifolia (family Oleaceae, subtribe Oleinae) can promote the transition from hermaphroditism to androdioecy. If widespread and stable in Oleaceae, DSI may explain the exceptionally high rate of androdioecious species reported in this plant family. Here, we set out to determine whether DSI occurs in another Oleaceae lineage. We tested for DSI in subtribe Fraxininae, a lineage that diverged from subtribe Oleinae c. 40 million yr ago. We explored the compatibility relationships in Fraxinus ornus using 81 hermaphrodites and 25 males from one natural stand and two naturalized populations using intra- and interspecific stigma tests performed on F. ornus and P. angustifolia testers. We uncovered a DSI system with hermaphrodites belonging to one of two self-incompatibility (SI) groups and males compatible with both groups, making for a truly androdioecious reproductive system. The two human-founded populations contained only one of the two SI groups. Our results provide evidence for the evolutionary persistence of DSI. We discuss how its stability over time may have affected transitions to other sexual systems, such as dioecy., (© 2016 European Union. New Phytologist © 2016 New Phytologist Trust.)
- Published
- 2016
- Full Text
- View/download PDF
48. Functional analyses of cellulose synthase genes in flax (Linum usitatissimum) by virus-induced gene silencing.
- Author
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Chantreau M, Chabbert B, Billiard S, Hawkins S, and Neutelings G
- Subjects
- Chromosome Mapping, Flax enzymology, Gene Expression Profiling, Gene Expression Regulation, Plant genetics, Gene Silencing, Genes, Plant physiology, Phylogeny, Plant Stems metabolism, Flax genetics, Genes, Plant genetics, Glucosyltransferases genetics
- Abstract
Flax (Linum usitatissimum) bast fibres are located in the stem cortex where they play an important role in mechanical support. They contain high amounts of cellulose and so are used for linen textiles and in the composite industry. In this study, we screened the annotated flax genome and identified 14 distinct cellulose synthase (CESA) genes using orthologous sequences previously identified. Transcriptomics of 'primary cell wall' and 'secondary cell wall' flax CESA genes showed that some were preferentially expressed in different organs and stem tissues providing clues as to their biological role(s) in planta. The development for the first time in flax of a virus-induced gene silencing (VIGS) approach was used to functionally evaluate the biological role of different CESA genes in stem tissues. Quantification of transcript accumulation showed that in many cases, silencing not only affected targeted CESA clades, but also had an impact on other CESA genes. Whatever the targeted clade, inactivation by VIGS affected plant growth. In contrast, only clade 1- and clade 6-targeted plants showed modifications in outer-stem tissue organization and secondary cell wall formation. In these plants, bast fibre number and structure were severely impacted, suggesting that the targeted genes may play an important role in the establishment of the fibre cell wall. Our results provide new fundamental information about cellulose biosynthesis in flax that should facilitate future plant improvement/engineering., (© 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.)
- Published
- 2015
- Full Text
- View/download PDF
49. Beyond Rational Decision-Making: Modelling the Influence of Cognitive Biases on the Dynamics of Vaccination Coverage.
- Author
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Voinson M, Billiard S, and Alvergne A
- Subjects
- Communicable Diseases epidemiology, Humans, Cognition, Decision Making, Models, Biological, Vaccination
- Abstract
Background: Theoretical studies predict that it is not possible to eradicate a disease under voluntary vaccination because of the emergence of non-vaccinating "free-riders" when vaccination coverage increases. A central tenet of this approach is that human behaviour follows an economic model of rational choice. Yet, empirical studies reveal that vaccination decisions do not necessarily maximize individual self-interest. Here we investigate the dynamics of vaccination coverage using an approach that dispenses with payoff maximization and assumes that risk perception results from the interaction between epidemiology and cognitive biases., Methods: We consider a behaviour-incidence model in which individuals perceive actual epidemiological risks as a function of their opinion of vaccination. As a result of confirmation bias, sceptical individuals (negative opinion) overestimate infection cost while pro-vaccines individuals (positive opinion) overestimate vaccination cost. We considered a feedback between individuals and their environment as individuals could change their opinion, and thus the way they perceive risks, as a function of both the epidemiology and the most common opinion in the population., Results: For all parameter values investigated, the infection is never eradicated under voluntary vaccination. For moderately contagious diseases, oscillations in vaccination coverage emerge because individuals process epidemiological information differently depending on their opinion. Conformism does not generate oscillations but slows down the cultural response to epidemiological change., Conclusion: Failure to eradicate vaccine preventable disease emerges from the model because of cognitive biases that maintain heterogeneity in how people perceive risks. Thus, assumptions of economic rationality and payoff maximization are not mandatory for predicting commonly observed dynamics of vaccination coverage. This model shows that alternative notions of rationality, such as that of ecological rationality whereby individuals use simple cognitive heuristics, offer promising new avenues for modelling vaccination behaviour.
- Published
- 2015
- Full Text
- View/download PDF
50. Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.
- Author
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Billiard S, Ferrière R, Méléard S, and Tran VC
- Subjects
- Adaptation, Biological genetics, Biodiversity, Computer Simulation, Ecosystem, Feedback, Physiological, Genetic Markers, Genetics, Population, Mathematical Concepts, Mutation, Population Dynamics, Selection, Genetic, Evolution, Molecular, Models, Genetic, Stochastic Processes
- Abstract
How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.
- Published
- 2015
- Full Text
- View/download PDF
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