Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

Saubin, Méline; Tellier, Aurélien; Stoeckel, Solenn; Andrieux, Axelle; Halkett, Fabien

doi:10.1101/2022.10.24.513475

Cited by 2 publications

(11 citation statements)

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“…In turn, the inference of demographic parameters may be used to infer the evolutionary forces acting during rapid adaptation of pathogens to their hosts. Saubin et al (2023) The authors conclude thus that, contrary to expectations, eco-evo feedbacks may positively affect genetic diversity over time in antagonistic species rapidly co-adapting to one another.…”

Section: Role Of Eco -E Vo Feedback In R Apid Adap Tati On During Coe...mentioning

confidence: 75%

“…In recent years, studies of the model insect Drosophila melanogaster , which undergoes several generations per year, suggest that rapid allele fluctuations are more common than previously thought (Bergland et al., 2014; Wittmann et al., 2017) and are often driven by some form of balancing selection, such as temporally fluctuating or sexually antagonistic selection. Fluctuation in allele frequencies can be observed at the loci under selection as well at linked neutral loci, which has been demonstrated for Drosophila melanogaster (Glaser‐Schmitt et al., 2023) and for a fungal pathogen of poplars (Saubin et al., 2023).…”

Section: Role Of Eco‐evo Feedback In Rapid Adaptation During Coevolut...mentioning

confidence: 91%

“…Saubin et al. (2023) develop a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual‐based model with temporal genetic data to disentangle genetic changes and demographic variation in a case of rapid adaptation. They study the evolution of a fungal pathogen of crops, which overcomes resistant cultivars within a few years of their introduction.…”

Section: Role Of Eco‐evo Feedback In Rapid Adaptation During Coevolut...mentioning

confidence: 99%

“…We present a range of empirical studies generating coevolution/fluctuating selection in controlled set‐ups using species with short generation time. Fluctuating selection is chiefly characterised by fast changes in allele frequencies at the loci under selection and across the whole genome as documented and analysed in Drosophila melanogaster (Glaser‐Schmitt et al., 2023) and in a fungal pathogen of poplars (Saubin et al., 2023). Furthermore, fluctuating selection in host–parasite systems also coincide with eco‐evo feedback which affects the population sizes of antagonistic species over time, which in turn has consequences on the available genetic diversity (Le Pennec et al., 2023).…”

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confidence: 99%

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Rapid evolutionary adaptation: Potential and constraints

Tellier,

Hodgins,

Stephan

et al. 2024

Molecular Ecology

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The vast diversity of life on earth is the result of evolutionary processes that acted over billions of years. Historically it was assumed that adaptation and the origin of new species required long periods of time. However, it is now well established that adaptation to new environments can occur rapidly and sometimes even within a few generations. We define here rapid adaptation as a selective process, which allows a population or species to substantially improve its average fitness in the short time scale of few tens of generations, typically within a hundred years for annual species. More precisely, rapid adaptation occurs through natural selection acting on the phenotype (and ultimately on the underlying genetic variants) over short time scale and therefore encompasses both ecological (demographic abundance and inter-specific interactions within a given habitat and species community) and evolutionary (genetic drift, mutation, recombination, gene flow and selection) processes (Hairston et al., 2005;Kokko et al., 2017). The occurrence and speed of rapid adaptation is thus determined by the feedback between ecological and evolutionary (eco-evo) processes. A large body of literature now documents

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Section: Role Of Eco -E Vo Feedback In R Apid Adap Tati On During Coe...mentioning

confidence: 75%

Section: Role Of Eco‐evo Feedback In Rapid Adaptation During Coevolut...mentioning

confidence: 91%

Section: Role Of Eco‐evo Feedback In Rapid Adaptation During Coevolut...mentioning

confidence: 99%

mentioning

confidence: 99%

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Rapid evolutionary adaptation: Potential and constraints

Tellier,

Hodgins,

Stephan

et al. 2024

Molecular Ecology

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“…Moreover, understanding the emergence of a genetic structure requires deciphering the temporal evolution of population genetic indices, which is rarely done both theoretically and empirically (Saubin et al, 2023b).…”

Section: Introductionmentioning

confidence: 99%

Neutral genetic structuring of pathogen populations during rapid adaptation

Saubin

Stoeckel

Tellier

et al. 2022

Preprint

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1AbstractThe demography and genetic structure of a population are closely linked. The study of this interplay is crucial, especially for organisms with frequent demographic fluctuations such as pathogen species responsible for emerging diseases. The joint study of demographic variations and genetic evolution of a pathogen population can be achieved by coupling epidemiology and population genetics. This framework is particularly suited to the study of genetic signatures of strong and rapid selective events, such as pathogen adaptation to plant genetic resistances. We have limited knowledge of how these events shape the genetic evolution of pathogens and what would be the typical genetic signatures of strong demographic and selective events on the pathogen population. In this study, we model pathogen population dynamics and genetic evolution at neutral loci to draw a typology of scenarios of eco-evolutionary dynamics. Using a clustering method dedicated to time-series variations, we identify three main scenarios: 1) small variations in the pathogen population size and small changes in genetic structure, 2) a strong founder event on the resistant host that in turn leads to a genetic structure on the susceptible host, and 3) evolutionary rescue that results in a strong founder event on the resistant host, preceded by a bottleneck on the susceptible host. Beyond the selective event itself, the demographic trajectory imposes specific changes in the genetic structure of the pathogen population. Most of these genetic changes are transient, with a signature of resistance overcoming that vanishes in a few years only. Considering time series is therefore of utmost importance for accurate tracking of the evolutionary trajectories of pathogen populations.

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Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

Cited by 2 publications

References 73 publications

Rapid evolutionary adaptation: Potential and constraints

Rapid evolutionary adaptation: Potential and constraints

Neutral genetic structuring of pathogen populations during rapid adaptation

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