Fisher–Wright model with deterministic seed bank and selection

Koopmann, Bendix; Müller, Johannes; Tellier, Aurélien; Živković, Daniel

doi:10.1016/j.tpb.2016.11.005

Cited by 39 publications

(80 citation statements)

References 55 publications

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“…To test this hypothesis, we simulated the trajectory of a beneficial allele in a population subject to the strong seed-bank effect and examined the dormant and active portions of the population separately (see Supplemental Materials: Selection simulation). As expected, we found that the average amount of time required for a beneficial allele to reach fixation increases with the average number of generations that an individual spends in the seed bank (Figure 4a,b) (Koopmann et al, 2017).…”

Section: Selectionsupporting

confidence: 82%

“…In a population with a seed bank, there are active and dormant subpopulations, where individuals enter and exit a dormant state in a manner analogous to migration between subpopulations (Blath, González-Casanova, Eldon, Kurt, & Wilke-Berenguer, 2015;Lennon & Jones, 2011) (Figure 1). Seed banks are sometimes viewed simply as an evolutionary buffer (Koopmann, Müller, Tellier, & Živković, 2017). Dormancy preserves existing genetic diversity by decreasing the rate that genetic diversity is removed from the population (Hairston & De Stasio, 1988;Koopmann et al, 2017;Vitalis, Glémin, & Olivieri, 2004), in turn increasing in the effective size of the population (Nunney, 2002).…”

Section: Population Genetic Consequences Of Dormancymentioning

confidence: 99%

“…Seed banks are sometimes viewed simply as an evolutionary buffer (Koopmann, Müller, Tellier, & Živković, 2017). Dormancy preserves existing genetic diversity by decreasing the rate that genetic diversity is removed from the population (Hairston & De Stasio, 1988;Koopmann et al, 2017;Vitalis, Glémin, & Olivieri, 2004), in turn increasing in the effective size of the population (Nunney, 2002). However, when individuals remain dormant for extremely long periods of time, dormancy can have complex and nonintuitive effects on evolutionary dynamics (Blath et al, 2015).…”

Section: Population Genetic Consequences Of Dormancymentioning

confidence: 99%

See 2 more Smart Citations

Evolution with a seed bank: The population genetic consequences of microbial dormancy

Shoemaker

Lennon

2018

Evolutionary Applications

101

128

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Dormancy is a bet‐hedging strategy that allows organisms to persist through conditions that are suboptimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long‐term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence the evolutionary dynamics of microorganisms as well as other taxa.

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Section: Selectionsupporting

confidence: 82%

Section: Population Genetic Consequences Of Dormancymentioning

confidence: 99%

Section: Population Genetic Consequences Of Dormancymentioning

confidence: 99%

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Evolution with a seed bank: The population genetic consequences of microbial dormancy

Shoemaker

Lennon

2018

Evolutionary Applications

101

128

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“…It has been suggested early on that due to the storage effect, seed banking slows down the action of selection (Templeton & Levin, 1979;Hairston & De Stasio, 1988). Recent theory shows that a positively (negatively) selected allele has indeed a longer time to fixation (loss) under a persistent seed bank, but only by a factor 1/b compared with 1/b² for neutral alleles (Koopmann et al, 2017) because plants are exposed to selection in the above-ground population as soon as the seeds germinate (with probability b). In other words, more persistent seed banks effectively: (1) slow down the time of fixation of advantageous alleles; but (2) decrease the probability for these alleles to be lost due to random drift (Koopmann et al, 2017;Shoemaker & Lennon, 2018).…”

Section: Seed Banks Influence the Rate And Signatures Of Natural mentioning

confidence: 99%

Persistent seed banking as eco‐evolutionary determinant of plant nucleotide diversity: novel population genetics insights

Tellier

2018

New Phytologist

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Contents Summary725I.Introduction725II.Seed banks decrease the population extinction rate726III.Seed banks define the effective population size727IV.Seed banks affect the mutation rate728V.Seed banks affect the effective recombination rate728VI.Seed banks influence the rate and signatures of natural selection729VII.Conclusion729Acknowledgements729References729 Summary Long‐term persistent seed banking is a common temporal bet‐hedging strategy in plants to adapt to unpredictable environments. The population genomics perspective developed in this article suggests that seed banking determines plant nucleotide diversity by decreasing the rate of genetic drift and the effect of linked selection while increasing mutational input. As a result, persistent seed banks are important factors determining the magnitude of the discrepancy between the census size of the above‐ground plant population and its genetic diversity, an effect known as the Lewontin paradox. The theoretical population genetics predictions presented here can be tested by combining genome‐wide polymorphism data with ecological studies of dormancy.

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“…Furthermore, neglecting seed banks may yield distorted results for the inference of past demography using for example the SFS (Živković and Tellier, 2012). Interestingly, the effect of (weak) selection is enhanced by the slow-down of the time scale due to seed banks (Blath et al, 2013(Blath et al, , 2016Koopmann et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Effects of population- and seed bank noise on neutral evolution and efficacy of natural selection

Heinrich¹,

Müller

Tellier³

et al. 2017

Preprint

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Population genetics models typically consider a fixed population size and a unique selection coefficient. However, population dynamics inherently generate noise in numbers of individuals and selection acts on various components of the individuals' fitness. In plant species with seed banks, the size of both the aboveand below-ground compartments present noise depending on seed production and the state of the seed bank. We investigate if this noise has consequences on 1) the rate of genetic drift, and 2) the efficacy of selection. We consider four variants of two-allele Moran-type models defined by combinations of presence and absence of noise in above-ground and seed bank compartments. Time scale analysis and dimension reduction methods allow us to reduce the corresponding Fokker-Planck equation to a one-dimensional diffusive Moran model. We first show that if the above-ground noise classically affects the rate of genetic drift, below-ground noise reduces the diversity storage effect of the seed bank. Second, we consider that selection can act on four different components of the plant fitness: plant or seed death rate, seed production or seed germination. Our striking result is that the efficacy of selection for seed death rate or germination rate is reduced by seed bank noise, whereas selection occurring on plant death rate or seed production is not affected. We derive the expected site-frequency spectrum reflecting this heterogeneity in selection efficacy between genes underpinning different plant fitness components. Our results highlight the importance to consider the effect of ecological noise to predict the impact of seed banks on neutral and selective evolution.

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Fisher–Wright model with deterministic seed bank and selection

Cited by 39 publications

References 55 publications

Evolution with a seed bank: The population genetic consequences of microbial dormancy

Evolution with a seed bank: The population genetic consequences of microbial dormancy

Persistent seed banking as eco‐evolutionary determinant of plant nucleotide diversity: novel population genetics insights

Effects of population- and seed bank noise on neutral evolution and efficacy of natural selection

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