Genealogical Properties of Subsamples in Highly Fecund Populations

Eldon, Bjarki; Freund, Fabian

doi:10.1007/s10955-018-2013-1

Cited by 7 publications

(4 citation statements)

References 81 publications

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“…Taking

for some

, Eldon and Wakeley (2006) obtain Λ-coalescents for which the Λ measure in Equation (2) is a point mass at ψ . The simplicity of this model does allow one to obtain some explicit mathematical results (see e.g ., Der et al 2012 ; Eldon and Freund 2018 ; Freund 2020 ; Matuszewski et al 2018 ), and the model has also been used to simulate gene genealogies within phylogenies ( Zhu et al 2015 ). As well as the haploid model of Eldon and Wakeley (2006) , provides the diploid version of Birkner et al (2013a ), in which individuals perish as above, but replacements are generated by sampling a single pair of diploid individuals as parents, with children sampling one chromosome from each parent.…”

Section: Mutation Generationmentioning

confidence: 99%

Efficient ancestry and mutation simulation with msprime 1.0

et al. 2021

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Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

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“…Taking

for some

Section: Mutation Generationmentioning

confidence: 99%

Efficient ancestry and mutation simulation with msprime 1.0

et al. 2021

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“…Viewing time in units of

scriptO ()(, N^{γ})

generations for some

γ \in (](, 0, 2)

, it can be shown that the model is in the domain of attraction of a

normalΛ

‐coalescent, indeed for

γ = 2

the limiting coalescent is a mixture of the Kingman‐coalescent and a multiple‐merger coalescent (Eldon & Wakeley, 2006). The model in Equation () is unrealistic in assuming that exactly the same fraction

()(, ψ)

of the population is replaced in each sweepstakes event, but it is among the simplest models of random sweepstakes, and its simplicity does facilitate some mathematical results to be obtained (Der et al, 2012; Eldon & Freund, 2018; Matuszewski et al, 2018). In particular, fixation probabilities under selection are studied for generalized Wright‐Fisher processes (Der et al, 2011).…”

Section: The Impact Of Random Sweepstakes On Selectionmentioning

confidence: 99%

Sweepstakes reproduction facilitates rapid adaptation in highly fecund populations

Eldon

Stephan²

2023

Molecular Ecology

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Adaptation enables natural populations to survive in a changing environment. Understanding the mechanics of adaptation is therefore crucial for learning about the evolution and ecology of natural populations. We focus on the impact of random sweepstakes on selection in highly fecund haploid and diploid populations partitioned into two genetic types, with one type conferring selective advantage. For the diploid populations, we incorporate various dominance mechanisms. We assume that the populations may experience recurrent bottlenecks. In random sweepstakes, the distribution of individual recruitment success is highly skewed, resulting in a huge variance in the number of offspring contributed by the individuals present in any given generation. Using computer simulations, we investigate the joint effects of random sweepstakes, recurrent bottlenecks and dominance mechanisms on selection. In our framework, bottlenecks allow random sweepstakes to have an effect on the time to fixation, and in diploid populations, the effect of random sweepstakes depends on the dominance mechanism. We describe selective sweepstakes that are approximated by recurrent sweeps of strongly beneficial allelic types arising by mutation. We demonstrate that both types of sweepstakes reproduction may facilitate rapid adaptation (as defined based on the average time to fixation of a type conferring selective advantage conditioned on fixation of the type). However, whether random sweepstakes cause rapid adaptation depends also on their interactions with bottlenecks and dominance mechanisms. Finally, we review a case study in which a model of recurrent sweeps is shown to essentially explain population genomic data from Atlantic cod.

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“…The simplicity of this model does allow one to obtain some explicit mathematical results (see e.g. Der et al (2012); Eldon and Freund (2018); Freund (2020); Matuszewski et al (2018)), and the model has also been used to simulate gene genealogies within phylogenies . As well as the haploid model of Eldon and Wakeley (2006), msprime provides the diploid version of Birkner et al (2013a), in which individuals perish as above, but replacements are generated by sampling a single pair of diploid individuals as parents, with children sampling one chromosome from each parent.…”

Section: Availabilitymentioning

confidence: 99%

Efficient ancestry and mutation simulation with msprime 1.0

Baumdicker

Bisschop

Goldstein

et al. 2021

Preprint

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Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and tskit library. We summarise msprime's many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

show abstract

Genealogical Properties of Subsamples in Highly Fecund Populations

Cited by 7 publications

References 81 publications

Efficient ancestry and mutation simulation with msprime 1.0

Efficient ancestry and mutation simulation with msprime 1.0

Sweepstakes reproduction facilitates rapid adaptation in highly fecund populations

Efficient ancestry and mutation simulation with msprime 1.0

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