Effect of beneficial sweeps and background selection on genetic diversity in changing environments

Kaushik, Sachin

doi:10.1016/j.jtbi.2023.111431

Cited by 2 publications

(1 citation statement)

References 29 publications

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“…A description of resampling simulations is omitted as it requires empirical data from existing samples, likely to contain non‐neutral regions and an unknown selection regime, from which the simulated data is generated. Given that the general aim of simulation in evolutionary genomics is to model specific modes of selection and their effect on the linked neutral background (Barton, 2000; Charlesworth, 2006; Charlesworth & Jensen, 2021; Kaushik, 2023; Smith & Haigh, 1974), this work will instead focus on coalescent and forward simulations.…”

Section: Introductionmentioning

confidence: 99%

Population genetic simulation: Benchmarking frameworks for non‐standard models of natural selection

Johnson,

Tobler,

Schmidt

et al. 2024

Molecular Ecology Resources

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Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high‐level model complexity has recently been developed, and the advancement of tree sequence recording now allows simulations to merge the efficiency and genealogical insight of coalescent simulations with the flexibility of forward simulations. However, frameworks utilizing these features have not yet been compared and benchmarked. Here, we evaluate various simulation workflows using the coalescent simulator msprime and the forward simulator SLiM, to assess resource efficiency and determine an optimal simulation framework. Three aspects were evaluated: (1) the burn‐in, to establish an equilibrium level of neutral diversity in the population; (2) the forward simulation, in which temporally fluctuating selection is acting; and (3) the final computation of summary statistics. We provide typical memory and computation time requirements for each step. We find that the fastest framework, a combination of coalescent and forward simulation with tree sequence recording, increases simulation speed by over twenty times compared to classical forward simulations without tree sequence recording, although it does require six times more memory. Overall, using efficient simulation workflows can lead to a substantial improvement when modelling complex evolutionary scenarios—although the optimal framework ultimately depends on the available computational resources.

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Section: Introductionmentioning

confidence: 99%

Population genetic simulation: Benchmarking frameworks for non‐standard models of natural selection

Johnson,

Tobler,

Schmidt

et al. 2024

Molecular Ecology Resources

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Genetic diversity during selective sweeps in non-recombining populations

Kaushik,

Jain,

Johri

2024

Preprint

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Selective sweeps, resulting from the spread of beneficial, neutral, or deleterious mutations through a population, shape patterns of genetic variation at linked neutral sites. While many theoretical, computational, and statistical advances have been made in understanding the genomic signatures of selective sweeps in recombining populations, substantially less is understood in populations with little/no recombination. We present a mathematical framework based on diffusion theory for obtaining the site frequency spectrum (SFS) at linked neutral sites immediately post and during the fixation of moderately or strongly beneficial mutations. We find that when a single hard sweep occurs, the SFS decays as 1/xfor low derived allele frequencies (x), similar to the neutral SFS at equilibrium, whereas at higher derived allele frequencies, it follows a 1/x2power law. These power laws are universal in the sense that they are independent of the dominance and inbreeding coefficient, and also characterize the SFS during the sweep. Additionally, we find that the derived allele frequency where the SFS shifts from the 1/xto 1/x2law, is inversely proportional to the selection strength: thus under strong selection, the SFS follows the 1/x2dependence for most allele frequencies, resembling a rapidly expanding neutral population. When clonal interference is pervasive, the SFS immediately post-fixation becomes U-shaped and is better explained by the equilibrium SFS of selected sites. Our results will be important in developing statistical methods to infer the timing and strength of recent selective sweeps in asexual populations, genomic regions that lack recombination, and clonally propagating tumor populations.

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Effect of beneficial sweeps and background selection on genetic diversity in changing environments

Cited by 2 publications

References 29 publications

Population genetic simulation: Benchmarking frameworks for non‐standard models of natural selection

Population genetic simulation: Benchmarking frameworks for non‐standard models of natural selection

Genetic diversity during selective sweeps in non-recombining populations

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