Allelic gene conversion softens selective sweeps

Daniel R. Schrider

doi:10.1093/genetics/iyag222

Abstract The prominence of positive selection, in which beneficial mutations are favored by natural selection and rapidly increase in frequency, is a subject of intense debate. Positive selection can result in selective sweeps, in which the haplotype(s) bearing the adaptive allele sweep through the population, thereby removing much of the genetic diversity from the region surrounding the target of selection. Two models of selective sweeps have been proposed: classic sweeps, or hard sweeps, in which a single copy of the adaptive allele sweeps to fixation, and soft sweeps, in which multiple distinct copies of the adaptive allele leave descendants after the sweep. Soft sweeps can be the outcome of recurrent mutation to the adaptive allele, or the presence of standing genetic variation consisting of multiple haplotypes bearing the adaptive allele prior to the onset of selection. Importantly, soft sweeps will be common when populations can rapidly adapt to novel selective pressures, either because of a high mutation rate or because adaptive alleles are already present. The prevalence of soft sweeps is especially controversial, and it has been noted that selection on standing variation or recurrent mutations may not always produce soft sweeps. Here, we show that the inverse is true: selection on single-origin de novo mutations may often result in an outcome that is indistinguishable from a soft sweep. This is made possible by allelic gene conversion, which “softens” hard sweeps by copying the adaptive allele onto multiple genetic backgrounds, a process we refer to as a “pseudo-soft” sweep. We carried out a simulation study examining the impact of gene conversion on sweeps from a single de novo allele in models of human, Drosophila, and Arabidopsis populations. The fraction of simulations in which gene conversion had produced multiple haplotypes with the adaptive allele upon fixation was appreciable. Indeed, under realistic demographic histories and gene conversion rates, even if selection always acts on a single-origin mutation, sweeps in large populations usually involve multiple haplotypes, especially when selection is not extremely strong. Thus, even when the mutation rate is low or there is no standing variation, signatures of hard sweeps are expected to be the exception rather than the rule in large populations. We also summarize patterns of haplotypic diversity following pseudo-soft sweeps, and show that they often resemble those produced by true soft sweeps. It follows that the presence of signatures of soft sweeps does not necessarily mean that adaptation has been especially rapid or is not mutation limited.

External reference records

A community-maintained standard library of population genetic models

10.7554/elife.54967 · 2020

Identifying the favored mutation in a positive selective sweep

10.1038/nmeth.4606 · 2018

Uncovering footprints of natural selection through spectral analysis of genomic summary statistics

10.1093/molbev/msad157 · 2023

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

10.1038/356519a0 · 1992

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

10.1371/journal.pbio.0050310 · 2007

Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome

10.1093/molbev/msy188 · 2018

A selective sweep across species boundaries in Drosophila

10.1093/molbev/mst123 · 2013

The hitchhiking effect on the site frequency spectrum of DNA polymorphisms

10.1093/genetics/140.2.783 · 1995

Estimating gene conversion rates from population data using multi-individual identity by descent

10.1016/j.ajhg.2025.07.019 · 2025

10.1101/2022.07.19.500702

10.1101/2022.07.19.500702 · 2022

Estimating the parameters of background selection and selective sweeps in drosophila in the presence of gene conversion

10.1073/pnas.1619434114 · 2017

How long does it take to fix a favorable mutation, and why should we care?

10.1086/708187 · 2020

Population differentiation as a test for selective sweeps

10.1101/gr.100545.109 · 2010

Signatures of selective sweeps in continuous-space populations

10.1093/genetics/iyaf183 · 2025

The many landscapes of recombination in Drosophila melanogaster

10.1371/journal.pgen.1002905 · 2012

Natural selection constrains neutral diversity across a wide range of species

10.1371/journal.pbio.1002112 · 2015

Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations

10.1093/genetics/iyae180 · 2025

Genome-wide signals of positive selection in human evolution

10.1101/gr.164822.113 · 2014

Hitchhiking under positive Darwinian selection

10.1093/genetics/155.3.1405 · 2000

The clarifying role of time series data in the population genetics of hiv

10.1371/journal.pgen.1009050 · 2021

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in hiv-1

10.7554/elife.10670 · 2016

Parameter scaling in population genetics simulations may introduce unintended background selection: considerations for scaled simulation design

10.1093/gbe/evaf097 · 2025

On detecting incomplete soft or hard selective sweeps using haplotype structure

10.1093/molbev/msu077 · 2014

Xxi.—on the dominance ratio

10.1017/s0370164600023993 · 1923

Adaptive protein evolution in animals and the effective population size hypothesis

10.1371/journal.pgen.1005774 · 2016

Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps

10.1371/journal.pgen.1005004 · 2015

Detection of hard and soft selective sweeps from drosophila melanogaster population genomic data

10.1371/journal.pgen.1009373 · 2021

Estimating meiotic gene conversion rates from population genetic data

10.1534/genetics.107.078907 · 2007

Genetic drift in an infinite population: the pseudohitchhiking model

10.1093/genetics/155.2.909 · 2000

Toward a selection theory of molecular evolution

10.1111/j.1558-5646.2007.00308.x · 2008

A mathematical theory of natural and artificial selection—i

10.1007/bf02459574 · 1924

A likelihood approach for uncovering selective sweep signatures from haplotype data

10.1093/molbev/msaa115 · 2020

On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses

10.1371/journal.pgen.1007859 · 2018

Soft sweeps molecular population genetics of adaptation from standing genetic variation

10.1534/genetics.104.036947 · 2005

Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation

10.1111/2041-210x.12808 · 2017

Classic selective sweeps were rare in recent human evolution

10.1126/science.1198878 · 2011

The effect of dna sequence polymorphisms on intragenic recombination in the rosy locus of drosophila melanogaster

10.1093/genetics/129.3.779 · 1991

Meiotic gene conversion tract length distribution within the rosy locus of drosophila melanogaster

10.1093/genetics/137.4.1019 · 1994

Gene expression drives the evolution of dominance

10.1038/s41467-018-05281-7 · 2018

Keeping it local: evidence for positive selection in swedish arabidopsis thaliana

10.1093/molbev/msu247 · 2014

Additional external references

Discovery of ongoing selective sweeps within anopheles mosquito populations using deep learning

10.1093/molbev/msaa259 · doi-reference

Evolution in mendelian populations

10.1093/genetics/16.2.97 · doi-reference

Soft selective sweeps in complex demographic scenarios

10.1534/genetics.114.165571 · doi-reference

Non-crossover gene conversions show strong gc bias and unexpected clustering in humans

10.7554/elife.04637 · doi-reference

The genomic landscape of meiotic crossovers and gene conversions in arabidopsis thaliana

10.7554/elife.01426 · doi-reference

Molecular parallelism underlies convergent highland adaptation of maize landraces

10.1093/molbev/msab119 · doi-reference

A map of recent positive selection in the human genome

10.1371/journal.pbio.0040072 · doi-reference

Robust forward simulations of recurrent hitchhiking

10.1534/genetics.113.156935 · doi-reference

Polygenic adaptation to an environmental shift: temporal dynamics of variation under gaussian stabilizing selection and additive effects on a single trait

10.1534/genetics.119.302662 · doi-reference

A second generation human haplotype map of over 3.1 million SNPs

10.1038/nature06258 · doi-reference

Allelic gene conversion softens selective sweeps | ResearchHub

Allelic gene conversion softens selective sweeps

Referenced works

Cited by

External reference records

Additional external references