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

Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.

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Soft selective sweeps in evolutionary rescue

10.1101/052993 ◽

2016 ◽

Cited By ~ 4

Author(s):

Benjamin A. Wilson ◽

Pleuni S. Pennings ◽

Dmitri A. Petrov

Keyword(s):

Drug Resistance ◽

Population Genetics ◽

Population Genetic ◽

Genetic Adaptation ◽

Selective Sweeps ◽

Adaptive Mutations ◽

Evolutionary Rescue ◽

Large Populations ◽

Genetic Signatures ◽

Soft Selective Sweeps

AbstractEvolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps in our model. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens.

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Architecture of parallel adaptation to freshwater in multiple populations of threespine stickleback

10.1101/381723 ◽

2018 ◽

Author(s):

Nadezhda V. Terekhanova ◽

Anna E. Barmintseva ◽

Alexey S. Kondrashov ◽

Georgii A. Bazykin ◽

Nikolai S. Mugue

Keyword(s):

Genetic Architecture ◽

White Sea ◽

Core Region ◽

Selective Sweeps ◽

The White Sea ◽

Threespine Sticklebacks ◽

White Sea Basin ◽

Soft Selective Sweeps ◽

Freshwater Environments

AbstractThreespine sticklebacks adapted to freshwater environments all over the Northern Hemisphere. This adaptation involved parallel recruitment of freshwater alleles in clusters of closely linked sites, or divergence islands (DIs). However, it is unclear to what extent the DIs involved in adaptation and the alleles within them coincide between populations adapting to similar environments. Here, we examine 10 freshwater populations of similar ages from the White Sea basin, and study the repeatability of patterns of adaptation in them. Overall, the 65 detected DIs tend to reside in regions of low recombination, underlining the role of reduced recombination in their establishment. Moreover, the DIs are clustered in the genome to the extent that is not explainable by the recombination rate alone, consistent with the divergence hitchhiking model. 21 out of the 65 DIs are universal; i.e., the frequency of freshwater alleles in them is increased in all analyzed populations. Universal DIs tend to have longer core region shared between populations, and the divergence between the marine and the freshwater haplotypes in them is higher, implying that they are older, also consistently with divergence hitchhiking. Within most DIs, the same set of sites distinguished the marine and the freshwater haplotypes in all populations; however, in some of the DIs, the genetic architecture of the freshwater haplotype differed between populations, suggesting that they could have been established by soft selective sweeps.

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Allele Surfing Promotes Microbial Adaptation from Standing Variation

10.1101/049353 ◽

2016 ◽

Cited By ~ 3

Author(s):

Matti Gralka ◽

Fabian Stiewe ◽

Fred Farrell ◽

Wolfram Möebius ◽

Bartek Waclaw ◽

...

Keyword(s):

Genetic Drift ◽

Selective Sweeps ◽

High Frequencies ◽

Microbial Adaptation ◽

Standing Variation ◽

Resource Limited ◽

Variation Range ◽

Mean Fitness ◽

Soft Selective Sweeps ◽

Uniform Population

AbstractThe coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from ‘soft’ selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges.

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Dominance shifts increase the likelihood of soft selective sweeps

10.1101/2021.02.22.432386 ◽

2021 ◽

Author(s):

Pavitra Muralidhar ◽

Carl Veller

Keyword(s):

Selective Sweep ◽

Primary Source ◽

Pesticide Use ◽

Selective Sweeps ◽

Multiple Alleles ◽

Standing Variation ◽

Haplotypic Diversity ◽

Evolutionary Rescue ◽

Genetics Of Adaptation ◽

Soft Selective Sweeps

AbstractGenetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from the standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.

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Soft Selective Sweeps in Evolutionary Rescue

Genetics ◽

10.1534/genetics.116.191478 ◽

2017 ◽

Vol 205 (4) ◽

pp. 1573-1586 ◽

Cited By ~ 27

Author(s):

Benjamin A. Wilson ◽

Pleuni S. Pennings ◽

Dmitri A. Petrov

Keyword(s):

Selective Sweeps ◽

Evolutionary Rescue ◽

Soft Selective Sweeps

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Examination of signatures of recent positive selection on genes involved in human sialic acid biology

10.1101/137034 ◽

2017 ◽

Author(s):

Jiyun M. Moon ◽

David M. Aronoff ◽

John A. Capra ◽

Patrick Abbot ◽

Antonis Rokas

Keyword(s):

Sialic Acid ◽

Positive Selection ◽

Transfer Functions ◽

Demographic History ◽

Neutral Evolution ◽

Human Lineage ◽

Selective Sweeps ◽

Frequency Spectra ◽

Recent Positive Selection ◽

Soft Selective Sweeps

AbstractSialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens). To test whether sialic acid biology genes have also experienced more recent positive selection during the evolution of the modern human lineage, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we examined whether their protein-coding regions showed evidence of recent hard and soft selective sweeps. This examination involved the calculation of four measures that quantify changes in allele frequency spectra, extent of population differentiation, and haplotype homozygosity caused by recent hard and soft selective sweeps for 55 sialic acid biology genes using publicly available whole genome sequencing data from 1,668 humans from three ethnic groups. To disentangle evidence for selection from confounding demographic effects, we compared the observed patterns in sialic acid biology genes to simulated sequences of the same length under a model of neutral evolution that takes into account human demographic history. We found that the patterns of genetic variation of most sialic acid biology genes did not significantly deviate from neutral expectations and were not significantly different among genes belonging to different functional categories. Those few sialic acid biology genes that significantly deviated from neutrality either experienced soft sweeps or population-specific hard sweeps. Interestingly, while most hard sweeps occurred on genes involved in sialic acid recognition, most soft sweeps involved genes associated with recycling, degradation and activation, transport, and transfer functions. We propose that the lack of signatures of recent positive selection for the majority of the sialic acid biology genes is consistent with the view that these genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically restricted pathogens.

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More efficacious drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

10.1101/024109 ◽

2015 ◽

Cited By ~ 1

Author(s):

Alison F Feder ◽

Soo-Yon Rhee ◽

Robert W Shafer ◽

Dmitri A Petrov ◽

Pleuni S Pennings

Keyword(s):

Drug Resistance ◽

Hiv Treatment ◽

Adaptive Mutation ◽

Selective Sweeps ◽

Consensus Sequences ◽

Adaptive Mutations ◽

Slow Evolution ◽

Soft Selective Sweeps ◽

Hiv 1 ◽

Evolution Proceeds

In the early days of HIV treatment, drug resistance occurred rapidly and predictably in all patients, but under modern treatments, resistance arises slowly, if at all. The probability of resistance should be controlled by the rate of generation of resistant mutations. If many adaptive mutations arise simultaneously, then adaptation proceeds by soft selective sweeps in which multiple adaptive mutations spread concomitantly, but if adaptive mutations occur rarely in the population, then a single adaptive mutation should spread alone in a hard selective sweep. Here we use 6,717 HIV-1 consensus sequences from patients treated with first-line therapies between 1989 and 2013 to confirm that the transition from fast to slow evolution of drug resistance was indeed accompanied with the expected transition from soft to hard selective sweeps. This suggests more generally that evolution proceeds via hard sweeps if resistance is unlikely and via soft sweeps if it is likely.

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discoal: flexible coalescent simulations with selection

10.1101/063453 ◽

2016 ◽

Cited By ~ 2

Author(s):

Andrew D. Kern ◽

Daniel R. Schrider

Keyword(s):

Programming Language ◽

Source Code ◽

Recurrent Mutation ◽

Supplementary Information ◽

Selective Sweeps ◽

C Programming Language ◽

Coalescent Simulations ◽

C Programming ◽

Soft Selective Sweeps ◽

General Public License

AbstractSummaryHere we describe discoal, a coalescent simulator able to generate population samples that include selective sweeps in a feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due to drift or either hard or soft selective sweeps—even those occurring a large genetic distance away from the simulated locus. discoal can simulate sweeps with recurrent mutation to the adaptive allele, recombination, and gene conversion, under nonequilibrium demographic histories and without specifying an allele frequency trajectory in advance.Availability and ImplementationAvailability and implementation: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kernlab/discoal_multipop) under a GNU General Public [email protected] informationSupplementary Figures and Text are appended below

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