scholarly journals Allele Surfing Promotes Microbial Adaptation from Standing Variation

2016 ◽  
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.

scholarly journals Dominance shifts increase the likelihood of soft selective sweeps

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.

scholarly journals Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

2017 ◽  
Vol 11 (7) ◽  
pp. e0005816 ◽  
Author(s):  
Stephen R. Doyle ◽  
Catherine Bourguinat ◽  
Hugues C. Nana-Djeunga ◽  
Jonas A. Kengne-Ouafo ◽  
Sébastien D. S. Pion ◽  
...  
Keyword(s):  
Genetic Drift ◽  
Drug Sensitivity ◽  
Onchocerca Volvulus ◽  
Selective Sweeps ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Soft Selective Sweeps

scholarly journals Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

2015 ◽  
Author(s):  
Florencia Schlamp ◽  
Julian van der Made ◽  
Rebecca Stambler ◽  
Lewis Chesebrough ◽  
Adam R Boyko ◽  
...  
Keyword(s):  
Artificial Selection ◽  
Population Sample ◽  
Population Bottlenecks ◽  
Selective Sweeps ◽  
Nucleotide Polymorphism ◽  
Genomic Signatures ◽  
Population Genomic ◽  
Dog Domestication ◽  
Soft Selective Sweeps ◽  
Positive Controls

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.

scholarly journals Soft selective sweeps in evolutionary rescue

2016 ◽  
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.

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

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.

scholarly journals Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

PLoS Genetics ◽  
2012 ◽  
Vol 8 (10) ◽  
pp. e1003011 ◽  
Author(s):  
Benjamin M. Peter ◽  
Emilia Huerta-Sanchez ◽  
Rasmus Nielsen
Keyword(s):  
De Novo ◽  
De Novo Mutation ◽  
Selective Sweeps ◽  
Standing Variation

scholarly journals Soft Selective Sweeps in Evolutionary Rescue

Genetics ◽  
2017 ◽  
Vol 205 (4) ◽  
pp. 1573-1586 ◽  
Author(s):  
Benjamin A. Wilson ◽  
Pleuni S. Pennings ◽  
Dmitri A. Petrov
Keyword(s):  
Selective Sweeps ◽  
Evolutionary Rescue ◽  
Soft Selective Sweeps

scholarly journals Population heterogeneity in mutation rate increases mean fitness and the frequency of higher order mutants

2016 ◽  
Author(s):  
Helen K. Alexander ◽  
Stephanie I. Mayer ◽  
Sebastian Bonhoeffer
Keyword(s):  
Mutation Rate ◽  
Relative Effect ◽  
Relative Increase ◽  
Higher Order ◽  
Population Heterogeneity ◽  
Arbitrary Distribution ◽  
Rate Heterogeneity ◽  
Standing Variation ◽  
A Genome ◽  
Mean Fitness

AbstractMutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, mutation rate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We explore the consequences of such mutation rate heterogeneity in a model allowing an arbitrary distribution of mutation rate among individuals, either with or without inheritance. We find that variation of mutation rate about the mean results in a higher probability of producing zero or many simultaneous mutations on a genome. Moreover, it increases the frequency of higher order mutants even under ongoing mutation and selection. We gain a quantitative understanding of how this frequency depends on moments of the mutation rate distribution and selection coefficients. In particular, in a two-locus model, heterogeneity leads to a relative increase in double mutant frequency proportional to the squared coefficient of variation of the mutation rate. Relative effect sizes increase with the number of loci. Finally, this clustering of deleterious mutations into fewer individuals results in a higher population mean fitness. Our results imply that mutation rate heterogeneity allows a population to maintain a higher level of adaptedness to its current environment, while simultaneously harboring greater genetic diversity in the standing variation, which could be crucial for future adaptation to a new environment. Our results also have implications for interpreting mutation rate estimates and mutant frequencies in data.

scholarly journals A genome-wide Approximate Bayesian Computation approach suggests only limited numbers of soft sweeps in humans over the last 100,000 years

2019 ◽  
Author(s):  
Guillaume Laval ◽  
Etienne Patin ◽  
Pierre Boutillier ◽  
Lluis Quintana-Murci
Keyword(s):  
Approximate Bayesian Computation ◽  
Population Data ◽  
Bayesian Computation ◽  
Selective Sweeps ◽  
Asian Populations ◽  
Standing Variation ◽  
Genome Wide ◽  
A Genome ◽  
Approximate Bayesian ◽  
False Discoveries

Over the last 100,000 years, humans have spread across the globe and encountered a highly diverse set of environments to which they have had to adapt. Genome-wide scans of selection are powerful to detect selective sweeps. However, because of unknown fractions of undetected sweeps and false discoveries, the numbers of detected sweeps often poorly reflect actual numbers of selective sweeps in populations. The thousands of soft sweeps on standing variation recently evidenced in humans have also been interpreted as a majority of mis-classified neutral regions. In such a context, the extent of human adaptation remains little understood. We present a new rationale to estimate these actual numbers of sweeps expected over the last 100,000 years (denoted by X) from genome-wide population data, both considering hard sweeps and selective sweeps on standing variation. We implemented an approximate Bayesian computation framework and showed, based on computer simulations, that such a method can properly estimate X. We then jointly estimated the number of selective sweeps, their mean intensity and age in several 1000G African, European and Asian populations. Our estimations of X, found weakly sensitive to demographic misspecifications, revealed very limited numbers of sweeps regardless the frequency of the selected alleles at the onset of selection and the completion of sweeps. We estimated ∼80 sweeps in average across fifteen 1000G populations when assuming incomplete sweeps only and ∼140 selective sweeps in non-African populations when incorporating complete sweeps in our simulations. The method proposed may help to address controversies on the number of selective sweeps in populations, guiding further genome-wide investigations of recent positive selection.

Sign in / Sign up

Export Citation Format

Share Document