scholarly journals Population genomics of rapid adaptation by soft selective sweeps

2013 ◽  
Vol 28 (11) ◽  
pp. 659-669 ◽  
Author(s):  
Philipp W. Messer ◽  
Dmitri A. Petrov
Keyword(s):  
Population Genomics ◽  
Selective Sweeps ◽  
Rapid Adaptation ◽  
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 Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

2019 ◽  
Author(s):  
Anna Tigano ◽  
Jocelyn P. Colella ◽  
Matthew D. MacManes
Keyword(s):  
North America ◽  
Population Genomics ◽  
Protein Denaturation ◽  
Gene Families ◽  
Small Rodent ◽  
Selective Sweeps ◽  
Cellular Mechanisms ◽  
Dietary Shift ◽  
Recent Emergence ◽  
Signature Of Selection

AbstractOrganisms that live in deserts offer the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for organisms living there. The cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration. To investigate the genomic basis of desert adaptation in cactus mice, we built a chromosome-level genome assembly and resequenced 26 additional cactus mouse genomes from two locations in southern California (USA). Using these data, we integrated comparative, population, and functional genomic approaches. We identified 16 gene families exhibiting significant contractions or expansions in the cactus mouse compared to 17 other Myodontine rodent genomes, and found 232 sites across the genome associated with selective sweeps. Functional annotations of candidate gene families and selective sweeps revealed a pervasive signature of selection at genes involved in the synthesis and degradation of proteins, consistent with the evolution of cellular mechanisms to cope with protein denaturation caused by thermal and hyperosmotic stress. Other strong candidate genes included receptors for bitter taste, suggesting a dietary shift towards chemically defended desert plants and insects, and a growth factor involved in lipid metabolism, potentially involved in prevention of dehydration. Understanding how species adapted to the recent emergence of deserts in North America will provide an important foundation for predicting future evolutionary responses to increasing temperatures, droughts and desertification in the cactus mouse and other species.

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

2017 ◽  
Author(s):  
Joachim Hermisson ◽  
Pleuni S Pennings
Keyword(s):  
Model Development ◽  
Rapid Evolution ◽  
Theoretical Models ◽  
List Type ◽  
Selective Sweeps ◽  
Rapid Adaptation ◽  
Contrast Model ◽  
Theoretical Concepts ◽  
Complex Adaptive

AbstractThe tempo and mode of adaptive evolution determine how natural selection shapes patterns of genetic diversity in DNA polymorphism data. While slow mutation-limited adaptation leads to classical footprints of “hard” selective sweeps, these patterns are different when adaptation responds quickly to a novel selection pressure, acting either on standing genetic variation or on recurrent new mutation. In the past decade, corresponding footprints of “soft” selective sweeps have been described both in theoretical models and in empirical data.Here, we summarize the key theoretical concepts and contrast model predictions with observed patterns in Drosophila, humans, and microbes.Evidence in all cases shows that “soft” patterns of rapid adaptation are frequent. However, theory and data also point to a role of complex adaptive histories in rapid evolution.While existing theory allows for important implications on the tempo and mode of the adaptive process, complex footprints observed in data are, as yet, insufficiently covered by models. They call for in-depth empirical study and further model development.

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

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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