scholarly journals Unpacking conditional neutrality: genomic signatures of selection on conditionally beneficial and conditionally deleterious mutations

2019 ◽  
Author(s):  
Jonathan A. Mee ◽  
Samuel Yeaman
Keyword(s):  
Allele Frequency ◽  
Local Adaptation ◽  
Home Environment ◽  
Cumulative Effect ◽  
Antagonistic Pleiotropy ◽  
Deleterious Mutations ◽  
Genome Scans ◽  
Beneficial Mutations ◽  
Local Environments ◽  
Non Local

AbstractIt is common to look for signatures of local adaptation in genomes by identifying loci with extreme levels of allele frequency divergence among populations. This approach to finding genes associated with local adaptation often assumes antagonistic pleiotropy, wherein alternative alleles are strongly favoured in alternative environments. Conditional neutrality has been proposed as an alternative to antagonistic pleiotropy, but conditionally neutral polymorphisms are transient and it is unclear how much outlier signal would be maintained under different forms of conditional neutrality. Here, we use individual-based simulations and a simple analytical heuristic to show that a pattern that mimics local adaptation at the phenotypic level, where each genotype has the highest fitness in its home environment, can be produced by the accumulation of mutations that are neutral in their home environment and deleterious in non-local environments. Because conditionally deleterious mutations likely arise at a rate many times higher than conditionally beneficial mutations, they can have a significant cumulative effect on fitness even when individual effect sizes are small. We show that conditionally deleterious mutations driving non-local maladaptation may be undetectable by even the most powerful genome scans, as differences in allele frequency between populations are typically small. We also explore the evolutionary effects of conditionally-beneficial mutations and find that they can maintain significant signals of local adaptation, and they would be more readily detectable than conditionally deleterious mutations using conventional genome scan approaches. We discuss implications for interpreting outcomes of transplant experiments and genome scans that are used to study the genetic basis of local adaptation.

scholarly journals Background selection and the statistics of population differentiation: consequences for detecting local adaptation

2018 ◽  
Author(s):  
Remi Matthey-Doret ◽  
Michael C. Whitlock
Keyword(s):  
Local Adaptation ◽  
Dna Sequences ◽  
Population Differentiation ◽  
False Positive Rate ◽  
Parameter Estimates ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Genome Scans ◽  
Positive Rate

AbstractBackground selection is a process whereby recurrent deleterious mutations cause a decrease in the effective population size and genetic diversity at linked loci. Several authors have suggested that variation in the intensity of background selection could cause variation in FST across the genome, which could confound signals of local adaptation in genome scans. We performed realistic simulations of DNA sequences, using parameter estimates from humans and sticklebacks, to investigate how variation in the intensity of background selection affects different statistics of population differentiation. We show that, in populations connected by gene flow, Weir & Cockerham’s (1984) estimator of FST is largely insensitive to locus-to-locus variation in the intensity of background selection. Unlike FST, however, dXY is negatively correlated with background selection. We also show that background selection does not greatly affect the false positive rate in FST outlier studies. Overall, our study indicates that background selection will not greatly interfere with finding the variants responsible for local adaptation.

scholarly journals Selfish Genes, Pleiotropy and the Origin of Recombination

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2089-2097 ◽  
Author(s):  
Jody Hey
Keyword(s):  
Natural Selection ◽  
Simple Model ◽  
Computer Simulations ◽  
Recombination Rate ◽  
Evolutionary Origin ◽  
Deleterious Mutations ◽  
Beneficial Mutations ◽  
Selfish Genes ◽  
Simple Interaction

Abstract If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination.

scholarly journals Molecularly Controlled Catalysis – Targeting Synergies Between Local and Non‐local Environments

ChemCatChem ◽  
2020 ◽  
Author(s):  
Basujit Chatterjee ◽  
Wei‐Chieh Chang ◽  
Christophe Werlé
Keyword(s):  
Local Environments ◽  
Non Local

scholarly journals The Advantages of Segregation and the Evolution of Sex

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1099-1118 ◽  
Author(s):  
Sarah P Otto
Keyword(s):  
Sexual Reproduction ◽  
Asexual Reproduction ◽  
Deleterious Mutations ◽  
Evolution Of Sex ◽  
Beneficial Mutations ◽  
Selection Regime ◽  
Strong Selection ◽  
Genome Wide ◽  
Low Levels

AbstractIn diploids, sexual reproduction promotes both the segregation of alleles at the same locus and the recombination of alleles at different loci. This article is the first to investigate the possibility that sex might have evolved and been maintained to promote segregation, using a model that incorporates both a general selection regime and modifier alleles that alter an individual’s allocation to sexual vs. asexual reproduction. The fate of different modifier alleles was found to depend strongly on the strength of selection at fitness loci and on the presence of inbreeding among individuals undergoing sexual reproduction. When selection is weak and mating occurs randomly among sexually produced gametes, reductions in the occurrence of sex are favored, but the genome-wide strength of selection is extremely small. In contrast, when selection is weak and some inbreeding occurs among gametes, increased allocation to sexual reproduction is expected as long as deleterious mutations are partially recessive and/or beneficial mutations are partially dominant. Under strong selection, the conditions under which increased allocation to sex evolves are reversed. Because deleterious mutations are typically considered to be partially recessive and weakly selected and because most populations exhibit some degree of inbreeding, this model predicts that higher frequencies of sex would evolve and be maintained as a consequence of the effects of segregation. Even with low levels of inbreeding, selection is stronger on a modifier that promotes segregation than on a modifier that promotes recombination, suggesting that the benefits of segregation are more likely than the benefits of recombination to have driven the evolution of sexual reproduction in diploids.

scholarly journals SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

2022 ◽  
Author(s):  
Tiago da Silva Ribeiro ◽  
José A Galván ◽  
John E Pool
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Genetic Variant ◽  
Real Data ◽  
Selective Sweeps ◽  
Functional Categories ◽  
Genome Scans ◽  
Genome Wide ◽  
A Genome ◽  
Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

scholarly journals Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data

2016 ◽  
Author(s):  
Paula Tataru ◽  
Maéva Mollion ◽  
Sylvain Glemin ◽  
Thomas Bataillon
Keyword(s):  
Molecular Evolution ◽  
Evolutionary Genetics ◽  
Deleterious Mutations ◽  
Probabilistic Framework ◽  
Evolutionary Trajectory ◽  
Beneficial Mutations ◽  
Fitness Effects ◽  
Polymorphism Data ◽  
Inference Methods ◽  
Biased Estimates

ABSTRACTThe distribution of fitness effects (DFE) encompasses deleterious, neutral and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (α). Inference of DFE and α from patterns of polymorphism (SFS) and divergence data has been a longstanding goal of evolutionary genetics. A widespread assumption shared by numerous methods developed so far to infer DFE and α from such data is that beneficial mutations contribute only negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and α is only predicted by contrasting the SFS with divergence data from an outgroup. Here, we develop a hierarchical probabilistic framework that extends on previous methods and also can infer DFE and α from polymorphism data alone. We use extensive simulations to examine the performance of our method. We show that both a full DFE, comprising both deleterious and beneficial mutations, and α can be inferred without resorting to divergence data. We demonstrate that inference of DFE from polymorphism data alone can in fact provide more reliable estimates, as it does not rely on strong assumptions about a shared DFE between the outgroup and ingroup species used to obtain the SFS and divergence data. We also show that not accounting for the contribution of beneficial mutations to polymorphism data leads to substantially biased estimates of the DFE and α. We illustrate these points using our newly developed framework, while also comparing to one of the most widely used inference methods available.

scholarly journals Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau

2021 ◽  
Vol 118 (17) ◽  
pp. e2017831118
Author(s):  
Qingyun Liu ◽  
Haican Liu ◽  
Li Shi ◽  
Mingyu Gan ◽  
Xiuqin Zhao ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Local Adaptation ◽  
Population Genomics ◽  
Genetic Evidence ◽  
The Tibetan Plateau ◽  
Lower Altitude ◽  
Local Environments ◽  
Plausible Model ◽  
Genes Encoding

During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host–pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.

scholarly journals Dynamics and Fate of Beneficial Mutations Under Lineage Contamination by Linked Deleterious Mutations

Genetics ◽  
2017 ◽  
Vol 205 (3) ◽  
pp. 1305-1318 ◽  
Author(s):  
Sophie Pénisson ◽  
Tanya Singh ◽  
Paul Sniegowski ◽  
Philip Gerrish
Keyword(s):  
Deleterious Mutations ◽  
Beneficial Mutations

scholarly journals A Simple Model of Unbounded Evolutionary Versatility as a Largest-Scale Trend in Organismal Evolution

2000 ◽  
Vol 6 (2) ◽  
pp. 109-128 ◽  
Author(s):  
Peter D. Turney
Keyword(s):  
Natural Selection ◽  
Simple Model ◽  
Computational Model ◽  
Local Adaptation ◽  
Large Scale ◽  
Changing Environment ◽  
Local Environments ◽  
Global Trend ◽  
Evolutionary Pace ◽  
Biological Organisms

The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model.

scholarly journals Dissection of the mutation accumulation process during bacterial range expansions

2020 ◽  
Author(s):  
Lars Bosshard ◽  
Stephan Peischl ◽  
Martin Ackermann ◽  
Laurent Excoffier
Keyword(s):  
Colony Size ◽  
Evolutionary Dynamics ◽  
Early Stage ◽  
Whole Genome ◽  
Spatial Expansion ◽  
Deleterious Mutations ◽  
Evolutionary Processes ◽  
Temporal Perspective ◽  
Linear Change ◽  
Beneficial Mutations

Abstract Background Recent experimental work has shown that the evolutionary dynamics of bacteria expanding across space can differ dramatically from what we expect under well-mixed conditions. During spatial expansion, deleterious mutations can accumulate due to inefficient selection on the expansion front, potentially interfering with and modifying adaptive evolutionary processes. Results We used whole genome sequencing to follow the genomic evolution of 10 mutator Escherichia coli lines during 39 days (∼1650 generations) of a spatial expansion, which allowed us to gain a temporal perspective on the interaction of adaptive and non-adaptive evolutionary processes during range expansions. We used elastic net regression to infer the positive or negative effects of mutations on colony growth. The colony size, measured after three day of growth, decreased at the end of the experiment in all 10 lines, and mutations accumulated at a nearly constant rate over the whole experiment. We find evidence that beneficial mutations accumulate primarily at an early stage of the experiment, leading to a non-linear change of colony size over time. Indeed, the rate of colony size expansion remains almost constant at the beginning of the experiment and then decreases after ∼12 days of evolution. We also find that beneficial mutations are enriched in genes encoding transport proteins, and genes coding for the membrane structure, whereas deleterious mutations show no enrichment for any biological process. Conclusions Our experiment shows that beneficial mutations target specific biological functions mostly involved in inter or extra membrane processes, whereas deleterious mutations are randomly distributed over the whole genome. It thus appears that the interaction between genetic drift and the availability or depletion of beneficial mutations determines the change in fitness of bacterial populations during range expansion.

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