scholarly journals Soft selective sweeps in complex demographic scenarios

2014 ◽  
Author(s):  
Benjamin A Wilson ◽  
Dmitri Petrov ◽  
Philipp W Messer
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
De Novo ◽  
Analytical Framework ◽  
De Novo Mutation ◽  
Selective Sweeps ◽  
Effective Population ◽  
Weak Selection ◽  
Adaptive Mutations ◽  
Soft Selective Sweeps

Recent studies have shown that adaptation from de novo mutation often produces so-called soft selective sweeps, where adaptive mutations of independent mutational origin sweep through the population at the same time. Population genetic theory predicts that soft sweeps should be likely if the product of the population size and the mutation rate towards the adaptive allele is sufficiently large, such that multiple adaptive mutations can establish before one has reached fixation; however, it remains unclear how demographic processes affect the probability of observing soft sweeps. Here we extend the theory of soft selective sweeps to realistic demographic scenarios that allow for changes in population size over time. We first show that population bottlenecks can lead to the removal of all but one adaptive lineage from an initially soft selective sweep. The parameter regime under which such 'hardening' of soft selective sweeps is likely is determined by a simple heuristic condition. We further develop a generalized analytical framework, based on an extension of the coalescent process, for calculating the probability of soft sweeps under arbitrary demographic scenarios. Two important limits emerge within this analytical framework: In the limit where population size fluctuations are fast compared to the duration of the sweep, the likelihood of soft sweeps is determined by the harmonic mean of the variance effective population size estimated over the duration of the sweep; in the opposing slow fluctuation limit, the likelihood of soft sweeps is determined by the instantaneous variance effective population size at the onset of the sweep. We show that as a consequence of this finding the probability of observing soft sweeps becomes a function of the strength of selection. Specifically, in species with sharply fluctuating population size, strong selection is more likely to produce soft sweeps than weak selection. Our results highlight the importance of accurate demographic estimates over short evolutionary timescales for understanding the population genetics of adaptation from de novo mutation.

scholarly journals Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors

2020 ◽  
Vol 38 (1) ◽  
pp. 244-262
Author(s):  
Alexander T Ho ◽  
Laurence D Hurst
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Stop Codon ◽  
Neutral Theory ◽  
Error Rates ◽  
Species Variation ◽  
Effective Population ◽  
Weak Selection ◽  
Error Mitigation ◽  
Good Proxy

Abstract In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.

scholarly journals Evidence that the rate of strong selective sweeps increases with population size in the great apes

2017 ◽  
Vol 114 (7) ◽  
pp. 1613-1618 ◽  
Author(s):  
Kiwoong Nam ◽  
Kasper Munch ◽  
Thomas Mailund ◽  
Alexander Nater ◽  
Maja Patricia Greminger ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Large Population ◽  
Great Apes ◽  
Genomic Diversity ◽  
Comparative Approach ◽  
Selective Sweeps ◽  
Effective Population ◽  
Intergenic Sequences ◽  
The Right

Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.

scholarly journals The global impact of Wolbachia on mitochondrial diversity and evolution

2017 ◽  
Author(s):  
Marie Cariou ◽  
Laurent Duret ◽  
Sylvain Charlat
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Synonymous Substitution ◽  
Selective Sweeps ◽  
Effective Population ◽  
Widespread Distribution ◽  
Global Impact ◽  
Synonymous Substitution Rates ◽  
Extinction Events

AbstractThe spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. Although suggested by a few case studies, the global consequences of this process on mitochondrial diversity and evolution remains to be assessed. Here we address this question using a mapping of Wolbachia acquisition / extinction events on a large mitochondrial DNA tree, including over 1,000 species. We show that the presence of Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in non-synonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red-queen-like cytonuclear coevolution through the fixation of deleterious mitochondrial alleles.

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