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 Does effective population size affect rates of molecular evolution: mitochondrial data for host/parasite species pairs in bees suggests not

2021 ◽  
Author(s):  
Nahid Shokri Bousjein ◽  
Simon Tierney ◽  
Michael Gardner ◽  
Michael Schwarz
Keyword(s):  
Molecular Evolution ◽  
Population Size ◽  
Effective Population Size ◽  
Parasite Species ◽  
Mitochondrial Protein ◽  
Neutral Theory ◽  
Mitochondrial Genes ◽  
Social Parasite ◽  
Effective Population ◽  
Rates Of Molecular Evolution

Adaptive evolutionary theory argues that organisms with larger effective population size (Ne) should have higher rates of adaptive evolution and therefore greater capacity to win evolutionary arm races. However, in some certain cases species with much smaller Ne may be able to survive beside their opponents for an extensive evolutionary time. Neutral theory predicts that accelerated rates of molecular evolution in organisms with exceedingly small Ne is due to the effects of genetic drift and fixation of slightly deleterious mutations. We test this prediction in two obligate social parasite species and their respective host species from the bee tribe Allodapini. The parasites (genus Inquilina) have been locked into a tight coevolutionary arm races with their exclusive hosts (genus Exoneura) for ~15 million years, even though Inquilina exhibit Ne that are an order of magnitude smaller than their host. In this study, we compared rates of molecular evolution between host and parasite using nonsynonymous to synonymous substitution rate ratios (dN/dS) of eleven mitochondrial protein coding genes sequenced from transcriptomes. Tests of selection on mitochondrial genes indicated no significant differences between host and parasite dN/dS, with evidence for purifying selection acting on all mitochondrial genes of host and parasite species. Several potential factors which could weaken the inverse relationship between Ne and rate of molecular evolution are discussed.

scholarly journals Background selection theory overestimates effective population size for high mutation rates

2022 ◽  
Author(s):  
Joseph D Matheson ◽  
Joanna Masel
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Deleterious Mutation ◽  
Neutral Theory ◽  
Mutation Rates ◽  
Background Selection ◽  
Effective Population ◽  
Selection Theory ◽  
Linkage Disequilibria ◽  
Genome Wide

Simple models from the neutral theory of molecular evolution are claimed to be flexible enough to incorporate the complex effects of background selection against linked deleterious mutations. Complexities are collapsed into an "effective" population size that specifies neutral genetic diversity. To achieve this, current background selection theory assumes linkage equilibrium among deleterious variants. Data do not support this assumption, nor do theoretical considerations when the genome-wide deleterious mutation is realistically high. We simulate genomes evolving under background selection, allowing the emergence of linkage disequilibria. With realistically high deleterious mutation rates, neutral diversity is much lower than predicted from previous analytical theory.

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 Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)

2020 ◽  
Vol 12 (2) ◽  
pp. 3803-3817 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Neutral Theory ◽  
Effective Population ◽  
Low Genetic Diversity

Abstract Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals Reconstructing the history of variation in effective population size along phylogenies

2019 ◽  
Author(s):  
Mathieu Brevet ◽  
Nicolas Lartillot
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Shape Parameter ◽  
Current Knowledge ◽  
Neutral Theory ◽  
Effective Population ◽  
Phylogenetic Structure ◽  
Frequency Spectra ◽  
Nearly Neutral Theory ◽  
History Of

AbstractThe nearly-neutral theory predicts specific relations between effective population size (Ne), and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward since Ne is difficult to estimate in practice. For that reason, indirect proxies for Ne have often been used to test the nearly-neutral theory, although with mixed results. Here, we introduce an integrative comparative framework allowing for an explicit reconstruction of the phylogenetic history of Ne, thus leading to a quantitative test of the nearly-neutral theory and an independent estimation of the shape parameter of the DFE. We applied our method to primates, for which the nearly-neutral predictions were mostly verified. Estimates of the shape parameter were compatible with independent measures based on site frequency spectra. The reconstructed history of Ne in primates seems consistent with current knowledge and shows a clear phylogenetic structure at the super-family level. Altogether, our integrative framework provides a quantitative assessment of the role of Ne in modulating patterns of genetic variation, while giving a synthetic picture of the long-term trends in Ne variation across a group of species.

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