Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals

ABSTRACTWhether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with the effective population size Ne. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species.We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover a weak negative correlation between ωa and θ at a larger taxonomic scale. This result is consistent with Fisher’s geometrical model predictions and suggests that the proportion of beneficial mutations scales negatively with species’ long-term Ne.

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Overestimation of the adaptive substitution rate in fluctuating populations

Biology Letters ◽

10.1098/rsbl.2018.0055 ◽

2018 ◽

Vol 14 (5) ◽

pp. 20180055 ◽

Cited By ~ 22

Author(s):

Marjolaine Rousselle ◽

Maeva Mollion ◽

Benoit Nabholz ◽

Thomas Bataillon ◽

Nicolas Galtier

Keyword(s):

Substitution Rate ◽

Population History ◽

Comparative Genomic ◽

Coding Sequences ◽

Potential Source ◽

Genomic Studies ◽

Demographic Fluctuations ◽

Fluctuating Populations ◽

Adaptive Substitution

Estimating the proportion of adaptive substitutions ( α ) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate α from patterns polymorphism and divergence in coding sequences. However, estimators of α can be biased when the underlying assumptions are not met. Here we focus on a potential source of bias, i.e. variation through time in the long-term population size ( N ) of the considered species. We show via simulations that ancient demographic fluctuations can generate severe overestimations of α , and this is irrespective of the recent population history.

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Counterbalancing the time-dependence effect on the Human Mitochondrial DNA Molecular Clock

10.21203/rs.2.17533/v3 ◽

2020 ◽

Author(s):

vicente M Cabrera

Keyword(s):

Mitochondrial Dna ◽

Molecular Clock ◽

Substitution Rate ◽

Demographic History ◽

Time Dependent ◽

Effective Population ◽

Modern Humans ◽

Human Mitochondrial Dna ◽

Dependent Effect ◽

Time Dependent Effect

Abstract Background: The molecular clock is an important genetic tool for estimating evolutionary timescales. However, the detection of a time-dependent effect on substitution rate estimates complicates its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study, I propose a new algorithm for estimating the coalescent age of phylogenetically related sequences, taking into account the observed time-dependent effect on the molecular rate detected by others.Results: By applying this method to real human mitochondrial DNA trees with shallow and deep topologies, I obtained significantly older molecular ages for the main events of human evolution than were previously estimated. These ages are in close agreement with the most recent archaeological and paleontological records favoring the emergence of early anatomically modern humans in Africa 315 ± 34 thousand years ago (kya) and the presence of recent modern humans outside of Africa as early as 174 ± 48 thousand years ago. Furthermore, during the implementation process, I demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size, which is in better accordance with the fact that under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift.Conclusions: I suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and I propose a new method that corrects for this effect.

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Viruses Without Borders: Global Analysis of the Population Structure, Haplotype Distribution, and Evolutionary Pattern of Iris Yellow Spot Orthotospovirus (Family Tospoviridae, Genus Orthotospovirus)

Frontiers in Microbiology ◽

10.3389/fmicb.2021.633710 ◽

2021 ◽

Vol 12 ◽

Author(s):

Afsha Tabassum ◽

S. V. Ramesh ◽

Ying Zhai ◽

Romana Iftikhar ◽

Cristian Olaya ◽

...

Keyword(s):

Genetic Diversity ◽

In Silico ◽

Substitution Rate ◽

Population Expansion ◽

Rflp Analysis ◽

Yellow Spot ◽

N Gene ◽

Gene Sequences ◽

Evolutionary Pattern ◽

Highest Posterior Density

Iris yellow spot, caused by Iris yellow spot orthotospovirus (IYSV) (Genus: Orthotospovirus, Family: Tospoviridae), is an important disease of Allium spp. The complete N gene sequences of 142 IYSV isolates of curated sequence data from GenBank were used to determine the genetic diversity and evolutionary pattern. In silico restriction fragment length polymorphism (RFLP) analysis, codon-based maximum likelihood studies, genetic differentiation and gene flow within the populations of IYSV genotypes were investigated. Bayesian phylogenetic analysis was carried out to estimate the evolutionary rate. In silico RFLP analysis of N gene sequences categorized IYSV isolates into two major genotypes viz., IYSV Netherlands (IYSVNL; 55.63%), IYSV Brazil (IYSVBR; 38.73%) and the rest fell in neither group [IYSV other (IYSVother; 5.63%)]. Phylogenetic tree largely corroborated the results of RFLP analysis and the IYSV genotypes clustered into IYSVNL and IYSVBR genotypes. Genetic diversity test revealed IYSVother to be more diverse than IYSVNL and IYSVBR. IYSVNL and IYSVBR genotypes are under purifying selection and population expansion, whereas IYSVother showed decreasing population size and hence appear to be under balancing selection. IYSVBR is least differentiated from IYSVother compared to IYSVNL genotype based on nucleotide diversity. Three putative recombinant events were found in the N gene of IYSV isolates based on RDP analysis, however, RAT substantiated two among them. The marginal likelihood mean substitution rate was 5.08 × 10–5 subs/site/year and 95% highest posterior density (HPD) substitution rate between 5.11 × 10–5 and 5.06 × 10–5. Findings suggest that IYSV continues to evolve using population expansion strategies. The substitution rates identified are similar to other plant RNA viruses.

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