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Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory.

ABSTRACT: Adaptation, where a population evolves increasing fitness in a fixed environment, is typically thought of as a hill-climbing process on a fitness landscape. With a finite genome, such a process eventually leads the population to a fitness peak, at which point fitness can no longer increase through individual beneficial mutations. Instead, the ruggedness of typical landscapes due to epistasis between genes or DNA sites suggests that the accumulation of multiple mutations (via a process known as stochastic tunneling) can allow a population to continue increasing in fitness. However, it is not clear how such a phenomenon would affect long-term fitness evolution. By using a spin-glass type model for the fitness function that takes into account microscopic epistasis, we find that hopping between metastable states can mechanistically and robustly give rise to a slow, logarithmic average fitness trajectory.

SUBMITTER: Guo Y

PROVIDER: S-EPMC6669011 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory.

Guo Yipei Y Vucelja Marija M Amir Ariel A

Science advances 20190731 7

Adaptation, where a population evolves increasing fitness in a fixed environment, is typically thought of as a hill-climbing process on a fitness landscape. With a finite genome, such a process eventually leads the population to a fitness peak, at which point fitness can no longer increase through individual beneficial mutations. Instead, the ruggedness of typical landscapes due to epistasis between genes or DNA sites suggests that the accumulation of multiple mutations (via a process known as s ...[more]

PMID: 31392265

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Project description:BackgroundSingle nucleotide substitutions in protein-coding genes can be divided into synonymous (S), with little fitness effect, and non-synonymous (N) ones that alter amino acids and thus generally have a greater effect. Most of the N substitutions are affected by purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases potentially could alleviate the deleterious effect of single substitutions, making them subject to positive selection. To elucidate the effects of selection on double substitutions in all codons, it is critical to differentiate selection from mutational biases.ResultsWe addressed the evolutionary regimes of within-codon double substitutions in 37 groups of closely related prokaryotic genomes from diverse phyla by comparing the fractions of double substitutions within codons to those of the equivalent double S substitutions in adjacent codons. Under the assumption that substitutions occur one at a time, all within-codon double substitutions can be represented as "ancestral-intermediate-final" sequences (where "intermediate" refers to the first single substitution and "final" refers to the second substitution) and can be partitioned into four classes: (1) SS, S intermediate-S final; (2) SN, S intermediate-N final; (3) NS, N intermediate-S final; and (4) NN, N intermediate-N final. We found that the selective pressure on the second substitution markedly differs among these classes of double substitutions. Analogous to single S (synonymous) substitutions, SS double substitutions evolve neutrally, whereas analogous to single N (non-synonymous) substitutions, SN double substitutions are subject to purifying selection. In contrast, NS show positive selection on the second step because the original amino acid is recovered. The NN double substitutions are heterogeneous and can be subject to either purifying or positive selection, or evolve neutrally, depending on the amino acid similarity between the final or intermediate and the ancestral states.ConclusionsThe results of the present, comprehensive analysis of the evolutionary landscape of within-codon double substitutions reaffirm the largely conservative regime of protein evolution. However, the second step of a double substitution can be subject to positive selection when the first step is deleterious. Such positive selection can result in frequent crossing of valleys on the fitness landscape.

Project description:ImportanceIndividuals with total joint arthroplasty (TJA) have long-term exposure to metal-containing implants; however, whether long-term exposure to artificial implants is associated with cognitive function is unknown.ObjectiveTo compare long-term cognitive trajectories in individuals with and without TJA.Design, setting, and participantsThis population-based cohort study assessed serial cognitive evaluations of 5550 participants (≥50 years of age) from the Mayo Clinic Study of Aging between November 1, 2004, and December 31, 2020.ExposuresTotal joint arthroplasty of the hip or the knee.Main outcomes and measuresLinear mixed-effects models were used to compare the annualized rate of change in global and domain-specific cognitive scores in participants with and without TJA, adjusting for age, sex, educational level, apolipoprotein E ε4 carrier status, and cognitive test practice effects.ResultsA total of 5550 participants (mean [SD] age at baseline, 73.04 [10.02] years; 2830 [51.0%] male) were evaluated. A total of 952 participants had undergone at least 1 TJA of the hip (THA, n = 430) or the knee (TKA, n = 626) before or after entry into the cohort. Participants with TJA were older, more likely to be female, and had a higher body mass index than participants without TJA. No difference was observed in the rate of cognitive decline in participants with and without TJA until 80 years of age. A slightly faster cognitive decline at 80 years or older and more than 8 years from surgery was observed (b = -0.03; 95% CI, -0.04 to -0.02). In stratified analyses by surgery type, the faster decline was observed primarily among older participants with TKA (b = -0.04; 95% CI, -0.06 to -0.02).Conclusions and relevanceIn this cohort study, long-term cognitive trajectories in individuals with and without TJA were largely similar except for a slightly faster decline among the oldest patients with TKA; however, the magnitude of difference was small and of unknown clinical significance.

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Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory.

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Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory.

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