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Beneficial Mutation–Selection Balance and the Effect of Linkage on Positive Selection
The results imply that mutator phenotypes are less effective in larger asexual populations, and have consequences for the advantages (or disadvantages) of sex via the Fisher–Muller effect.
The Speed of Evolution and Maintenance of Variation in Asexual Populations
The rate at which asexual populations cross fitness valleys.
High-Throughput Sequencing of the Zebrafish Antibody Repertoire
High-throughput sequencing of the variable domain of the antibody heavy chain from 14 zebrafish is used to provide insight into the breadth of the expressed antibody repertoire and immunological diversity at the level of an individual organism.
Quantitative evolutionary dynamics using high-resolution lineage tracking
- Sasha F. Levy, J. Blundell, S. Venkataram, D. Petrov, D. S. Fisher, G. Sherlock
- 12 March 2015
It is found that the spectrum of fitness effects of beneficial mutations is neither exponential nor monotonic, and early adaptation is a predictable consequence of this spectrum and is strikingly reproducible, but the initial small-effect mutations are soon outcompeted by rarer large- effect mutations that result in variability between replicates.
Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination
Global analysis of the immune system’s clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects, using high-throughput long read sequencing to characterize the human antibody response after influenza vaccination.
The Rate of Fitness-Valley Crossing in Sexual Populations
This work presents a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes and finds that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombinations slow down valley crossing.
Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche
Deep sequencing of a thermophilic cyanobacterial population and analysis of the statistics of synonymous single-nucleotide polymorphisms revealed a high rate of homologous recombination and departures from neutral drift consistent with the effects of genetic hitchhiking.
Denoising PCR-amplified metagenome data
A new denoising algorithm that is more accurate and over an order of magnitude faster than AmpliconNoise is introduced, which eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates.
Rate of Adaptation in Large Sexual Populations
The rate of adaptation, v, is calculated in several models of such sexual populations and it is shown that v is linear in NUb only in sufficiently small populations, and acceleration of adaptation by recombination implies a strong evolutionary advantage of sex.