Evolution and Genetic Dynamics

The paper constructs marked Neurospora crassa strains and develops a Bayesian method to estimate fitness in competition experiments, showing fitness differences related to mating type and a qde-2 mutation.

This paper introduces a new method to jointly estimate population size and sampling intensity dynamics from molecular sequences, showing improved accuracy over existing methods.

The paper models how the microbiome contributes to phenotype heritability by showing that host-microbiota interactions increase phenotypic variability and reduce missing heritability.

This study identifies deleterious mutations in Wrangel Island mammoths and shows their potential functional impacts on development, fertility, and sensory abilities.

The paper investigates the evolutionary history of the CDHR3 locus, finding that the protective variant against RV-C and asthma has been subject to selection in recent human evolution, though not as a classical selective sweep.

This paper develops algorithms to reconstruct clonal evolution from time course genomic sequencing data, achieving accurate results on both simulated and experimental data.

The paper identifies that both epistasis and physical linkage can drive correlated evolution detected computationally under antibiotic selection in Pseudomonas aeruginosa.

The paper compares parametric approximations to the Wright-Fisher model for inferring selection from genetic time series and finds the Beta-with-Spikes model performs best.

This study identifies beneficial alleles lost through LOH in yeast hybrids, showing how LOH can drive adaptation to new environments.

The paper shows that toxic environments with resource-waste dynamics promote cellular diversity through metabolic tradeoffs and spatial interactions.

The paper studies epistasis in a fluorescent protein by analyzing mutations linking two phenotypically distinct variants, revealing high-order interactions and sparse patterns.

This paper introduces an approximate full-likelihood method to infer selection and allele frequency trajectories from DNA sequence data, showing improved power to detect selection compared to existing methods.

The paper shows that changes in gene expression alter the strength and direction of genetic interactions between mutations in many genes.

GEMME predicts mutational effects by modeling evolutionary history, outperforming existing methods in speed and accuracy for viral and conserved sequences.

The paper quantifies reproductive success variability in bacterial populations and finds heavy-tailed offspring distributions due to stochastic dormancy exits.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

The paper models mutation dispersion in populations, estimating selective advantages using Dunbar's number and observed mutation prevalence.

This study shows that salicylate increases the fitness cost of MarA-mediated antibiotic resistance, leading to the rapid exclusion of resistant bacteria from mixed populations.

The paper develops a Bayesian method to detect host influences on pathogen evolution using large datasets, demonstrating improved precision in identifying HLA-induced selection in HIV-1.

This study shows desiccation increases recombination and interference in Drosophila melanogaster, with effects more pronounced in desiccation-sensitive genotypes, suggesting fitness-dependent plasticity in recombination.

This paper clarifies how convergent adaptive evolution manifests in coding sequences, reviews detection methods, and evaluates their power through simulations.

The paper investigates adaptive dependencies between enzymes in bacterial folate metabolism, showing that DHFR and TYMS form a modular unit that can adapt independently from the rest of the genome.

The paper shows that epistasis can be detected in genomic data within a narrow parameter window, but is masked by linkage outside this range unless recombination is strong.

The paper quantifies GC-biased gene conversion in great ape genomes using a new polymorphism-aware model that accounts for allelic selection and demography.

This study shows cis-regulatory changes predominantly drive gene expression divergence in sticklebacks, with parallel expression patterns linked to adaptive genomic regions and natural selection.

The paper investigates how proteostasis machinery influences higher-order epistasis in antibiotic resistance traits across different bacterial species.

The paper assesses the applicability of the mutation-selection balance model to human protein-truncating variants using simulations and data from exome datasets.

The paper estimates the probability that protein genes navigate fitness valleys during human evolution, finding that small protein motifs cross valleys of depth 2Ns ≳ 30 with probability ≳ 0.1.

The paper shows that the giant duckweed has extremely low genetic diversity due to its exceptionally low mutation rate despite a large population size.

The paper compares codon models that account for substitution rate variation and finds that ignoring rate variation leads to many false positives in positive selection detection.