Evolution and Genetic Dynamics

The paper shows that cellular adaptability is shaped by evolutionary history through a prioritization hierarchy of transcriptional responses to environmental cues.

This paper develops a theoretical framework to predict evolutionary dynamics in structured populations by integrating invasion determinants with a compressed ecological model.

The paper reassesses the positive growth effects of random sequence clones in E. coli, showing some clones confer genuine fitness advantages independent of vector artifacts or clone competition.

The paper integrates genotype-to-phenotype maps into ecological models to develop an ecology of metagenomes, revealing gene-level dynamics and metagenomic hitchhiking.

The paper analyzes selective pressures on virus-targeted host proteins by integrating PPI data and residue contacts, revealing spatial patterns of positive and negative selection across interaction interfaces.

The paper develops a hybrid model showing that recombinant viral lineages succeed based on timing and parental population dynamics, not just fitness.

This study uses experimental evolution to reduce yeast cell size and identifies genetic factors contributing to cell size regulation.

This paper proposes a topological framework explaining the origin of organismal forms through interfaces with the environment, validated by cross-kingdom empirical data.

This study investigates how modular genotype-phenotype-fitness maps constrain trait evolution, showing that modular systems reach a module-selection balance where traits improve at the same rate.

This study develops a unified Wright-Fisher model to analyze mutation fate on Y chromosomes and autosomes, showing overdominant mutations are more likely to fix on Y chromosomes due to segregation time effects.

This study shows that habitat reconstruction and genome mutation can equally increase bacterial fitness through experimental evolution and active learning.

The paper presents a simulation model demonstrating nonrandom, non-Lamarckian mutation in evolution using an estimation-of-distribution algorithm, highlighting the role of internal genomic information integration.

This study shows that unilateral cross-feeding interactions constrain adaptive evolution in both producer and consumer microbes, even when the producer experiences no direct fitness effects.

This study shows that genome architecture and gene-gene interactions influence the repeatability of polygenic adaptation in two copepod species with different chromosome numbers.

WINDEX improves detection of positive selective sweeps by integrating site- and window-based statistics in population genetic data, showing improved localization and genome-wide estimates of selective pressures.

This study shows that thermal adaptation across yeast species involves convergent changes in conserved regulatory networks, despite divergent phenotypic outcomes.

This study uses simulations to show that beneficial microbes, rather than parasites, drive the evolution and maintenance of adaptive immunity by reducing selection pressure on innate immunity.

This study evolves a plant RNA virus in age-diverse host populations and finds that host age structure drives virulence evolution by shaping disease progression, severity, and viral load.

This study investigates how genotype-to-phenotype architecture influences biodiversity dynamics in multilayer networks, showing that correlated and modular architectures affect diversity under different ecological conditions.

The paper uses a simplified Rough Mount Fuji model to show that adaptive walks on multi-peaked fitness landscapes can reach high-ranking peaks due to specific landscape features.

This study traces how natural selection on SARS-CoV-2 has shifted during the pandemic, favoring antibody escape and ACE2 binding, with dynamic pressures across antibody classes.

The paper shows that the history of symbiosis affects the evolutionary trajectory of hosts even after symbionts are removed in experimentally evolved amoebas.

The paper identifies deleterious mutations in sugar beet by combining evolutionary models and deep learning, showing a decline in genetic load over time due to breeding.

The paper examines recombination rates and linked selection efficiency in small and large stickleback populations, finding higher recombination in a small freshwater population and a polygenic basis for recombination rates.

This study models multicellular life cycles using intrinsic information sources and finds inherent trade-offs between flexibility and regularity in their regulation.

The paper shows that diverse microbial communities enable coexistence of closely-related strains through community-mediated feedbacks that equalize and stabilize their dynamics.

This study compares population genetics and adaptive dynamics frameworks to predict species interaction evolution, showing discrepancies in two-species competition models due to mutation supply, effect sizes, and population size.

The paper quantifies selection efficiency across Escherichia coli lineages by linking mutation scores to population genetics, showing significant variation in selection intensity between synonymous and non-synonymous mutations and pathogenic populations.

The paper investigates interallelic cis-regulatory dominance in Drosophila, showing it promotes robustness by masking deleterious variants and enables evolutionary innovation through cell-type-specific activity.

The paper investigates whether cheater nuclei in filamentous fungi can increase in frequency by exploiting public goods, and how this affects virulence and antifungal resistance.