Evolution and Genetic Dynamics

Between Friends and Foes: Evolutionary Diversification in Mutualistic-Antagonistic Networks

The paper uses an eco-evolutionary model to show how mutualism and antagonism interact to influence diversification in ecological networks, finding that trait correlation affects diversification rates across guilds.

Pervasive cryptic selection in the human noncoding genome

This study detects pervasive cryptic negative selection in human noncoding regions using a statistical test, finding that at least 7% of the genome is under negative selection, surpassing previous estimates from conservation-based methods.

The Gene Version Iteration Hypothesis reveals the Y chromosome-mediated closed-loop transmission and version selection mechanism of mutated genes

The paper proposes the Gene Version Iteration Hypothesis, suggesting mutant genes may cycle through chromosomes via the Y and X chromosomes, enabling version selection and evolutionary dynamics.

Evolution of an Aurora Kinase A Inhibitor from an Essential tRNA Synthetase

The paper shows how a duplicated tRNA synthetase evolved into a novel toxin by losing its ancestral function and acquiring a new role in targeting Aurora kinase A.

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The paper analyzes selection pressures on mammalian extracellular matrix proteins across species and develops an open-access browser to visualize evolutionary dynamics.

Mutation-biased adaptation is consequential even in large bacterial populations

This study shows mutation-biased adaptation can intensify in large bacterial populations and lead to unpredictable collateral sensitivity to antibiotics.

What sets the mutation rate of a cell type in an animal species?

The paper reviews patterns and theories on how natural selection shapes mutation rates in animal germline and somatic cells across species.

Evidence that many prokaryotic accessory genes are adaptive.

The paper tests whether prokaryotic accessory genes are adaptive by analyzing the ratio of non-synonymous to synonymous diversity in two bacterial species.

Additive Channels in Curved Fitness Landscapes

The paper introduces an additivity index [A]g to quantify local fitness landscape curvature and identifies additive channels where linear genetic predictions are effective for short-term evolutionary response.

Correcting for Global Synonymous Selection Improves the Accuracy of Episodic Positive Selection Inference

This paper shows that accounting for global synonymous selection improves the accuracy of detecting episodic positive selection in protein evolution.

Constraining pesticide resistance using evolution-informed selection regimes

This study tests how pesticide deployment regimes affect resistance evolution in C. elegans, finding that compound mixtures with refuge most effectively constrain resistance.

Replaying germinal center evolution on a quantified affinity landscape

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

Adaptive laboratory evolution of a minimal cell to low temperature

This study evolves a minimal genome bacterium to grow at a lower temperature, revealing genetic and non-genetic adaptation mechanisms.

Genetic Information Processing Complexity as a Determinant of Virus Diversity

The paper quantifies viral genome expression and replication complexity using a propagation index and finds it correlates with viral diversification across multiple taxonomic levels.

Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.

The paper identifies epistatic constraints on adaptive evolution in Drosophila Trio protein by reconstructing evolutionary intermediates and showing reduced viability and locomotor defects.

Explaining the rapid evolution of mammalian meiotic recombination proteins

The paper analyzes evolutionary rates of 100 meiotic recombination proteins across 400 placental mammals, finding that rapid evolution is driven by reduced purifying selection and linked to chromosome pairing proteins in long-lived species.

De novo mutation of an RNA virus is increased in the presence of engineered synonymous mutations that disrupt RNA structural elements

The paper shows that engineered synonymous mutations disrupting RNA structural elements increase de novo mutations in a virus, suggesting structural perturbations affect genomic stability.

Horizontal gene transfer by plasmids relaxes the evolutionary constraints of its own tradeoff

The paper examines the evolutionary tradeoff between horizontal and vertical gene transfer in plasmids, finding mixed evidence and proposing that HGT relaxes constraints by introducing plasmids into novel hosts.

Ecological interactions mediate evolutionary responses to temperature in microbial communities

The paper shows that temperature-induced evolutionary responses in microbial populations depend on both intraspecific and interspecific ecological interactions.

Effects of deleterious mutations on the fixation of chromosomal inversions on autosomes and sex chromosomes

The paper uses simulations to show that deleterious mutations reduce inversion fixation probabilities, but lucky inversions can still fix and influence macroevolution.

Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation

The paper compares the effects of mutational drought and meltdown on extinction risk in small populations, finding mutational drought is more significant in stable and changing environments.

Eco-evolutionary dynamics are shaped by competition in experimental range expansions

This study tests if interspecific competition during range expansion leads to pushed wave dynamics and alters evolutionary patterns in duckweed species.

Molecular pet or parasite? Exploring selection for vertical and horizontal plasmid transfer

This study develops a mathematical model to understand selection for horizontal plasmid transfer and shows that modifying lab protocols can tip selection towards horizontal gene transfer.

Evolution of the highest fidelity DNA replication systems

The paper analyzes factors influencing mutation rates across species and suggests evolutionary mechanisms for reducing mutation rates to mitigate cancer risk.

Do plasmid-dependent phages enable the survival of costly plasmids?

The paper shows that plasmid-dependent phages can help high-cost plasmids persist by reducing their abundance and neutralizing their costs in host populations.

The evolution of condition-dependent self-fertilisation

This study shows condition-dependent selfing generates within-population variation in selfing rates and contributes to mating-system diversity.

Persistent trade-offs balance competition and colonization across centuries

The paper shows a trade-off between competitive ability and host colonization in Pseudomonas populations has persisted for centuries.

Variable jackpot individuals provide most alleles for repeated, rapid adaptation to freshwater by anadromous Threespine Stickleback

The paper shows that a few individuals with large adaptive haploblocks drive rapid adaptation of anadromous sticklebacks to freshwater in multiple lakes.

MKado: a toolkit for McDonald-Kreitman tests of natural selection

MKado performs McDonald-Kreitman tests of natural selection using aligned coding sequences, offering extensions and visualization tools.

Two decades of resurrection studies: What have we learned about contemporary evolution of plant species?

This study reviews 52 resurrection studies to assess plant evolutionary responses to global change, finding rapid evolution in annual plants and reduced plasticity in some traits.