Evolution and Genetic Dynamics

Accounting for recurrent mutation in the frequency spectrum of rare alleles

The paper introduces the single mutation frequency spectrum (SMFS) to account for recurrent mutations in the site frequency spectrum of rare alleles, showing its application to human exome data.

Modes of natural selection on maternal and zygotic gene expression in Drosophila melanogaster embryos

The paper investigates selection pressures on maternal and zygotic gene expression in Drosophila melanogaster embryos using single-embryo RNA sequencing and variance tests, finding directional selection is more common than stabilizing selection.

The phylodynamic threshold of measurably evolving populations

This study shows that determining if a population is measurably evolving or has reached the phylodynamic threshold depends on model assumptions and sampling strategies, not just data, and emphasizes prior sensitivity over tests of temporal signal.

Buffering of developmental noise provides a mechanism for heterosis in both polyploid and diploid hybrids

The paper uses a computational model to show that increased ploidy buffers gene expression noise, explaining hybrid vigor and inbreeding depression through developmental robustness.

De-novo promoters emerge more readily from random DNA than from genomic DNA

The paper compares the emergence of de-novo promoters in random DNA versus genomic DNA, finding that random DNA generates them more readily due to fewer proto-binding sites in genomic DNA.

An analytical framework for phenotypic selection of fitness-conferring genes

The paper develops an analytical framework to understand how phenotypic selection enriches fitness-conferring genes under stress, showing symmetry breaking and noise-driven enrichment mechanisms.

Pleiotropy constrains the evolution of immune system plasticity while promoting domain modularity

The paper examines how pleiotropy affects evolutionary rates and plasticity in immune system genes across six Drosophila species, finding domain-specific evolution can reduce gene-level constraints.

A quantitative framework for bacterial competition during starvation

The paper develops a quantitative framework to model bacterial competition during starvation, showing that physiological traits influence competitive outcomes through necromass recycling.

Evolution induced state shifts in a long-term microbial community experiment

This study tracks four-year microbial community evolution in two environments, showing how adaptive mutations in one species can cause abrupt community state shifts.

Pervasive bacterial and prophage hybridization during chronic gut inflammation

The paper shows that chronic gut inflammation drives bacterial and prophage hybridization in E. coli, leading to new genetic lineages associated with inflammatory bowel disease.

Amino acid cross-feeding in E. coli globally and idiosyncratically alters mutant fitness

This study shows that cross-feeding between E. coli auxotrophs globally and idiosyncratically changes mutant fitness by altering selection pressures on specific genetic variants.

Phenotypic complexity makes the molecular basis of evolutionary convergence predictable

The paper shows that phenotypic complexity determines whether convergent evolution leads to molecular convergence, using simulations of regulatory gene expression.

Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?

The paper develops a mathematical model to explore why mobile genetic elements (MGEs) frequently carry defense systems, finding that the strength of inter-MGE interference determines whether these systems are beneficial or costly.

A theoretical framework for how ecological interactions between microbes affect mutant fitness

This paper develops a theoretical framework to explain how ecological interactions between microbes influence the distribution of fitness effects of mutations.

How do mate-finding Allee effects affect evolutionary rescue?

This study examines how mate-finding Allee effects influence evolutionary rescue in populations below their Allee threshold, showing that mate limitation can impede rescue and alter optimal strategies.

Microbial cross-feeding interactions reshape evolutionary trajectories of consumers by preserving motility.

This study shows that cross-feeding interactions influence consumer evolution by altering selective pressures on motility, with resource origin determining whether flagellar genes are lost or maintained.

The danger hypothesis of virulence evolution

The paper develops a mathematical model based on danger theory to show that cost-based immune activation favors avirulence in microbes, proposing the danger hypothesis of virulence evolution.

Drosophila-virus genotype interactions dominate transmission, virulence and load, eroding additive fitness variance

The paper quantifies how host-virus genetic interactions shape fitness variance in Drosophila and sigma virus, showing that interactions dominate over additive effects.

Entrenchment of germline amino-acid differences in antibody affinity maturation

This study uses deep learning to detect entrenchment in antibody germline genes, revealing epistatic constraints from both intra-chain and genetically uncoupled partners.

Multiple molecular and cellular properties jointly affect protein and site-specific evolutionary rates

The paper uses neural networks to predict protein evolutionary rates by integrating molecular and cellular features across multiple scales, showing that protein-level and site-level properties contribute additively to evolutionary rate variance.

A simple model captures key characteristics of biological non-deterministic genotype-phenotype maps

The paper introduces a synthetic non-deterministic genotype-phenotype map that captures key features observed in biophysical models, highlighting the role of non-linearities in GP maps.

Unexpected changes in reproductive barriers between incipient species after experimental evolution in sympatry

This study shows that sympatric evolution in spider mites reduced reproductive barriers rather than reinforcing them, suggesting evolutionary changes are driven by non-hybridization-related factors.

A competition-protection balance explains the evolution of resistance within simple microbial communities

This study identifies how competition and protection in microbial communities influence resistance evolution, using mathematical models and experiments with E. coli and M. liquefaciens.

Additive effects of environmental and demographic variation shape the repeatability of evolution across replicated experiments

This study shows that environmental and demographic variation additively reduce the repeatability of evolution in replicated experiments with Caenorhabditis elegans.

Interplay between purging and admixture shapes genetic load in an invasive guppy population

The paper examines how purging and admixture affect genetic load in an invasive guppy population, finding that strongly and weakly deleterious mutations respond differently to these processes.

The dynamics of silent variation in Mimulus guttatus: Codon usage bias and linked selection

The paper examines codon usage bias and linked selection in Mimulus guttatus, finding weak codon selection for most genes and strong selection for specific functional genes, with linked selection affecting nucleotide diversity.

Phylogenetically estimated neutral rates and fitness effects of mutations to influenza proteins

The paper estimates neutral mutation rates and fitness effects of mutations in influenza proteins using phylogenetic analysis of over 100,000 sequences, revealing context-dependent patterns across viruses.

Coevolutionary dynamics of viruses and their defective interfering particles

This paper develops a mathematical model of virus-DIP coevolution, revealing population-level oscillations and trait-level coevolutionary chases, with implications for DIP-based antiviral therapies.

Bursts of reproduction can create genetic structure in frequently recombining bacterial populations

The paper shows that bursts of reproduction can create genetic structure in bacterial populations with high recombination rates, even when recombination would otherwise eliminate such structure.

Negative frequency-dependent selection maintains partner quality variation in a keystone nutritional mutualism

This study shows negative frequency-dependent selection maintains genetic variation in legume-rhizobium mutualisms by favoring high-quality strains when rare.