464 papers
This study demonstrates that frequency-dependent fitness effects are ubiquitous in *E. coli* populations, challenging the assumption of constant selection by revealing that competitive advantages typically decline as mutant frequency increases and that these dynamics significantly alter evolutionary trajectories.
This study demonstrates that alternative splicing is a widespread mechanism driving sexual dimorphism in *Timema* stick insects, particularly in male gonads, and that the transition to asexuality leads to a systematic erosion of this splicing complexity, suggesting sexual selection plays a key role in maintaining isoform diversity.
This study utilizes comprehensive genomic analyses to reveal that the widely studied ctenophore *Mnemiopsis leidyi* actually comprises two distinct cryptic species, *M. leidyi* and *M. gardeni*, which diverged during the Pleistocene and are shaped by genomic rearrangements and environmental adaptation along the US Atlantic coast.
This paper introduces wQFM-GDL, a novel quartet-based species tree inference method that extends the QFM framework to handle gene duplication and loss by leveraging species-driven quartets, demonstrating superior accuracy and scalability compared to leading tools like ASTRAL-Pro3 on large-scale genomic datasets.
Using machine learning to analyze *Aedes aegypti* populations from Africa and the Americas, this study reveals that soft selective sweeps predominate over hard sweeps, indicating the mosquito's rapid adaptive potential to environmental stressors like insecticides and highlighting specific resistance genes critical for vector control.
This study utilizes single-cell RNA sequencing to characterize the transcriptional diversity of *Holothuria forskali* perivisceral fluid coelomocytes, identifying ten distinct clusters including progenitor-like cells and carotenocytes, and elucidating their specific immune functions to advance the understanding of holothuroid immunity and deuterostome immune evolution.
This study reveals that adaptive evolution in the essential enzyme Topoisomerase II within *Drosophila simulans* creates a lethal incompatibility with *D. melanogaster* by failing to resolve topological stress from species-specific satellite DNA, thereby driving reproductive isolation.
This study reveals that the ciliate *Paramecium sonneborni* has repeatedly overcome extreme genetic divergence barriers through interspecific mating and genomic introgression, a process facilitated by its unique nuclear dualism which allows the elimination of incompatible foreign DNA from the somatic genome while retaining it in the germline.
This study presents the earliest evidence of *Yersinia pestis* in Southern Europe from a 4,950-year-old Italian individual who was co-infected with *Erysipelothrix rhusiopathiae* and Hepatitis B virus, while also expanding the ancient genomic record of *Erysipelothrix* species to better understand prehistoric zoonotic disease dynamics and transmission.
This study introduces the "covariomorph" model in RevBayes to address lineage-specific rate variation in morphological evolution, demonstrating through simulations and empirical analysis that accounting for such heterogeneity significantly improves phylogenetic inference accuracy and impacts divergence time estimation.
This paper demonstrates that evolutionary rescue in consumer-resource systems depends critically on the specific ecological traits affected by environmental change, the population's resident life-history, and the genetic architecture of evolving traits, revealing that intrinsic growth rates alone are insufficient to predict persistence probabilities.
This study presents the first large-scale population genomic survey of wild house mice, utilizing a novel bioinformatics pipeline to identify over 100,000 non-reference endogenous retrovirus insertions, thereby revealing significant subspecies-specific diversity and highlighting the role of these dynamic elements in structural variation and adaptive evolution, such as the adaptive introgression of the resistance-conferring Fv4 locus.
This study demonstrates that while selection consistently favors larger rosette diameter in *Fragaria vesca* across European environments, evolutionary responses in both growth and herbivore resistance are highly context-dependent, shaped by variable selection pressures and genetic covariances that can either constrain or facilitate adaptation under changing precipitation regimes.
By integrating multi-omics data, this study reveals that ancient, reciprocal adaptive introgression of immune and osmoregulatory genes during Miocene geoclimatic oscillations, rather than strict isolation, has been a key driver in shaping the evolutionary trajectories and long-term persistence of threatened *Coilia* species.
By generating chromosome-level genomes and integrating multi-omics analyses, this study reveals how *Stemona* species evolved distinct fatty acid partitioning mechanisms between elaiosomes and seeds to produce specific attractants and nutrients that facilitate the transition from ant- to wasp-mediated seed dispersal.
The paper introduces PEINT, a deep learning framework that models protein evolution over time by capturing complex site interactions and indel dynamics from raw sequences, enabling the generation of realistic evolutionary trajectories and novel, functional proteins that overcome the limitations of traditional independent-site models.
This paper proposes and validates a pleiotropic hitchhiking model demonstrating that univariate selection on wing size, acting through the structure of mutational variance, can explain both the alignment of Drosophila wing divergence with mutational lines of least resistance and the observed rate paradox without requiring hidden deleterious pleiotropic costs.
This global study demonstrates that publicly available single-locus genetic data can effectively map bat phylogenetic diversity and reveals that historical and current temperature variables are the primary drivers of these patterns, with Southeast Asia and South America identified as key hotspots for conservation.
Using population-genetic models, this study demonstrates that even weak sexual antagonism dramatically accelerates the evolution of recombination suppression on sex chromosomes compared to neutrality, with mating systems and the genomic origin of suppressors (heterogametic vs. homogametic) critically shaping the rate and direction of this evolutionary process in both XY and ZW systems.
This study demonstrates that in the social pine sawfly *Neodiprion sertifer*, collective defense against predation provides both direct and indirect (kin-selected) survival benefits, with individuals strategically modulating their contributions based on group size, sex ratio, and kinship to balance cooperation against the risk of exploitation.