466 papers
This paper introduces DDGeoSSE, a deep learning-based generative model that enables the estimation of diversity-dependent biogeographic rates and reveals how local species richness shapes diversification dynamics in Caribbean Anolis lizards and Viburnum plants.
This study demonstrates that the teleost-specific whole-genome duplication generated long-term redundant olfactory marker protein genes, which, through dosage-constrained functional divergence, ultimately drove molecular diversity in the teleost olfactory signaling system over 300 million years.
This study introduces and validates a novel high-throughput targeted paleoproteomics method using MALDI-CASI-FTICR mass spectrometry for rapid and accurate biological sex estimation, successfully applying it to 130 medieval Great Moravia individuals to improve efficiency and correct previous osteomorphological errors.
This study analyzes 33 barn owl parent-offspring trios to establish a mutation rate of 5.6 x 10⁻⁹, revealing that fathers transmit twice as many mutations as mothers and that paternal age significantly increases mutation rates, providing direct evidence of germline senescence in birds.
Through a year-long experimental evolution study of legume-rhizobia mutualisms, researchers demonstrated that negative frequency-dependent selection maintains genetic variation in partner quality by favoring high-quality strains only when they are rare, thereby providing a key mechanism for the ecological and evolutionary persistence of mutualisms under changing environmental conditions.
This study demonstrates that machine learning models trained on raw genotype data do not outperform traditional summary statistics in inferring the time to fixation of hard selective sweeps, suggesting that few undiscovered signals remain in single-population genomic data for distinguishing sweep timing from sweep age.
This paper introduces a two-timescale analytical framework to demonstrate that Diversity-Generating Retroelements (DGRs) provide a significant evolutionary fitness advantage over standard mutagenesis in switching environments, particularly clarifying the conditions under which constitutive DGR activation is favored in systems like human-gut Bacteroides.
By integrating new data from 390 individuals across 30 Sub-Saharan African populations with global datasets and employing ancestry-aware models, this study challenges the long-held "agriculture hypothesis" by demonstrating that demographic history, rather than dietary shifts to starch-rich farming, is the primary driver of human AMY1 copy number evolution.
This study identifies the evolutionary mechanisms behind the unique heat and chemical stress tolerance of the yeast *Kluyveromyces marxianus*, revealing that adaptive expansions and variants in membrane transporters, coupled with divergent lipid processing, underpin its extremotolerant traits.
By reanalyzing 29 mycorrhizal networks, this study reveals that while closely related plants and fungi interact (cophylogenetic signal), their evolutionary histories do not match (no phylogenetic congruence), indicating that previous evidence for host-symbiont codiversification was misinterpreted and that these symbioses are actually driven by diffuse coevolution via trait-matching.
This paper demonstrates that functional bottlenecks in protein fitness landscapes, which restrict evolutionary transitions between distinct phenotypes, can emerge from simple global epistasis acting on an additive underlying trait driven by a heterogeneous distribution of mutational effects, rather than requiring complex networks of interacting mutations.
This paper presents a generalizable analytical model that predicts the accumulation of ancestry junctions in admixed genomes based on recombination rates, ancestry heterozygosity, and effective population size, demonstrating strong agreement with both simulations and empirical data from African American populations to enable the study of recombination and demography without requiring parental source separation.
By integrating multi-omics analyses of polyploid peanut and its diploid progenitors, this study elucidates the lineage-specific evolution of regulatory landscapes, revealing that while most accessible chromatin regions remain stable after polyploidization, a subset of novel or divergent regions drives homeolog expression bias through de novo emergence and sequence variation.
This study utilizes low-coverage whole-genome sequencing of 140 purple sea urchins across seven populations to identify nine putative chromosomal inversions, three of which show signatures of local adaptation and functional enrichment in biomineralization and development, thereby establishing inversions as a key mechanism for adaptation in this high-gene-flow marine species.
Based on 47 years of data, this study reveals that the long-term decline in adult great tit body mass is driven by phenotypic plasticity resulting from increased early-life competition rather than temperature or food mismatch, demonstrating how early environmental conditions can shape long-term population-level phenotypic trends.
This study reveals that the nerveless sponge *Spongilla lacustris* utilizes an ancient monoaminergic signaling system, involving tryptamine, phenethylamine, and tyramine, to coordinate body-wide contractility through GPCR-mediated remodeling of actomyosin networks, representing a pre-neuronal evolutionary precursor to chemical neurotransmission.
TriMouNet is a novel algorithm that infers level-1 phylogenetic networks from multi-locus gene tree distributions by statistically selecting best-fitting trinets to assemble a full network, thereby outperforming concatenation-based methods like TriLoNet in accurately identifying reticulations while minimizing false positives.
This paper demonstrates through population-genetic modeling that selection favors condition-dependent self-fertilization, where high-condition individuals self-fertilize and low-condition individuals outcross, thereby generating stable within-population variation in mating systems and reducing mutation load.
This study identifies transcriptomic differences in neural and sensory tissues between two *Heliconius melpomene* subspecies that explain their natural variation in aversive mate-preference learning, suggesting that selection on these genetic networks could drive reproductive isolation and speciation.
This study demonstrates that in wild female-philopatric vervet monkeys, maternal age and dominance rank shape sex-specific life histories not through biased sex allocation at birth, but by driving divergent postnatal investment strategies where high-rank mothers enhance daughters' social integration while sons rely more heavily on direct maternal presence.