460 papers
This study demonstrates that in the liverwort *Marchantia polymorpha*, alternative splicing of a single exon alters the C-terminal TPR domain configuration of the sole CLU family protein, thereby determining its specific targeting to either mitochondria or plastids and compensating for the loss of gene duplication through genome reformatting.
This study reveals that ticks acquired a bacterial kinase gene (*anmK*) via horizontal gene transfer, which has since evolved to play a critical role in their blood-feeding and reproductive success by localizing to ovaries and supporting endosymbiont maintenance.
This study provides the first direct genomic evidence that strong sexual selection in *Tribolium castaneum* populations effectively purges deleterious mutations and reduces extinction risk without eroding overall genetic diversity, thereby enhancing population viability.
This paper introduces a fast and memory-efficient Empirical Bayes maximum likelihood approach implemented in the R package mvMORPH that enables the analysis of high-dimensional phenotypic traits and complex evolutionary models, such as multi-optima Ornstein-Uhlenbeck processes, overcoming the computational limitations of existing phylogenetic comparative methods.
This paper introduces Probabilistic Phenotype Genetics (ProP Gen), a new theoretical framework and simulation algorithm that revises classical evolutionary dynamics by incorporating ubiquitous phenotypic uncertainty, revealing novel mechanisms like "phenotypic buoying" and accelerated valley crossing that better explain complex biological phenomena such as bacterial persistence and cancer treatment evasion.
This study reveals that rapid adaptation to desert conditions in house mice is driven by context-dependent, tissue-specific *cis*-regulatory evolution, which alters gene expression in response to dehydration, particularly within the arachidonic acid and lipid metabolism pathways.
This study presents the most comprehensive evolutionary map of vertebrate selenoproteins to date, revealing that while tetrapods experienced convergent gene losses and Sec-to-Cys conversions, ray-finned fishes underwent extensive expansions driven by whole-genome duplications, highlighting a stronger selective advantage for selenoproteins in aquatic environments.
By analyzing 47,000 global *Klebsiella pneumoniae* genomes and applying hypercubic transition path sampling, this study maps and predicts the diverse evolutionary pathways of antimicrobial resistance, revealing how drug policies and public health contexts drive both consistent and divergent resistance patterns across countries.
Contrary to the expectation of widespread dosage compensation in iguanian lizards, this study reveals that male-female expression imbalance on the X chromosome is phylogenetically conserved across phrynosomatids, driven by female overexpression in ancestral regions and male underexpression in recently evolved neo-X regions.
This paper introduces and validates neural posterior estimation (NPE) as an efficient, accurate, and flexible simulation-based inference method for population genetics that overcomes the computational limitations of Approximate Bayesian Computation (ABC) and the lack of uncertainty quantification in standard supervised machine learning by training neural networks to directly estimate posterior distributions from raw genotypes or summary statistics.
This paper demonstrates that the exponential growth of evolutionary lineages creates a geometric packing problem that forces the Tree of Life to embed into a hyperbolic manifold with a universal dimension of approximately 2 and a specific curvature determined by the genetic code's information rate, a prediction rigorously confirmed across diverse biological datasets and protein alphabets.
This study reveals that *Varroa destructor* mites associated with varroa-resistant honey bee colonies across Europe consistently exhibit a significant reduction in body size compared to those from non-resistant colonies, suggesting a host-driven phenotypic shift that could serve as a new selection marker for breeding resistant bees.
This paper proposes that Neandertals originated from a sex-biased range expansion of modern humans utilizing Levallois tools between 400 and 250 ka, which resulted in massive introgression with local archaic populations in Europe to create a distinct lineage while simultaneously explaining shared genetic markers and tool technologies.
This study quantifies the phylogenetic signal across 35 primate traits and reveals that dental development, particularly permanent teeth, exhibits the strongest evolutionary conservation, challenging the expectation that earlier-developing traits are more phylogenetically constrained.
This study demonstrates that while song divergence between laurel and pine forest populations of the Canary Islands Chaffinch elicits slightly weaker territorial responses to cross-habitat songs, these acoustic differences are currently insufficient to act as a strong pre-mating barrier, suggesting that other ecological or morphological factors may drive the observed population differentiation.
This study analyzes six years of SARS-CoV-2 genomic data to demonstrate that shifts in mutational fitness costs across evolving variants are largely driven by pairwise epistatic interactions between new mutations and the distinct genetic backgrounds of those variants.
This study demonstrates that asymmetric reproductive character displacement in *Ischnura* damselflies, driven by reinforcement in hybrid zones, results in morph-specific divergence in prothorax shape and size, particularly affecting gynochrome females and males in *I. elegans*.
This study introduces a high-throughput platform for characterizing full-length human proteins on native cells to reveal how conformation-mediated epistasis resolves multidimensional biophysical trade-offs, thereby constraining antibody evolutionary trajectories to specific mutational orders that enable the acquisition of diverse antigen recognition without compromising folding or self-reactivity.
The paper introduces SHEPHERD, a novel framework combining Wright-Fisher population genetics and Markov Decision Processes to design optimal adaptive drug policies that effectively mitigate therapeutic resistance in heterogeneous, evolving populations beyond the limitations of traditional homogeneous models.
By integrating Approximate Bayesian Computation with X-chromosome diversity analyses, this study reveals that grey reef sharks in the Indo-Pacific comprise two ancient, deeply separated metapopulations shaped by extreme sex-biased dispersal and recent secondary contact, supporting their designation as distinct Evolutionary Significant Units.