445 papers
This study introduces a novel inference framework using multi-population two-locus statistics derived from single unphased genomes to reconstruct complex hominin demographic history, revealing multiple episodes of gene flow between early modern humans and Neanderthals, introgression from an unsampled lineage into Denisovans, and specific ancestry patterns in early European farmers.
This study characterizes *Candidatus* Centrionella anaeramoebae, a rare anaerobic Legionellales symbiont of *Anaeramoeba pumila* that has undergone genome reduction, acquired host-derived GTPase genes via horizontal transfer, and lost the symbiosome structure, thereby offering a unique model for the evolutionary transition from aerobic pathogenesis to anaerobic mutualism.
By leveraging a rare natural hybrid population in a karst window cave, researchers identified a specific nonsynonymous mutation in the Connexin-50 (Cx50) gene as a primary driver of eye loss in Mexican cavefish, demonstrating molecular convergence across diverse subterranean vertebrates.
This study reconstructs the evolutionary history of prokaryotic transcription factors using a large-scale dataset, revealing that ancestral prokaryotes possessed a diverse TF repertoire that expanded steadily through early innovation and later horizontal gene transfer, contrasting sharply with the burst-like emergence of TF families observed in eukaryotic evolution.
This study identifies a female-specific growth hormone receptor gene (GHR-W) on the W chromosome that has been retained in certain bird lineages, such as hawks and owls, and demonstrates a robust correlation between the presence of this gene and reverse sexual size dimorphism where females are larger than males.
Using population genomics and a chromosome-level assembly, researchers identified three cryptic, strongly reproductively isolated lineages of the mosquito *Aedes notoscriptus*, revealing that a single lineage (VIC1) drove international invasions while coexisting with a distinct lineage (VIC2) in Australia that exhibits hybridization barriers and a massive structural variant.
This study on Trinidadian guppies demonstrates that while increased polygyny boosts male reproductive output, it also imposes significant costs on both sexes, including delayed reproduction and higher failure rates, suggesting that male mating performance is limited and sexual selection pressures may be more balanced between sexes than traditionally assumed.
This study introduces phylogenetic comparative interaction methods to demonstrate that competition with darter clades likely drove the repeated colonization of caves by North American blind cavefishes, offering a new framework for testing macroevolutionary ecological interactions using living taxa.
By analyzing near-complete mitochondrial genomes and nuclear loci, this study resolves the previously conflicting phylogenetic placement of the bat-restricted genera *Nycteria* and *Polychromophilus* as a strongly supported monophyletic clade, demonstrating that expanded genomic data is essential for accurately reconstructing the evolutionary history of Haemosporida.
This study demonstrates that freshwater sponges acquired the microbial rhodoquinone biosynthesis gene *rquA* via lateral gene transfer, enabling them to synthesize rhodoquinone and potentially enhancing their tolerance to low-oxygen environments.
By reconstructing the eukaryotic Tree of Life using a largely independent, marker-rich dataset that minimizes shared biases with previous studies, this research confirms most major supergroups while proposing revised phylogenetic positions for specific lineages, thereby supporting the hypothesis that extant eukaryotic diversity is organized into a small number of high-rank supergroups.
This study provides robust experimental evidence that a subset of random sequence clones genuinely confers fitness advantages to *E. coli* under specific growth conditions, thereby validating the capacity of non-coding sequences to generate adaptive functions and supporting the mechanism of *de novo* gene evolution.
Analysis of preindustrial Finnish data reveals that while having more sons does not immediately reduce maternal survival in small families, it significantly increases short-term mortality risks for mothers with larger families, suggesting accumulated physiological costs that are often overlooked in studies focusing on post-reproductive lifespans.
This study identifies and characterizes a novel, lineage-specific venom gene family called *deca-ctx* in decapodiform cephalopods, revealing its evolutionary history, structural diversity, and localization in specialized glands, thereby redefining the golden cuttlefish's SE-CTX as part of a complex and chemically diverse venom system.
This study elucidates the molecular mechanisms of triploid seed failure in natural *Arabidopsis arenosa* populations by revealing that the triploid block involves the preferential misregulation of imprinted genes and a recurrent, cell-signaling-related defense response in the endosperm and seed coat.
This paper proposes a single epidemiological model explaining how the composition of a pathogen environment drives the evolution of divergent lifespan strategies in eusocial species, where chronic parasites favor caste-specific aging and altruistic worker death, while benign pathogens lead to negligible senescence across all castes.
This study demonstrates that in the fungus gnat *Bradysia coprophila*, a maternal genetic sex-determining region drives the adaptive divergence of female reproductive morphs into distinct life history and gene expression profiles, thereby extending core principles of sexual dimorphism and sex chromosome evolution to maternal sex-determination systems.
By analyzing three independent hybrid zones between *Ischnura elegans* and *Ischnura graellsii*, this study reveals that while demographic history drives geographic heterogeneity in introgression patterns, genomic architecture imposes consistent constraints, resulting in repeatable functional outcomes rather than identical gene flow across zones.
This study demonstrates that two distinct ecotypes of the wood-decay fungus *Meruliopsis taxicola* exhibit contrasting ecological strategies, with the Continental ecotype favoring competitive growth and decomposition while the Coastal ecotype prioritizes stress tolerance, a divergence that is largely maintained in their hybrid offspring.
This paper introduces *demestats*, a differentiable software library that computes first-coalescence and cross-coalescence rates for complex demographic models to overcome the limitations of pairwise summaries in resolving recent population history, demonstrating improved accuracy in simulations and new insights into human expansion using 1000 Genomes Project data.