458 papers
WINDEX is a novel hierarchical method that integrates site- and window-based statistics to more accurately detect and localize adaptive mutations and estimate the proportion of genomes under positive selection compared to existing approaches.
Using a nested co-evolutionary model, this study demonstrates that parasite coinfection drives the joint evolution of lower virulence and reduced host resistance through kin selection effects, with the magnitude of these outcomes contingent on the spatial coupling of host populations.
This study demonstrates that species traits, particularly diet specialization and body size, along with historical demographic patterns, dictate the vulnerability of tropical island endemic birds to climate change, revealing that most entered the Holocene with low effective population sizes and highlighting the need to integrate these factors into conservation strategies.
This study utilizes long-read and short-read sequencing to identify species-specific structural variants in North American deer, revealing that these genomic changes, particularly those affecting reproduction and sensory adaptation, likely play a significant role in adaptive divergence and reproductive isolation during speciation.
This study uses individual-based simulations to propose that the evolution of adaptive immunity was driven not by the need to combat diverse parasites, but by the necessity to manage beneficial and neutral gut microbes while minimizing the risks of rare parasitic infections.
This paper argues that traditional phylogenetic linear models suffer from "Occam's bias," a statistical distortion caused by neglecting relationships among predictors, and demonstrates through an analysis of vertebrate extinction risk that adopting multi-response models is essential for accurate ecological and evolutionary inference.
This study reveals that brain-related traits, including psychiatric disorders, exhibit distinct genetic architectures characterized by weaker GWAS associations and higher allele frequencies due to strong selective constraints acting on their large mutational target sizes, suggesting that the tissues mediating complex traits fundamentally shape their genetic underpinnings.
This study demonstrates that the architecture linking genotypes to phenotypes—specifically whether traits evolve in a correlated or modular fashion—fundamentally constrains biodiversity patterns by acting as a critical filter that determines species coexistence and persistence across varying regimes of selection, migration, and environmental or biotic pressures.
This study characterizes the TLR gene repertoire in elasmobranchs using genomic and transcriptomic data, revealing lineage-specific evolutionary patterns, evidence of adaptive selection driven by pathogen and environmental pressures, and a conserved genomic association between TLRs and MHC regions.
By integrating automated image-based phenotyping with comparative pan-genomics, this study reveals that convergent wing color patterns in *Heliconius erato* and *H. melpomene* arise through distinct, lineage-specific genetic variants acting within conserved regulatory architectures, demonstrating how repeated adaptive outcomes can emerge via different molecular paths.
This study utilizes a comprehensive genomic dataset to demonstrate that the diversification of Australian diplodactylid geckos was driven by mid-Eocene origins in mesic environments followed by repeated transitions into arid habitats, which generated ecological opportunities for morphological divergence and lineage expansion across the continent.
This paper introduces "structural evolutionary invasion analysis," a unified framework that combines an algebraic "invasion determinant" and a "Projected Next-Generation Matrix" to rigorously reduce high-dimensional structured population models while preserving key evolutionary properties, thereby enabling tractable analysis of complex life cycles under weak selection.
By developing an evolutionarily informed gene-set framework to analyze single-cell data across eleven vertebrate species, this study reveals that forebrain evolution proceeds through lineage-specific tuning of deeply conserved transcriptional programs within stable cellular architectures rather than the emergence of entirely new cell types.
To resolve the phylogenetic relationships within the recalcitrant clusioid clade of Malpighiales, researchers developed the Clusioids626 probe set by combining universal Angiosperms353 targets with 273 lineage-specific nuclear orthologs, which successfully outperformed the universal panel alone in generating high-resolution nuclear and plastid data while revealing significant cyto-nuclear conflicts.
This study demonstrates that host age structure acts as a primary ecological driver of plant virus evolution, experimentally showing that diverse demographic regimes in *Arabidopsis thaliana* populations select for distinct viral strategies regarding disease timing, severity, and host-stage specialization through both parallel and demography-specific genomic changes.
By analyzing the distribution of fitness effects across 38 catarrhine primates, this study demonstrates that interspecific differences in deleterious mutations are primarily driven by variation in effective population size rather than clade-specific factors, supporting the nearly neutral theory and confirming the robustness of these findings to demographic history and dominance effects.
This study demonstrates that while antibiotic resistance evolution is generally predictable across most genetic backgrounds, specific disruptions to cellular functions induce idiosyncratic, function-specific epistasis that alters evolutionary trajectories and often slows resistance development, offering a potential strategy to improve treatments through targeted inhibitors.
Ancient DNA analysis of Song Dynasty melon seeds from China reveals that these fruits were introduced from the broader Asian domestication pool rather than independently domesticated locally, and were likely consumed as fresh or culinary fruits with green flesh and jade-green aesthetics rather than as sweet dessert melons.
This study demonstrates that ancient human dental calculus contains identifiable dental enamel matrix proteins, such as amelogenin, thereby expanding the biomolecular potential of calculus analysis beyond diet and microbiome research to include new avenues for sex estimation.
This study reconstructs mobility patterns among Eneolithic-Bronze Age populations in the North Pontic steppe by establishing a regional strontium isotope baseline and analyzing human remains to identify individuals who migrated from the eastern or western Caspian steppes or experienced physiological stress.