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PubMed2026

A complex of MAST1 and 14-3-3η regulates Tau phosphorylation in the developing cortex.

The MAST family of serine/threonine kinases has been implicated in a spectrum of human neurodevelopmental disorders. However, little is known about their biological function or regulation. Seeking to fill these gaps in our knowledge, we have identified upstream and downstream partners of MAST1. 14-3-3η, a neuronal 14-3-3 paralog, specifically interacts with MAST1 at two regulatory serines, S90 and S161. p21-activated kinase (PAK), a neuronal regulator of the actin cytoskeleton, phosphorylates MAST1 to regulate its interaction with 14-3-3η. Exploiting mouse models of human Mega-Corpus-Callosum Syndrome (MCC) and whole brain phosphoproteomics, we identify the microtubule-associated protein Tau as a candidate substrate of MAST1. We show that pathogenic MAST1 mutations perturb protein function either through misfolding or attenuation of kinase activity. Our data are consistent with a model in which the MAST kinases couple PAK, a neuronal regulator of the actin cytoskeleton, to microtubule remodeling during the differentiation and specification of cortical neurons.

Animals↗

PubMed2026

Metagenomic Deep Sequencing Identifies Gene Mutations Associated with Chemotherapeutic Resistance in Vitreoretinal Lymphoma.

PURPOSE: To identify gene mutations associated with chemotherapeutic resistance in patients with vitreoretinal lymphoma (VRL) using metagenomic deep sequencing (MDS) of intraocular specimens. METHODS: Patients with VRL confirmed by cytopathology and immunohistochemistry, flow cytometry, and/or polymerase chain reaction for MYD88, were included. Intraocular specimens underwent MDS of the host genome. Gene mutations were identified and cross-referenced with the Catalogue of Somatic Mutations in Cancer database to determine associations with chemotherapeutic resistance. RESULTS: Forty-nine patients with VRL underwent MDS, with six specimens from four patients revealing eight gene mutations associated with chemotherapeutic resistance. Four specimens from three patients harbored mutations associated with methotrexate resistance, the mainstay of VRL treatment. In one patient, serial sampling from the initial vitrectomy and two subsequent recurrences revealed distinct resistance-associated mutations at each time point. Despite multi-agent therapy including rituximab, consolidation regimens, and lenalidomide, this patient ultimately succumbed to the disease, whereas the other three patients remained in long-term remission. CONCLUSIONS: Our findings demonstrated that specific gene mutations associated with chemotherapeutic resistance may be harbored by VRL. The detection of different resistance mutations at sequential time points in one patient may reflect clonal selection, treatment pressure, or variable detection sensitivity. The ability to easily sample ocular fluid and detect different mutations associated with tumor recurrence or persistence may provide insights into tumor pathogenesis and could inform prognosis and influence treatment decisions. These findings establish a foundation for developing targeted PCR assays for identified resistance genes, which could transform clinical practice in VRL.

Chemotherapeutic resistance-associated mutations↗

PubMed2026

Bacterial Outer Membrane Vesicles in Colorectal Cancer: Interdomain Communication Hubs in Pathogenesis and Immunotherapy.

The complex interaction between the intestinal microbiota and host mucosal immunity plays a defining role in colorectal cancer (CRC) development and therapeutic outcomes. Recently, bacterial outer membrane vesicles (OMVs)-nano-sized, lipid-bilayered extracellular particulates released by both commensal and pathogenic microorganisms-have emerged as critical long-range signaling vehicles within the gut. This review provides a comprehensive synthesis of the dual functionalities of OMVs in CRC pathogenesis and oncology. Mechanistically, pathogenic OMVs cross compromised mucosal barriers to drive horizontal gene transfer (HGT) of chimeric episomes, such as SPHINX DNAs and Bovine Meat and Milk Factors (BMMFs), thereby promoting genomic instability and neoplastic transformation. Conversely, there is a paradigm shift toward exploiting next-generation probiotic and engineered OMVs as highly tunable therapeutic platforms. By combining cutting-edge bioengineering strategies-such as biomimetic mineralization to neutralize local tissue acidity and chemotherapeutic packaging-these nanovectors effectively reprogram the immunosuppressive tumor microenvironment (TME). Specifically, optimized OMVs modulate macrophage polarization from an M2 to an M1 phenotype and stimulate CXCL10-mediated CD8+ T-cell infiltration, effectively turning immunologically "cold" tumors "hot." Finally, the great translational challenges regarding systemic endotoxicity, scalability, and target delivery, providing a strategic approach for the integration of OMV-based platforms into synergistic immune checkpoint inhibition regimens.

Colon cancer↗

PubMed2026

Novel potential treatment options for infections caused by multi-drug and extensively drug-resistant Neisseria gonorrhoeae strains.

INTRODUCTION: Neisseria gonorrhoeae has evolved antimicrobial resistance (AMR) since antimicrobial treatment of gonorrhea was introduced. The AMR development is driven by the bacterium's high capacity for genetic adaptation, antimicrobial overuse and misuse, and insufficient surveillance. Novel therapeutic options are urgently needed. AREAS COVERED: This review summarizes novel gonorrhea treatment options, with special emphasis on the novel oral antimicrobials zoliflodacin and gepotidacin that obtained US FDA-approval for treatment of uncomplicated urogenital gonorrhea in December 2025. It also highlights compounds in early clinical or preclinical development that have demonstrated promising in vitro activity against N. gonorrhoeae. EXPERT OPINION: Zoliflodacin and gepotidacin have the potential to optimize gonorrhea management as oral alternatives to current injectable ceftriaxone. Their successful long-term use will depend on optimized use strategies, including indications, evidence-based approved dosing, adherence, surveillance, and population-specific considerations. Public-health agencies and clinicians will need to balance broad clinical access with antimicrobial stewardship measures to delay the AMR emergence. Looking ahead, gonorrhea management will hopefully shift from empirical, syndromic treatment toward etiology-guided and AMR-informed therapy, driven by advances in rapid point-of-care testing and whole-genome sequencing technologies. Continuous phenotypic and genomic surveillance remains essential to detect early AMR signals, transmission of AMR strains, and inform treatment guidelines.

AMR↗

PubMed2026

β-carotene enhances drought tolerance in fenugreek by modulating antioxidant defense and redox homeostasis.

Drought stress is one of the main abiotic factors that modulates the morphology and physiology of crops. This study investigated the effect of foliar application of β-carotene on the growth, physiological, and biochemical responses of fenugreek (Trigonella foenum-graecum L.) under drought stress conditions. A pot experiment was conducted using two varieties, Kasuri and Local, under two drought stress levels (control and 50% field capacity), and three β-carotene concentrations (0, 100, and 200 ppm) were applied. Drought stress significantly declined shoot fresh weight up to 35.02% and 58.04%, and shoot length to 17.12% and 17.14%, while increasing the root fresh weight by 133% and 26.2% and the root length to 109.1% and 13.4%, respectively, in the Kasuri methi and Local. Drought stress decreases the total Chl. by 55.4% and 59.3% and carotenoids 42.1% and 59.3% and increased the MDA by 6.35% and 24.2%, respectively, and the content of hydrogen peroxides increased by 12.05% and 44.2% in Kasuri and Local as compared to control. By the application of 200  ppm β-carotene, the shoot fresh weight increased by 95.06% and 66.7%, the shoot length increased by 49.6% and 44.5%, and the total Chl. increased by 194.3% and 144.3%, and carotenoids 71.6% and 63%, and MDA decreased by 14.7% and 15.8%, hydrogen peroxides 26.6% and 27.8%, in Kasuri methi and Local under drought stress conditions. Additionally, with the application of β-carotene, antioxidant enzyme activities (SOD, POD, and CAT) and osmoprotectants (total soluble proteins and sugars) improved significantly, indicating enhanced oxidative defense. Overall, foliar β-carotene application, especially at 200 ppm, proved highly effective in improving fenugreek's drought tolerance by enhancing antioxidant capacity, maintaining pigment stability, and supporting metabolic homeostasis, thereby highlighting its potential role in sustainable crop management under water-limited conditions.

beta Carotene↗

PubMed2026

Epigenetic age acceleration is not strongly associated with cardiorespiratory fitness in heart failure: a pilot study.

BACKGROUND: In heart failure (HF), standard measures such as left ventricular ejection fraction and cardiopulmonary exercise testing incompletely capture interindividual differences in disease status or prognosis. DNA methylation (DNAm) epigenetic clocks, which estimate biological age and epigenetic age acceleration (EAA), may provide complementary insight into cardiorespiratory fitness and systemic aging in HF. RESEARCH DESIGN AND METHODS: We analyzed peripheral blood DNAm from fourteen patients enrolled in REDHART2, a clinical trial of interleukin-1 blockade following hospitalization for acute systolic HF. Genome-wide DNAm was assayed using Illumina EPIC arrays and several clocks were applied to these data. Associations between biological age or EAA and cardiorespiratory fitness measures, inflammatory markers, and clinical parameters were evaluated. RESULTS: All epigenetic clocks demonstrated moderate to strong correlations with chronological age. Biological age was consistently associated with measures of cardiorespiratory fitness, particularly oxygen consumption normalized to fat free mass (VO2_FFM). However, chronological age showed similar associations, and biological age did not significantly improve prediction of VO2 parameters beyond chronological age alone. EAA was not significantly associated with cardiorespiratory fitness for any clock. CONCLUSIONS: In this pilot study, neither biological age nor EAA provided significant predictive value beyond chronological age for cardiorespiratory fitness in patients with HF. CLINICAL TRIAL REGISTRATION NUMBER: NCT03797001.

DNA methylation↗

PubMed2026

ALPHA-1 antitrypsin genotype, sex, and lung cancer: Clinical and molecular characterisation.

INTRODUCTION AND OBJECTIVES: Alpha-1 antitrypsin deficiency is associated with lung and liver disease, but its role in lung carcinogenesis remains unclear. This study aimed to compare the clinical, functional, and molecular characteristics of lung cancer according to alpha-1 antitrypsin (AAT) genotype and, additionally, to explore differences by sex and the possible influence of environmental exposures. PATIENTS AND METHODS: We conducted a cross-sectional, single-centre study including 407 patients with incident lung cancer diagnosed between 2020 and 2023. Clinical, functional, radiological, molecular, and environmental variables were collected. Comparisons were performed between carriers and non-carriers of altered AAT alleles and between women and men. RESULTS: Of the 394 patients with available genotyping, 24.4% carried at least one altered allele. No significant differences were observed by genotype in smoking status, radon exposure, comorbidities, lung function, or histological subtype. Carriers showed significantly lower serum AAT levels and a higher frequency of values < 116 mg/dL (p < 0.001). PD-L1 expression ≥ 50% was more common in carriers (28.1% vs. 19.4%; p = 0.036). In the multivariable analysis, the altered AAT genotype remained independently associated with a higher probability of PD-L1 expression ≥ 50% (aOR = 2.04; 95% CI: 1.09-3.80; p = 0.026). Women had lower cumulative tobacco exposure, lower prevalence of emphysema and COPD, greater biomass exposure, higher frequency of adenocarcinoma, and more EGFR mutations (p < 0.001). CONCLUSIONS: Patients carrying altered AAT alleles did not exhibit a distinctly different clinical profile, although they showed higher PD-L1 expression (≥50%). Furthermore, significant differences were observed between women and men in terms of exposure, histology and molecular alterations.

Humans↗

PubMed2026

The Human Breath Volatilome Responds to Exercise and Recovery: An Untargeted Profiling Study.

Exercise induces metabolic and physiological changes across multiple organs. These changes have been studied via several human biofluids, including urine and blood; however, they remain mainly underexplored in exhaled breath. In this exploratory pilot study, we performed untargeted profiling of breath volatile compounds (VCs) to investigate how exercise and recovery influence breath chemical composition. Breath samples were collected from 71 university athletes from three sporting disciplines. Across 143 breath samples, a total of 1,204 unique breath VCs were detected. There were distinct volatilomic responses to physical activity and recovery, regardless of the athlete's sport. Comparison of paired samples using volcano analysis collected before and during exercise identified 80 breath VCs that significantly increased and 182 that significantly decreased. Similarly, a comparison of samples collected before and after exercise identified 11 compounds that decreased significantly. These findings demonstrate that exercise induces measurable changes in the breath volatilome. However, due to the lack of standardized exercise intensity measures and physiological monitoring, the results should be considered exploratory and interpreted cautiously within the field of exercise science.

Exhaled breath analysis↗

PubMed2026

CoSAG-nf: A Scalable Nextflow Pipeline for Co-assembly, Optimization, and Interactive Visualization of High-Throughput Single-Cell Genomes.

MOTIVATION: Single-cell amplified genomes (SAGs) are crucial for resolving intra-population microbial heterogeneity and accurately understanding the metabolic potential of microbial dark matter populations. However, SAGs generated through multiple displacement amplification (MDA) of genomic DNA from single cells with single-copy chromosomes are highly fragmented and prone to contamination, severely hindering high-quality genome reconstruction and functional analysis, which greatly limits their scientific utility. Co-assembly of related SAGs can substantially improve genome quality, but to our knowledge no automated pipeline exists for high-throughput processing, forcing manual implementation of complex workflows that scale poorly to modern dataset sizes. RESULTS: We present CoSAG-nf, an automated high-throughput co-assembly and optimization pipeline for SAGs, implemented following the nf-core framework standards. The pipeline performs alignment-free clustering using sourmash MinHash signatures, then employs iterative tetranucleotide frequency profiling to identify and exclude outlier SAGs from co-assembly groups. CheckM2 quality assessment guides dynamic selection of optimal SAG combinations to optimize genome completeness and minimize contamination. Fully containerized, CoSAG-nf ensures reproducibility and scalability for the high-throughput processing of large-scale SAG datasets across diverse computing environments, including HPC and cloud platforms. The pipeline generates comprehensive HTML reports with quality metrics and taxonomic annotations, providing an end-to-end solution for automated high-throughput single-cell genome reconstruction. AVAILABILITY: CoSAG-nf is freely available under the MIT License at: https://github.com/linfengxu/CoSAG-nf. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.21525244. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Journal Article↗

PubMed2026

Ultra-processed Foods, Cancer, and Early-onset Cancer: A Comprehensive Review.

The classification of foods according to their degree of processing, and particularly the concept of ultra-processed foods, is relatively new. Consumption of ultra-processed foods has increased markedly worldwide in recent decades. Their growing consumption has coincided with a rising global burden of cancer, including marked increases in several cancers diagnosed before age 50 years. In this comprehensive review, we summarize trends in ultra-processed food consumption and the sociodemographic, psychological, and behavioral characteristics associated with higher intake. We further review the epidemiological evidence linking ultra-processed foods with cancer incidence and mortality, with particular attention to the limited but emerging evidence relevant to early-onset cancer. Potential mechanisms linking ultra-processed foods to cancer include unfavorable nutrient displacement, changes in body composition and fat deposition, and increased exposure to additives, processing by-products, and other chemicals. These influences may converge on a range of biological pathways, including metabolic dysfunction, chronic inflammation, immune dysregulation, gut microbiome disruption, DNA damage and genomic instability, and epigenetic alterations. Substantial uncertainties remain, including heterogeneous exposure definitions and classification practices, limitations in dietary assessment and temporal exposure capture, residual confounding, and the complexity of putative biological mechanisms. We conclude by highlighting key research challenges and future directions, along with considerations related to policy, regulation, and industry practices.

Ultra-processed foods↗

PubMed2026

Epistasis and the changing fitness landscapes of SARS-CoV-2.

Since its emergence in late 2019, millions of SARS-CoV-2 genomes have been generated as part of global efforts to monitor the evolution and spread of the virus. This unprecedented volume of data provides a unique opportunity to study viral evolution at unparalleled resolution. In particular, individual genomic sites can be observed to have mutated independently thousands of times. These mutation counts have been used to estimate site-specific mutation rates and fitness effects for most mutations across the viral genome. Here, we use these data to investigate how the landscape of mutational fitness costs has changed over the course of the pandemic. SARS-CoV-2 evolution over the past 6 years has been characterized by the emergence of distinct variants separated by long branches corresponding to evolutionary saltations involving up to 50 mutations. We compare inferred fitness landscapes of the Spike protein across these variants and find that shifts in the estimated effects of non-synonymous mutations are linked to genetic differences between them. Sites with altered fitness costs are enriched near positions where the genetic backgrounds differ. To explain the observed changes, we introduce a model with pairwise epistatic interactions between mutations and residues that differ between variants. This model is able to explain about half of the variance in the shifts of fitness effects and suggests that each mismatch between variants substantially alters mutation effects at typically 1 to 3 additional positions.

SARS-CoV-2↗

PubMed2026

A Molecularly Anchored Spatial Transcriptomic Framework for Precise CA1-Subiculum Parcellation and Region-Resolved Analysis in Alzheimer's Disease.

BACKGROUND: The precise molecular delineation of the interface between the Subiculum (Sub) and cornu ammonis 1 (CA1) is a challenge in hippocampal research, as conventional cytoarchitectural boundaries are often ambiguous and limit reproducible regional annotation. Here, we developed a molecularly anchored spatial transcriptomic framework to define CA1-Sub regional identities using high-definition spatial transcriptomics (Stereo-seq) and single-nucleus RNA sequencing (snRNA-seq) references. FINDINGS: Using a human hippocampal Stereo-seq dataset from 12 donors, we established a data-driven parcellation framework that defines reproducible molecular features distinguishing CA1 and Sub while capturing the transition between these regions. FN1 was identified as a Sub-enriched marker in a subset of EX_Sub and, together with ETV1 and additional regional markers, enabled molecular assignment of CA1 and Sub identities across datasets. The Sub association of FN1 and ETV1 was further supported by human 10X Genomics spatial transcriptomics, mouse in situ hybridization data, and a mouse spatial transcriptomic dataset. Applying this framework to Alzheimer's disease (AD) tissues revealed region-specific transcriptional alterations across CA1 and Sub, including enrichment of mitochondrial energy metabolism-related transcripts in the Sub, suggesting exploratory transcriptional associations of altered metabolic function. CONCLUSIONS: This study provides a molecularly anchored framework for human CA1-Sub parcellation that complements conventional annotation. By defining regional molecular states while preserving the biological continuum across CA1-Sub interface, this approach enables more consistent regional analysis of human hippocampus tissue across donors, datasets, and disease conditions.

Journal Article↗

PubMed2026

Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.

Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here we examine ecological and evolutionary responses to 33 years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium ASVs, and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.

ecology↗

PubMed2026

Institutional data commons: a federated Data Use Certification-aware architecture for secure and scalable data use in biomedical data ecosystems.

BACKGROUND: Modern biomedical data ecosystems increasingly rely on global cloud platforms to coordinate access to large-scale genomic and clinical datasets. However, operational governance remains largely investigator-centric, shifting the responsibility for complex security, compliance, and infrastructure management to individual laboratories. As data volumes and regulatory requirements expand, this approach fails to scale across the research enterprise. This disjointed approach creates a substantial governance burden and can slow down scientific progress. In centralized cloud environments, investigators face siloed identity management and high costs, leading to inefficient data use and increased risk when integrating local and global datasets. MATERIALS AND METHODS: We examine limitations in the current infrastructure and propose reframing institutional data commons as governance-aware intermediaries to ensure secure, efficient and sustainable use of controlled-access biomedical data. RESULTS: This federated architecture decouples storage from authorization, enabling dynamic access linked to active certifications, whether data are analyzed in situ on global platforms or in local governance-aware institutional access environments. DISCUSSION: Shifting governance from investigators to institutional infrastructure ensures that biomedical research remains both secure and economically sustainable.

biomedical data ecosystems↗

PubMed2026

Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome.

High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared to a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.

FISH↗

PubMed2026

Isolation and Characterization of Lytic Bacteriophages Targeting Clinical Staphylococcus Other Than S. aureus.

Staphylococcus spp., other than S. aureus (SOSA, formerly CoNS), are opportunistic pathogens often linked to biofilm infections on indwelling devices. Their rising antibiotic resistance highlights the need for novel therapies. Bacteriophages are promising due to their specificity and ability to inhibit cell growth and biofilm formation. In this study, lytic phages isolated from swab pools were characterized against six clinical S. epidermidis and S. warneri isolates. Two distinct groups were identified via their host range, transmission electron microscopy, and genome sequencing. Group 1 phage ΘBRJ9 belongs to genus Sepunavirus (Myoviridae), while Group 2 phage ΘBRJ18 belongs to genus Andhravirus (Podoviridae). Both showed rapid adsorption, short latent periods (20 min), and high burst sizes (79 and 60 PFU/cell). They strongly inhibited planktonic SOSA growth at MOI 10, with efficacy comparable to or better than vancomycin, and their genomes lacked lysogeny, virulence, or resistance genes. These phages display a lytic lifestyle and are candidates for targeted SOSA therapies. Future work will assess biofilm efficacy, antibiotic synergies, and in vivo performance.

Antibiotic resistance↗

PubMed2026

An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes.

Admixture between populations is a common feature of human history. Admixture events introduce new genetic variation that can fuel evolution. Characterizing the significance of admixture events on the evolution of populations across various species is of great interest to evolutionary geneticists. Local Ancestry Inference (LAI) methods infer genetic ancestry of an individual at a particular chromosomal location. Certain methods specialize in detecting archaic introgression, which consists of interbreeding between modern and archaic humans like Neanderthals and Denisovans. Most current LAI methods allow the detection of a single archaic ancestry, and post-processing may distinguish between multiple waves of introgression. These methods vary in how they choose archaic or modern reference genomes for the inference. Here, we present a new HMM-based method (DAIseg), which has the advantage of simultaneously distinguishing between multiple waves of ancient and recent admixture, using only modern human reference genomes. Simulations demonstrate that DAIseg achieves higher overall performance than state-of-the-art methods. We also apply DAIseg to Papuan populations to jointly detect Denisovan and Neanderthal introgressed segments, and identify a higher number of archaic segments than previous methods. Analysis of inferred introgressed segments, shows that we can identify evidence for two Denisovan introgression events in Papuans. Overall, on top of being able to deal with both Archaic and recent admixture, DAIseg provides a more principled approach for detecting and classifying Denisovan and Neanderthal segments which will improve downstream analysis of introgressed segments to infer the impact of archaic introgression in humans.

Denisovan↗

PubMed2026

Local ancestry inference identifies robust evidence of selection in Neolithic Europe.

During the European Neolithic, migrating Anatolian farmers admixed with local hunter-gatherers, coinciding with major shifts in diet, environment, and lifestyle that imposed strong selective pressures. Local ancestry inference is widely used to detect selection following admixture, but most methods were developed and validated on present-day populations. Their performance in ancient DNA - where reference panels are smaller, data are sparser, and admixture is more ancient - remains unresolved. We benchmark eight local ancestry inference methods on 176 imputed Neolithic genomes. While individual-level ancestry estimates are highly correlated across methods, inferred tract lengths and admixture time estimates vary by an order of magnitude. Overall, we recommend Gnomix or RFMix for general use. We also investigated our ability to detect natural selection using LAI. Integrating results across methods and replicating across methods and in two independent datasets (n=378 and 1,121) we identify a robust ancestry deviation at FADS1/2, consistent with adaptation on metabolism. We also identify IRAK4 (innate immunity) as a candidate locus, but with less consistent signal across methods. Finally, we replicate previous reports of excess hunter-gatherer ancestry at the HLA, but these results are inconsistent across methods and suggest that they may be affected by bias in local ancestry inference. Our findings demonstrate that while local ancestry inference recovers biologically meaningful signals in ancient genomes, results can be sensitive to the methods used for inference, particularly in complex regions like the HLA. Method choice critically influences inferred ancestry patterns and selection signals, underscoring the importance of multi-method validation.

Journal Article↗