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PubMed2026

Genetically predicted childhood traits and parental health and risk of pediatric psychiatric disorders: A 2-sample Mendelian randomization study.

The etiology of pediatric psychiatric disorders is complex, involving intergenerational influences and a child's own developmental health. We aimed to investigate the potential effects of genetically predicted childhood traits (childhood obesity, absence epilepsy, intelligence) and parental health traits (longevity, Alzheimer disease, severe depression) on the risk of several childhood and adolescent psychiatric disorders. We employed a 2-sample Mendelian randomization (MR) design using summary statistics from large-scale genome-wide association studies. Data for parental health exposures were primarily from the UK Biobank. Data for childhood trait exposures were from various consortia. Data for outcomes - conduct disorder, mixed conduct and emotional disorders, attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and broader behavioral/emotional and social disorders - were sourced from FinnGen and the Psychiatric Genomics Consortium, among others. We used the inverse-variance weighted method for the primary analysis, with MR-Egger, weighted median, and weighted mode as additional analyses. To test the robustness of the results, we conducted sensitivity analyses using MR-Egger regression, Cochran Q test for heterogeneity, the MR-pleiotropy residual sum and outlier test, and a leave-one-out analysis. Genetic liability for childhood obesity was associated with an increased risk of ASD (odds ratio = 1.06, P = .016) and ADHD (odds ratio = 1.09, P = .026), even though these associations did not withstand multiple testing correction. No other robust, statistically significant causal associations were identified. Sensitivity analyses showed limited evidence of bias from horizontal pleiotropy for the main findings. Our findings provide MR evidence supporting potential links from genetic liability for childhood obesity to increased risks of ASD and ADHD. These results highlight the importance of considering a child's early-life health trajectory in the etiology of pediatric psychiatric disorders.

Humans↗

PubMed2026

Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers.

Carers in cooperatively breeding vertebrates increase food acquisition for offspring; however, they also impact the developmental social environment. One means of linking early-life environments, such as nutrition and social structure, with later-life phenotypes is DNA methylation. Here, using whole-genome methylation sequencing, we measured how additional carers influence DNA methylation in nestlings of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps). A comparison of nestlings raised by their parents (two carers) and those raised by parents plus additional helpers ('three plus' carers; mean = 4.3 ± 1.4 s.d.) revealed that additional care is associated with genome-wide differences in DNA methylation. Overall, 570 cytosine-phosphate-guanine sites from the regulatory regions of 487 genes were differentially methylated, with 85% being more methylated in nestlings reared by groups. Specifially, sites associated with genes that are integral for metabolism, growth, the regulation and promotion of sociality, the ability to cope with stressors, and cell communication were differentially methylated between the groups. Furthermore, gene ontology-term analysis revealed that differentially methylated sites were over-represented in multiple pathways, including those important for protein binding, metabolism and cell-to-cell and environment-to-cell communication. Our results suggest that the effects of being reared by groups as opposed to pairs in cooperative breeders can extend beyond those typically attributed to nutritional benefits and that these effects are molecularly mediated. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.

Animals↗

PubMed2022

Adolescents hospitalised for suicidality: biomarkers, social and affective predictors: a cohort study.

OBJECTIVES: The present research examines genomics and in vivo dynamics of family context and experienced affect following discharge from psychiatric hospitalisation for suicidal thoughts and behaviours (STBs). The purpose of this paper is to provide an overview of a new model, description of model-guided integration of multiple methods, documentation of feasibility of recruitment and retention and a description of baseline sample characteristics. DESIGN: The research involved a longitudinal, multimethod observational investigation. SETTING: Participants were recruited from an inpatient child and adolescent psychiatric hospital. 194 participants ages 13-18 were recruited following hospitalisation for STB. PRIMARY AND SECONDARY OUTCOME MEASURES: Participants underwent a battery of clinical interviews, self-report assessments and venipuncture. On discharge, participants were provided with a phone with (1) the electronically activated recorder (EAR), permitting acoustic capture later coded for social context, and (2) ecological momentary assessment, permitting assessment of in vivo experienced affect and STB. Participants agreed to follow-ups at 3 weeks and 6 months. RESULTS: A total of 71.1% of approached patients consented to participation. Participants reported diversity in gender identity (11.6% reported transgender or other gender identity) and sexual orientation (47.6% reported heterosexual or straight sexual orientation). Clinical interviews supported a range of diagnoses with the largest proportion of participants meeting criteria for major depressive disorder (76.9%). History of trauma/maltreatment was prevalent. Enrolment rates and participant characteristics were similar to other observational studies. CONCLUSIONS: The research protocol characterises in vivo, real-world experienced affect and observed family context as associated with STB in adolescents during the high-risk weeks post discharge, merging multiple fields of study.

Adolescent↗

PubMed2025

Genetic and genomic resources for turfgrasses: status, applications, and prospects.

Turfgrasses are integral to urban landscapes, providing social, economic, and ecological benefits. With increasing urbanization, there is a growing demand for turfgrasses that remain visually appealing while being resilient to environmental stresses. In this review, we highlight the current state of genetic and genomic resources for turfgrasses, focusing on advancements in the understanding of genes and pathways associated with traits such as disease resistance, stress tolerance, and environmental adaptability. Additionally, we discuss recent progress in implementing genome editing technologies for turfgrasses and their transformative potential for breeding and functional genomics. We examine progress, challenges, and future prospects in leveraging genomic tools for turfgrass improvement. By synthesizing knowledge from diverse studies, we provide a comprehensive overview of the techniques, discoveries, and innovations shaping the future of turfgrass breeding and management.

Poaceae↗

PubMed2025

Biochemical and Genomic Underpinnings of Carotenoid Colour Variation Across a Hybrid Zone Between South Asian Flameback Woodpeckers.

Colouration and patterning have been implicated in lineage diversification across various taxa, as colour traits are heavily influenced by sexual and natural selection. Investigating the biochemical and genomic foundations of these traits therefore provides deeper insights into the interplay between genetics, ecology and social interactions in shaping the diversity of life. In this study, we assessed the pigment chemistries and genomic underpinnings of carotenoid colour variation in naturally hybridising Dinopium flamebacks in tropical South Asia. We employed reflectance spectrometric analysis to quantify species-specific plumage colouration, High-Performance Liquid Chromatography (HPLC) to elucidate the feather carotenoids of flamebacks across the hybrid zone, and Genome-Wide Association Study (GWAS) using next-generation sequencing data to uncover the genetic factors underlying carotenoid colour variation in flamebacks. Our analysis revealed that the red mantle feathers of D. psarodes primarily contained astaxanthin, with small amounts of other 4-keto-carotenoids. In contrast, the yellow mantle feathers of D. benghalense predominantly contained lutein and 3'-dehydro-lutein, alongside minor amounts of zeaxanthin, β-cryptoxanthin and canary-xanthophylls A and B. Hybrids with an intermediate, orange colouration deposited all of these pigments in their mantle feathers, with notably higher concentrations of carotenoids with ε-end rings. The GWAS analysis identified the CYP2J2 gene, which plays a role in carotenoid ketolation, as associated with the expression of carotenoid colouration. Read depth data suggested variation in copy number of this gene in flamebacks. These findings contribute to the growing knowledge of avian carotenoid metabolism and highlight how genomic architecture can influence phenotypic diversity.

Animals↗

PubMed2026

Large-Scale Neuroimaging and Genetic Analyses of the Human Thalamus in Loneliness.

BACKGROUND: Although loneliness is prevalent and significantly impacts society globally, its neural and genetic bases remain poorly understood. The thalamus, which receives sensory information from the environment, may have a more significant role in social interactions than previously recognized. Here, we integrate neuroimaging and genetic approaches to characterize structural differences within the thalamus associated with loneliness. METHODS: We obtained thalamic nuclei volumes on brain scans from 45,834 individuals (age range: 45-82 years) in the UK Biobank and grouped them into 6 anatomical groups. We investigated effects of loneliness and social isolation using self-reported data. Then, we performed a genome-wide association study (GWAS) analysis on the genetic overlap between thalamic volumes and loneliness. RESULTS: The volumes of the whole thalamus and its medial, lateral, and posterior nuclei are significantly reduced in individuals with loneliness compared with those who do not feel lonely. Loneliness with frequent social contact is associated with smaller volumes, whereas social isolation without loneliness shows no such reduction in thalamus volumes. Leveraging data from GWASs on thalamic volumes (n = 30,114) and loneliness (n = 370,342) in the UK Biobank, we identified shared loci between thalamus structure and loneliness. CONCLUSIONS: Our findings support the emerging view that the thalamus plays important roles in social interactions and in the experience of loneliness.

Genetic architecture↗

PubMed2025

SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.

BACKGROUND: Persistent SARS-CoV-2 infections in hospitalised immunocompromised individuals are known to facilitate accelerated within-host viral evolution, potentially contributing to the emergence of highly divergent variants. However, little is known about the evolutionary dynamics and transmission risks of persistent infections in the general population. We aimed to characterise the within-host evolution of SARS-CoV-2 during persistent infections identified through a large community surveillance study. METHODS: We used data from the Office for National Statistics COVID-19 Infection Survey (ONS-CIS), a large-scale, longitudinal, population-based surveillance study conducted in the UK from April, 2020, to March, 2023. For this analysis, we focused on infections with high viral load (cycle threshold ≤30) and available genome sequences, from seven major SARS-CoV-2 lineages (alpha, delta, BA.1, BA.2, BA.4, BA.5, and XBB). ONS-CIS participants were randomly selected from the general population and tested regularly by RT-PCR, regardless of symptoms. We defined persistent infections as those with sustained or rebounding high viral RNA titres for 26 days or longer. We examined associated host characteristics and used raw sequence data to identify de novo mutations and estimate within-host synonymous and non-synonymous evolutionary rates across the SARS-CoV-2 genome. FINDINGS: Between Nov 2, 2020, and March 21, 2023, we identified 576 persistent infections with at least two sequences, including 11 alpha, 106 delta, 102 BA.1, 204 BA.2, 16 BA.4, 133 BA.5, and 4 XBB. Persistent infections were more common in males than females (p<0·0001) and individuals older than 60 years (p=0·0027). The median within-host genome-wide evolutionary rate was 7·9 × 10-4 substitutions per site per year (IQR 7·0-9·0 × 10-4), with high inter-individual variability driven largely by non-synonymous mutations, particularly in the N-terminal and receptor-binding domains of the spike protein. Longer infection duration was associated with higher evolutionary rates, while no associations were found with age, sex, vaccination status, previous infection, or virus lineage. We found no clear evidence of transmission beyond the first month of infection in any of the 84 persistent infections lasting 56 days or longer. In total, we identified 379 recurrent mutations, including many with known or predicted negative fitness effects and low prevalence at the population level, as well as de novo reversions to the Wuhan-Hu-1 reference sequence, which were likely under positive selection within those individuals. INTERPRETATION: This study highlights the heterogeneous nature of within-host SARS-CoV-2 evolution in individuals with persistent infection in the community. Notably, a small subset of persistent infections with high viral loads underwent accelerated viral evolution or recurrently acquired hallmark mutations found in novel variants. In addition, onward transmission from a persistent infection during the later stages of infection is likely to be rare. These insights have important implications for prioritising genomic surveillance and managing patients with persistent infections. FUNDING: Department of Health and Social Care.

Humans↗

PubMed2026

How the social lives of bacteria affect their pangenome.

Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.

Bacteria↗

PubMed2026

Social evolution and diminished olfactory function in larval honey bees.

Social evolution made larval honey bees dependent on adult colony members for feeding; they are confined to cells in waxen honeycombs and visited about 100 times per day by adult "nurse" bees. Based on organismal resource conservation theory, we predicted larvae have diminished olfactory capabilities at both the molecular and behavioral levels. Consistent with theory, larvae expressed very low levels of Orco, an essential gene for olfactory receptor (OR) function. By contrast, they showed higher expression of Ir25a, essential for other forms of sensory perception including gustation. Also consistent with theory, behavioral assays demonstrated that larvae cannot find food via olfaction, suggesting they use taste for feeding. By contrast, it is known that adult honey bees use OR-based olfaction extensively for a variety of behavioral functions, and the honey bee genome contains many OR-encoding genes. Comparative transcriptomic analyses of social and nonsocial insects suggest that this developmentally regulated suppression of olfactory function is related to social evolution, especially systems of offspring care.

Animals↗

PubMed2025

Dynamic clustering of genomics cohorts beyond race, ethnicity-and ancestry.

BACKGROUND: Recent decades have witnessed a steady decrease in the use of race categories in genomic studies. While studies that still include race categories vary in goal and type, these categories already build on a history during which racial color lines have been enforced and adjusted in the service of social and political systems of power and disenfranchisement. For early modern classification systems, data collection was also considerably arbitrary and limited. Fixed, discrete classifications have limited the study of human genomic variation and disrupted widely spread genetic and phenotypic continuums across geographic scales. Relatedly, the use of broad and predefined classification schemes-e.g. continent-based-across traits can risk missing important trait-specific genomic signals. METHODS: To address these issues, we introduce a dynamic approach to clustering human genomics cohorts based on genomic variation in trait-specific loci and without using a set of predefined categories. We tested the approach on whole-exome sequencing datasets in ten cancer types and partitioned them based on germline variants in cancer-relevant genes that could confer cancer type-specific disease predisposition. RESULTS: Results demonstrate clustering patterns that transcend discrete continent-based categories across cancer types. Functional analysis based on cancer type-specific clusterings also captures the fundamental biological processes underlying cancer, differentiates between dynamic clusters on a functional level, and identifies novel potential drivers overlooked by a predefined continent-based clustering. CONCLUSIONS: Through a trait-based lens, the dynamic clustering approach reveals genomic patterns that transcend predefined classification categories. We propose that coupled with diverse data collection, new clustering approaches have the potential to draw a more complete portrait of genomic variation and to address, in parallel, technical and social aspects of its study.

Humans↗

PubMed2026

Social isolation and 59 common health conditions: insights from observational and genetics analyses.

BACKGROUND: The impacts of social isolation on diverse health conditions and how it contributes to health risks remain unclear. We aimed to investigate the associations of social isolation with 59 health conditions among older adults. METHODS: Participants from the UK Biobank without baseline diagnosis of the included diseases were selected. Social isolation was assessed with three questions. The 59 health conditions included all-cause mortality, 5 cause-specific mortalities, and 53 diseases. We used an instrumental variable from multivariable common factor GWAS in Mendelian randomization (MR) to explore causal links of social isolation with diseases. Omics analyses were conducted to assess the roles of Olink plasma proteins and metabolomics, and PERM was calculated to evaluate the influence of other factors. RESULTS: A total of 489,741 individuals [266,706 (54.5%) women; mean age 56.5 years (SD 8.1)] were included. During a median follow-up of 12.5 years, social isolation was uncorrelated with the majority of 59 health conditions. Significantly, it was associated with increased risks of all-cause [adjusted HR (aHR) 1.28, 95% CI 1.25-1.32], 5 cause-specific mortalities (aHR range, 1.18-1.38), and 11 specific diseases (aHR range, 1.08-1.17). Living alone was the strongest item of isolation in predicting mortality (aHR range, 1.18-1.45) and selected diseases. MR analyses offered little evidence to support a causal link between social isolation and these diseases. The proteins involved in these associations are predominantly related to "response to stimulus". Proteomic signatures (PERM, 36%-49%), health behaviours (32%-59%), and socioeconomic factors (22%-42%) were the main explanatory factors linking social isolation to 8 health outcomes. CONCLUSIONS: Social isolation is associated with elevated risks of 17 out of the 59 examined adverse health outcomes, predominantly mortality-related conditions; however, MR analyses indicate an absence of evidence supporting causality for these associations.

Humans↗

PubMed1978

[Epidemiology of Burkitt's lymphoma in tropical areas - its relationship with malaria (author's transl)].

Epidemiology of tropical Burkitt's lymphoma shows the concomitant existence of the three following characteristics in endemic areas: - fairly dense rural population with a low standard of living; - early occurrence of primary infection by the Epstein-Barr virus (whose genome is always present in all tumour cells); - stable malaria. The social and economic level of these areas accounts for the specific features of the viral infection. Climatic factors determine permanent of prolonged transmission of malaria which could be mediated through a mitogen. Eradication of malaria could be a useful way to induce a fall in Burkitt's lymphoma incidence.

Africa↗

PubMed2025

Transcriptional interference gates monogenic odorant receptor expression in ants.

Communication is crucial to social life, and in ants, it is mediated primarily through olfaction. Ants have more odorant receptor (OR) genes than any other group of insects, generated through tandem duplications that produce large genomic arrays of related genes. The mechanism by which olfactory sensory neurons (OSNs) produce a single functional OR from these arrays remains unclear. In ant OSNs, only mRNA from one OR in an array is exported into the cytoplasm, while upstream genes are silent and transcripts from downstream genes remain nuclear. Here, we show that readthrough transcription in the downstream direction generates non-translated transcripts. We also find that OR promoters are bidirectional, producing antisense long non-coding RNAs. We suspect that neither readthrough nor antisense transcription produces functional RNA but that bidirectional transcription alone is critical to suppressing the expression of all other OR genes in a tandem array. Finally, we present evidence that this regulatory architecture is conserved across ants and bees, suggesting that this mechanism for functionally monogenic OR expression is widespread in insects with expanded OR repertoires.

Animals↗

PubMed2026

Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics.

Ancient DNA (aDNA) has transformed evolutionary biology and anthropology by providing direct, chronologically validated genetic evidence over millennia. This review synthesizes significant findings from the paleogenomic era (2010-2025), demonstrating how ancient DNA has resolved persistent debates across four interconnected themes: (i) human migration and admixture, revealing complex population transitions from archaic hominins to Holocene expansions; (ii) adaptation, tracking allele frequency changes during domestication and selection; (iii) pathogen history, clarifying the origins of pandemics and the evolution of microbiomes; and (iv) ecosystem dynamics, identifying extinction causes through sedimentary DNA and conservation genomics. We contend that scientific rigor and ethical stewardship are crucial for accurate conclusions, given ancient DNA study requires the destructive collection of culturally significant remains. This review argues that continued advancement will depend on the integration of genomic data with archaeological, isotopic, and proteomic evidence, and highlights the necessity for equitable involvement with descendant communities. By conceptualizing the past as a continuum of dynamic processes rather than static events, ancient DNA provides a revised historical narrative and insights relevant to contemporary concerns in conservation, health, and social justice.

Evolution↗

PubMed2025

The landscape of suicide risk factors in Latin America.

Suicide is a leading cause of death globally, with over 75 % of cases occurring in low- and middle-income countries (LMICs). Latin America, a severely underrepresented region in suicide research, has experienced a 6 % increase in its suicide rate from 2010 to 2016, contrasting with a global decline. In this commentary, we provide an overview of the epidemiological, social, and clinical factors influencing suicide in Latin America. We highlight the distinct trends in Latin America compared to other world regions, including the significant disparities in mental health care accessibility. Our review also considers the role of sociocultural factors such as strong family ties, traditional gender norms, and the impact of religiosity on stigma and care-seeking behaviors. Additionally, we address the lack of representation of Latin American populations in genetic studies on suicide, which hinders the identification of relevant biological markers and the development of tailored interventions. We call for increased research on the clinical, genetic, and social determinants of suicide in this region to better understand risk factors and ultimately inform suicide prevention strategies. Addressing this gap is critical for reducing suicide rates in Latin America.

Humans↗

PubMed2025

A Sociotechnical Approach to Genomic Data Privacy: A Comparative Analysis.

The sharing of genomic data across international borders presents significant privacy law challenges.Secured computed environments on smartphones allow the storing and processing of sensitive data without the underlying data being shared with processors.A novel technology, described here, to process genomic data within a secured computing environment seems to comport with EU and US privacy laws, despite their differing aims and rules.This technology suggests there may be technological solutions to privacy law fragmentation across jurisdictions, so long as data subjects socially trust the technology and have control over their data.

genome↗

PubMed2025

Multi-Omics and Integrative Analytics in Natural Products Discovery.

Natural products (NPs) have long been an essential source of new bioactive compounds for drug discovery; however, traditional methods for screening and isolating these compounds can be slow and often yield diminishing returns. Fortunately, advanced multi-omics and computational approaches present powerful solutions to these challenges. This review highlights innovative methodologies that integrate metabolomics, genomics, transcriptomics, and proteomics with bioinformatics and analytical chemistry to accelerate NP discovery. For instance, untargeted metabolomics platforms like high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Global Natural Products Social (GNPS) molecular networking allow for comprehensive profiling of new compounds, while targeted isotope-labeling strategies enhance this process. Additionally, genome and metagenome mining tools such as antibiotics and secondary metabolite analysis shell (antiSMASH), Deep Biosynthetic Gene Cluster (DeepBGC), and Pipeline for Reconstructing Integrated Syntheses of Metabolites (PRISM) quickly identify biosynthetic gene clusters (BGCs) in both cultured and uncultured organisms, often using heterologous expression to validate products. Transcriptomic analyses, including RNA sequencing (RNA-seq), co-expression networks, and fluxomics, help clarify how pathways are regulated, while quantitative proteomics techniques like tandem mass tags/isobaric tags for relative and absolute quantitation (TMT/iTRAQ) and label-free methods, along with chemoproteomics approaches such as cellular thermal shift assay and thermal proteome profiling (TPP), uncover molecular targets and their mechanisms of action. This review also places significant emphasis on the role of artificial intelligence (AI) and machine learning (ML) in integrating multi-omics data, spanning activities from constructing gene-metabolite correlation networks to leveraging knowledge graphs and graph neural networks for data fusion and functional prediction. Finally, this review concludes by discussing the synergistic benefits of multi-omics for natural-product discovery, addressing current technical challenges, and exploring future directions toward high-throughput, intelligent data integration for next-generation NP research.

Biological Products↗

PubMed2025

Education, socioeconomic status, leisure sedentary behaviors and female infertility: mendelian randomization study.

BACKGROUND: Previous studies have indicated that education, socioeconomic status, and leisure sedentary behavior may be associated with female infertility. However, it remains unclear whether these associations imply causal relationships. METHODS: Genetic variants from genome-wide association studies (GWAS) of education, socioeconomic status, and leisure sedentary behaviors were obtained from the UK Biobank and MRC-IEU database (Medical Research Council Integrative Epidemiology Unit), female infertility data was acquired from the FinnGen Biobank. Univariable and multivariable MR analyses were performed to explore the relationships between these traits and female infertility. RESULTS: The results of the univariate MR analysis indicated that age of full-time education had a protective effect on female infertility (odds ratio [OR] 0.471; 95% confidence interval [CI] 0.24 to 0.93; p = 0.03). Multivariable MR and reverse MR studies support the existence of a relationship between them. However, no causal correlation was found between other traits and female infertility. No significant heterogeneity or horizontal pleiotropy was detected, and the stability of the results was confirmed through sensitivity analysis and the leave-one-out test. CONCLUSIONS: A later age of completion of full-time education may be causally related to a reduced risk of female infertility, but no causality is established between other educational levels factors, socioeconomic status, or sedentary behaviors and infertility risk.

Humans↗