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PubMed2025

Comparison of phylogenetic metrics of transmission in symptomatic and asymptomatic tuberculosis.

BACKGROUND: Understanding drivers of Mycobacterium tuberculosis (Mtb) transmission remains a critical challenge in high-burden settings. Tuberculosis control efforts traditionally target symptomatic individuals, yet the role of asymptomatic cases in sustaining transmission is increasing recognized. METHODS: We conducted a genomic and epidemiological analysis of Mtb isolates collected in Mato Grosso do Sul, Brazil, between 2008 and 2024. From 2017 to 2022, active case finding was performed in three of the state's largest prisons, whereby sputum was collected from individuals irrespective of symptoms and tested by GeneXpert and culture. We evaluated several metrics of recent transmission from symptomatic and asymptomatic individuals, including phylogenetic clustering, Time-scaled Haplotype Density (THD), Local Branching Index (LBI), and transmission probabilities inferred using the Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH). FINDINGS: We sequenced 2,362 Mtb strains, of which 3.5% (115/2,362) were resistant to at least one drug, and 0.6% (16/2,362) were multi-drug resistant. Most strains were lineage 4, and 78.2% of all isolates were part of a genomic cluster. Among 2,362 individuals with tuberculosis, 1,137 were incarcerated at the time of diagnosis. Among these, 505 were identified through active case finding: 277 had symptomatic disease and 228 had asymptomatic tuberculosis. There was no significant difference in phylogenetic clustering proportion (77% vs. 85%; p= 0.816), THD (median 0.50 vs. 0.39; p = 0.120), or LBI (median 0.00863 vs. 0.00871; p = 0.086) between symptomatic and asymptomatic individuals. Bayesian transmission trees revealed no significant difference in the number of secondary infections inferred from symptomatic compared with asymptomatic individuals (p = 0.56). These findings were consistent across genomic clusters and robust to model assumptions. INTERPRETATION: We identified no differences in transmission from symptomatic compared with asymptomatic individuals, using several genomic measures of transmission, underscoring the substantial contribution that asymptomatic tuberculosis makes to transmission at the population level.

Asymptomatic↗
PubMed2026

Getting to the Core of the Matter-Assessing the Role of Replication in Metabarcoding-Based sedaDNA.

Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained > 70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.

DNA Barcoding, Taxonomic↗
PubMed2025

Germline stem cell isolation, lineage tracing, and aging in a protochordate.

Germline stem cells (GSCs), the source of gametes, are the only stem cells capable of passing genes to future generations and are therefore considered units of natural selection. Yet, the factors that influence GSC fitness, and thus govern GSC competition, which exist in both protochordates and mammals, remain poorly understood. We studied how aging affects GSC fitness in the protochordate Botryllus schlosseri, an evolutionary crosspoint between invertebrates and vertebrates. GSCs were isolated and distinguished from developing and mature gametes using flow cytometry and scRNA-Seq, facilitated by a new PacBio genome assembly. Moreover, their function was validated through a novel lineage tracing approach that combines membrane-labeled GSC transplantation with scRNA-Seq. Leveraging our method to isolate them, single-cell transcriptomics showed significant age-related changes between young and old GSCs. Spermatids and sperm, however, showed minimal changes, suggesting that reproductive aging is governed by GSCs rather than by gametes. Reduced expressions of markers like DDX4 and PIWIL1 in aged GSCs mirrored trends in mammalian datasets, pointing to a conserved GSC-driven aging mechanism across chordate evolution. This study provides new techniques that lay the foundation to investigate further drivers of GSC fitness and highlights fertility-related genes as promising targets for therapies to preserve reproductive health.

Journal Article↗
PubMedDate not supplied

The influence of UV radiation on protistan evolution.

Ultraviolet radiation has provided an evolutionary challenge to life on Earth. Recent increases in surficial ultraviolet B fluxes have focused attention on the role of UV radiation in protistan ecology, cancer, and DNA damage. Exploiting this new wealth of data, I examine the possibility that ultraviolet radiation may have played a significant role in the evolution of the first eukaryotes, that is, protists. Protists probably arose well before the formation of a significant ozone shield, and thus were probably subjected to substantial ultraviolet A, ultraviolet B, and ultraviolet C fluxes early in their evolution. Evolution consists of the generation of heritable variations and the subsequent selection of these variants. Ultraviolet radiation has played a role both as a mutagen and as a selective agent. In its role as a mutagen, it may have been crucial in the origin of sex and as a driver of molecular evolution. As a selective agent, its influence has been broad. Discussed in this paper are the influence of ultraviolet radiation on biogeography, photosynthesis, and desiccation resistance.

Animals↗
PubMed2026

Biocontrol potential and molecular basis of predation in a marine raptorial ciliate.

Predator-prey interactions are widespread across organisms and are key drivers of morphological and behavioral evolution. Despite this, predation remains poorly understood among microbial eukaryotes, mostly due to the absence of a tractable experimental system that allows quantitative, reproducible investigation. This study establishes the marine raptorial ciliate Chaenea vorax as a highly efficient predator, with Rosenzweig-MacArthur model simulations based on predation data showing that only a few dozen individuals can eliminate the vast majority of the facultatively pathogenic ciliate Uronema marinum within 1-2 days, providing a quantitative basis for developing predator-based biocontrol strategies in aquaculture. Genomic analysis shows that C. vorax possesses a highly fragmented macronuclear genome enriched with predation-related pathways, including calcium-mediated contractility, cellular proteolysis, toxin expulsion systems, among others. Transcriptomic profiling during predation events further demonstrates significant upregulation of genes involved in cytoskeletal remodeling, proteolytic activity, and cellular detoxification. Evolutionary analyses suggest that C. vorax has an extremely long evolutionary history, exceptionally high nucleotide diversity even among ciliates, and gene family expansions linked to predatory adaptation. Although the prey possesses certain defensive mechanisms (e.g. trichocysts), these are largely ineffective against short-term predation in closed aquatic environments. These findings provide fundamental insights into the molecular basis of predation in ciliates and suggest the potential utility of C. vorax in biocontrol applications targeting pathogenic ciliates.

Ciliophora↗
PubMed2026

Ancient DNA and Human Physiology.

Ancient DNA (aDNA) enables the reconstruction of chronologically sampled genomes from ancient humans, animals, plants, pathogens, and microorganisms, as well as environmental DNA, providing a record of biological changes through time. Improvements in short and degraded DNA extraction methods and low-cost sequencing now enable the generation of broad, cross-regional datasets that expand evolutionary analyses from past population demography to biological mechanisms. By tracking temporal shifts of allele frequencies, integrating functional genomics resources (e.g., gene expression, chromatin structure variation), modeling population demography to separate selection from genetic drift, and aligning genetic changes with archaeological, cultural, and climatic data, aDNA has the potential to link sequence variation to physiological function within their temporal and environmental contexts. In this review, we summarize illustrative case studies from aDNA research spanning complex traits, dietary adaptations, and responses to pathogens and other environmental changes, showing how human biology has evolved under multiple selective pressures through time. These dated signals help triage experimental work and expose mechanisms that are rare or absent in living cohorts. Although some challenges remain, such as geographic and temporal sampling disparities, limitations in data resolution and variant detection, and genotype-phenotype uncertainties, rapid methodological progress and stronger ethical frameworks are expanding what can be inferred, making aDNA a promising tool for refining physiological pathways, their timing, and their drivers.

Humans↗
PubMed2026

PIK3CA in Cancer: Structure, Biology, Alterations, and Actionability.

PIK3CA, which encodes the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K), is one of the most frequently altered oncogenes in human cancer and a major driver of tumor initiation, progression, metastasis, and therapeutic resistance. Over the past two decades, advances in structural biology, cancer genomics, and translational research have substantially expanded our understanding of PIK3CA function and established the PI3K pathway as a clinically actionable therapeutic target. This review provides an overview of the structural organization and physiological functions of the PI3Kα complex, the molecular mechanisms underlying oncogenic activation, and the diverse spectrum of PIK3CA alterations across human malignancies. We also summarize the current landscape of PI3K-targeted therapies, highlighting both approved agents and emerging therapeutic strategies. Clinical evidence supports the rational integration of PI3K inhibitors with endocrine therapy, CDK4/6 inhibitors, MAPK pathway inhibitors, dual PI3K/mTOR inhibition, and immune checkpoint blockade. In addition, accumulating evidence indicates that PIK3CA plays a pivotal role in shaping the tumor immune microenvironment, providing a biological rationale for combining PI3K inhibition with immunotherapy. Finally, we discuss future directions in precision oncology, emphasizing integrated molecular profiling, liquid biopsy, single-cell and spatial technologies, functional genomics, and evolutionary approaches as complementary strategies to refine patient selection, overcome therapeutic resistance, and optimize clinical outcomes.

PI3K signaling↗
PubMed1986

Human cellular sequences detectable with adenovirus probes. I. Evidence for novel repeat sequences and a possible E1a-like cellular "gene".

Previous studies suggesting homology between human cellular DNA and the DNAs from adenovirus types 2 and 5 are extended in the present paper. A clone (ChAdh), isolated from a human genomic DNA library using an adenovirus probe, hybridized to discrete regions of adenovirus 2 DNA, including part of the transforming genes E1a and E1b, as well as to repeated sequences within human DNA. The E1a and E1b genes both hybridize to the same 300 base pair Sau3AI fragment within ChAdh although there is no obvious homology between E1a and E1b. The Ad 2 E1a gene was also used as a probe to screen other cellular DNAs to determine whether repeated sequences detectable with Ad2 DNA probes were conserved over long evolutionary periods. Hybridization was detected to the genomes of man, rat, mouse and fruit fly, but not to those of yeast and bacteria. In addition to a "smear" hybridization, discrete fragments were detected in both rodent and fruit fly DNAs. The experiments reported suggest the existence of two different types of cellular sequences detected by Ad 2 DNA: (1) repeated sequences conserved in a variety of eukaryote genomes and (2) a possible unique sequence detected with an E1a probe different from that responsible for hybridization to repeated sequences. This unique sequence was detected as an EcoRI fragment in mouse DNA and had a molecular size of about 8.8 kb.

Adenoviruses, Human↗
PubMed2026

Viral community structure in New Zealand's aquatic birds is associated with scavenging behavior.

Wild migratory birds play a major role in the global spread of viruses, yet the ecological drivers underpinning viral diversity and transmission, particularly host behavior, remain poorly understood. Aotearoa/New Zealand provides a powerful system to address this, including unique species that reflect its geographical isolation, yet with international connections provided by migratory birds across the East Asian-Australasian Flyway and Antarctic regions. Herein, we conducted a large-scale metatranscriptomic survey of wild birds across New Zealand and its subantarctic islands, in which we collected 1,348 samples from 690 individuals across 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, expanding our knowledge of avian viral diversity. Notably, viral community composition was most strongly associated with bird scavenging behavior, which explained more variation than host taxonomy, geography, or migratory status. Scavenging birds and opportunistic scavengers harbored more diverse viromes than non-scavengers, consistent with increased viral exposure across trophic levels. This was supported by the detection of 12 mammalian-associated viruses, primarily in scavengers, including hedgehog hepatovirus, rabbit hemorrhagic disease virus 2, and sea lion astroviruses, with host sequence data confirming dietary origin. We also detected viruses of epidemiological and evolutionary interest, including a low-pathogenic avian influenza A(H1N9) virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), which represented the first putative avian member of the Tobaniviridae. These findings suggest that virome structure in wild birds is associated with scavenging behavior, thus highlighting the importance of incorporating host ecology into viral surveillance and risk assessment.

New Zealand↗
PubMed2026

Evolution of virulence of a plant RNA virus in developmental stage-structured host populations.

Natural host populations are age-structured, and developmental stages differ in susceptibility and within-host pathogen dynamics, potentially imposing distinct selective pressures on viruses. However, the evolutionary consequences of host age structure remain poorly understood. We experimentally evolved turnip mosaic potyvirus for 5 passages in Arabidopsis thaliana populations spanning 7 demographic regimes, from juvenile- to mature-dominated cohorts. We quantified disease progression, symptom severity, and viral load, cross-inoculated evolved lineages across host stages to construct infection matrices, and performed whole-population sequencing at passages 1 and 5. Disease traits changed markedly with passage, demography, and their interaction. Disease progression evolved faster in older populations, whereas symptom severity was independent of median age, indicating demographic reweighting of virulence components. Viral load increased across passages and positively correlated with severity, linking within-host fitness to symptoms. Cross-inoculation assays revealed a modular infection network: juvenile-evolved lineages specialized on juvenile hosts, whereas lineages from intermediate and older populations were more generalist. Genomically, we detected both parallel and demography-specific adaptations, including recurrent changes in the viral protein VPg (involved in translation, replication, and host interactions) as well as synonymous variants showing consistent or opposing selection across host population stage structures. Overall, host age structure emerges as a major ecological driver of virulence evolution, shaping tradeoffs between disease progression and severity and determining specialization versus generalism. These results integrate phenotypic and genomic responses and suggest that manipulating crop age structure could steer virus evolution toward less damaging outcomes.

Virulence↗
PubMed2025

Genetic diversity of Murray Valley encephalitis virus 1951-2020 identified via phylogenetic and evolutionary analyses.

Murray Valley encephalitis virus (MVEV) is a mosquito-borne orthoflavivirus endemic to Australia that can cause fatal neurological disease. The enzootic focus of MVEV is believed to reside in northern Western Australia (WA). We sequenced whole genomes of 70 MVEV sampled over 51 years, 1969-2020, from locations across Australia and Papua New Guinea (PNG) and identified greater MVEV diversity than previously recognized. Genotype 1 (G1) demonstrated greatest intra-genotype diversity and was predominant over the sampling period with sub-lineage G1B circulating in WA and seeding activity across Australia. G1A included viruses sampled across northern WA, as well as the Northern Territory (NT). A newly identified sub-lineage G1C circulated in northern WA in 1993 and was detected again in 2003. G2 viruses were distributed across the Kimberley and Pilbara regions of northern WA, and in the NT. Although no new G3 and G4 viruses, previously identified only in PNG, were detected in the present study, other MVEV originating in PNG clustered with G1A. We confirm MVEV is enzootic in northern WA, with transmission occurring more frequently and across a wider geographical area than previously recognised. Additionally, we identify evidence of regular genotype replacement that has occurred over many decades where the major genotypes G1 and G2 have circulated in northern WA since the late 1960s. We also show that WA MVEV likely seeded an MVE outbreak in Victoria in 1974, further supporting the notion that the enzootic focus of MVEV lies in northern WA. Recent increases in MVEV detections, MVE cases and deaths in WA and across Australia highlight the need for enhanced surveillance and more frequent sampling to understand viral origin and genomic diversity, to identify potential virulence motifs, and to understand the ecological drivers that determine emergence of MVEV in northern WA and movement of MVEV across the country.

Encephalitis Virus, Murray Valley↗
PubMed2025

Homoploid Hybrid Speciation in a Marine Pelagic Fish.

Homoploid hybrid speciation (HHS) is an enigmatic evolutionary process where new species arise through hybridisation of divergent lineages without changes in chromosome number. Although increasingly documented in various taxa and ecosystems, convincing cases of HHS in marine fishes have been lacking. This study presents a possible case of HHS in a pelagic marine fish based on comprehensive genomic, morphological, and ecological analyses. Population genomics, species tree estimation, and tests of introgression and admixture identified three sympatric clusters in Megalaspis cordyla in the western Pacific and the admixed nature of one cluster between the others. Moreover, model-based demographic inference favoured a hybrid speciation scenario over introgression for the origin of the admixed cluster. While contemporary gene flow suggested partial reproductive isolation, examination of occurrence data and ecologically relevant morphological characters suggested ecological differences between the clusters, potentially contributing to the reproductive isolation and niche partitioning in sympatry. The clusters are also morphologically distinguishable and thus can be taxonomically recognised as separate species. The hybrid cluster is restricted to the coasts of Taiwan and Japan, where all three clusters coexist. The parental clusters are additionally found in lower latitudes, where they display non-overlapping distributions. Given the geographical distributions, estimated times of species formation, and patterns of historical demographic changes, we propose that the Pleistocene glacial cycles were the primary driver of HHS in this system. We also develop an ecogeographic model of HHS in marine coastal ecosystems, including a novel hypothesis to explain the initial stages of HHS.

Animals↗
PubMed2006

Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis.

BACKGROUND: The Gram-negative bacterium Burkholderia pseudomallei (Bp) is the causative agent of the human disease melioidosis. To understand the evolutionary mechanisms contributing to Bp virulence, we performed a comparative genomic analysis of Bp K96243 and B. thailandensis (Bt) E264, a closely related but avirulent relative. RESULTS: We found the Bp and Bt genomes to be broadly similar, comprising two highly syntenic chromosomes with comparable numbers of coding regions (CDs), protein family distributions, and horizontally acquired genomic islands, which we experimentally validated to be differentially present in multiple Bt isolates. By examining species-specific genomic regions, we derived molecular explanations for previously-known metabolic differences, discovered potentially new ones, and found that the acquisition of a capsular polysaccharide gene cluster in Bp, a key virulence component, is likely to have occurred non-randomly via replacement of an ancestral polysaccharide cluster. Virulence related genes, in particular members of the Type III secretion needle complex, were collectively more divergent between Bp and Bt compared to the rest of the genome, possibly contributing towards the ability of Bp to infect mammalian hosts. An analysis of pseudogenes between the two species revealed that protein inactivation events were significantly biased towards membrane-associated proteins in Bt and transcription factors in Bp. CONCLUSION: Our results suggest that a limited number of horizontal-acquisition events, coupled with the fine-scale functional modulation of existing proteins, are likely to be the major drivers underlying Bp virulence. The extensive genomic similarity between Bp and Bt suggests that, in some cases, Bt could be used as a possible model system for studying certain aspects of Bp behavior.

Burkholderia↗
PubMed2025

Mapping Species Birth Across the Recombination Landscapes of Marine Snails.

Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study, we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula. These results challenge traditional theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population-specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.

Genetic Introgression↗
PubMed2026

Novelty, diversity, and genetic dark matter in enterococci of invertebrates.

Enterococci appear to have originated in the guts of early terrestrializing arthropods and invertebrates over 425 million years ago-hosts that are now highly diverse and widespread in nature today. Yet most knowledge of the genus comes from human infection-associated lineages with genomes swollen by the recent accretion of foreign DNA conveyed by mobile elements. Because invertebrates dominate terrestrial animal diversity and biomass, they would be predicted to constitute a major but little-explored reservoir of enterococcal diversity. We therefore systematically examined Enterococcus association and species diversification in invertebrate hosts of the comparatively natural, isolated, but well-characterized environment of the Azorean island of Terceira. Over 100 invertebrate specimens were examined for associated enterococci, which were taxonomically classified by whole-genome sequencing. Supporting the existence of a large pool of uncharacterized enterococci and Enterococcus-adapted genes, 40% (eight of 20) of the Enterococcus species identified were either undescribed, including four candidate new species described here, or very recently discovered. In contrast, control isolates from vertebrates were exclusively of known species typical of sampling elsewhere, discounting geographic isolation as a main driver of the novelty observed. Further, because of the abundance of E. casseliflavus and E. flavescens in this collection, we obtained the resolution necessary to quantify the divergence and decipher the drivers of speciation in the controversial division between these naturally vancomycin-resistant species. These findings provide robust support for the existence of a large pool of new species and unexplored adaptive traits in invertebrate-associated enterococci-diverse environmental survival traits optimized for expression in an enterococcal background, and well positioned for transmission into human-associated enterococcal strains.IMPORTANCEEnterococci are auxotrophic gut-associated bacteria that co-evolved with their terrestrial hosts over many eons. In the last 75 years-the "antibiotic era"-E. faecalis and E. faecium gained genes for antibiotic resistance and enhanced virulence, emerging as leading causes of multidrug-resistant infection. Little is known about the source of those genes or the pathway by which they entered human-associated strains. A recent global survey suggested a potentially large repository of uncharacterized genetic diversity in the enterococci of invertebrates. We directly tested this prospect by examining enterococci of invertebrate hosts in a largely natural and pastoral environment. Our findings provide clear evidence that invertebrates naturally harbor vast unexplored enterococcal diversity. Moreover, associations are likely driven by intrinsic host selection factors rather than geographic isolation. This expands our knowledge of Enterococcus biodiversity, including the identification of four novel species, identifying a vast reservoir of enterococcal genes available to species that colonize and infect humans.

Animals↗