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At least 19 recordsLinked to original sources
PubMed2025

Reproductive Isolation due to Divergent Ecological Selection Is Accompanied by Vast Genomic Instability in Experimentally Evolved Yeast Populations.

Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1 and F2 intraspecific hybrids. We found evidence for large-scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability-a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations, on the other hand, remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, that is, new structural variants (especially insertions, deletions and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.

Reproductive Isolation↗
PubMed2026

Hidden genomic structure and widespread structural polymorphism across environmental gradients in the spiny sea star Marthasterias glacialis.

Genomic regions of reduced recombination can preserve linkage among co-adapted alleles, facilitating local adaptation despite high connectivity. Such regions-often generated by chromosomal inversions-may be especially important in highly dispersive marine taxa yet remain poorly documented in echinoderms. Here, we combined a chromosome-level reference genome with genome-wide ddRAD-seq from 296 Marthasterias glacialis individuals across 19 Atlantic-Mediterranean locations to quantify population structure and scan for recombination-suppressed haploblocks. Genome-wide neutral markers showed significant population differentiation together with evidence of high connectivity, revealed by the presence of inter-ecoregion migrants. Additionally, we identified 16 polymorphic haploblocks with patterns consistent with putative chromosomal inversions spanning 18.6% of the genome. Haploblock haplotypes were strongly environmentally and geographically structured and contained genes with key functions in stress response, osmoregulation and thermal tolerance. Haplotype distributions also paralleled previously described mitochondrial lineages despite nuclear gene flow, consistent with a model of ancient divergence followed by secondary contact. Overall, our results suggest a role for widespread structural polymorphism in adaptive differentiation in Echinodermata, providing a framework for linking echinoderm genome rearrangements to ecological divergence. Marthasterias glacialis thus emerges as a promising system to explore how structural variation contributes to adaptation and genome evolution in highly dispersive organisms.

Animals↗
PubMed2026

Genomic signatures of host-range divergence in the generalist Beauveria bassiana and the specialist Beauveria brongniartii.

Entomopathogenic fungi of the genus Beauveria are widely used biological control agents that infect diverse insect hosts and can also associate with plants as rhizosphere colonizers and endophytes. Within this genus, Beauveria bassiana is a cosmopolitan generalist, whereas Beauveria brongniartii exhibits a narrower host range, primarily targeting soil-dwelling coleopteran larvae with limited evidence of plant colonization. To explore genomic differentiation associated with this ecological divergence, the commercially exploited B. brongniartii strain BIPESCO2 and B. bassiana ATHUM 4946 were sequenced using Oxford Nanopore technology, followed by comparative genomic analyses across multiple strains. Orthology identified species-specific gene families, although overall genome architecture and core gene content were highly conserved. The CAZyme repertoires were nearly identical, indicating retention of a versatile enzymatic toolkit supporting plant association, saprotrophy, and insect pathogenicity. In contrast, biosynthetic gene clusters displayed substantial variation, including structural remodeling of Beauveria-specific virulence-associated clusters and expansion of type I polyketide synthase clusters in B. brongniartii. Effector prediction revealed a conserved core of largely uncharacterized proteins alongside species-specific orthogroups enriched in adhesion-, immunity-, and cuticle-interaction domains. Together, these findings indicate that host-range divergence in Beauveria is associated with compartmentalized genomic differentiation, particularly in secondary metabolism and a limited subset of lineage-specific virulence factors, rather than in the conserved core infection machinery.

Beauveria↗
PubMed2025

Comparative genomic analysis of Acer tsinglingense and A. davidii provides insights into nervonic acid biosynthesis, population evolution and genome vulnerability of endangered A. tsinglingense.

Global biodiversity is facing threats from climate change, habitat fragmentation, and anthropogenic activities-pressures that particularly endanger endemic and narrowly distributed species. In this study, the high-quality chromosome-level genomes of two ecologically divergent maples were assembled: the endangered and range-restricted Acer tsinglingense (791.40 Mb) and its widespread congener Acer davidii (1291.99 Mb). Phylogenomic analysis indicates that the two species diverged ~16.3 million years ago, with A. tsinglingense showing notable gene family expansions in secondary metabolite pathways. Notably, the 3-ketoacyl-CoA synthase gene family, which is involved in nervonic acid biosynthesis, underwent significant expansion and tandem duplication in A. tsinglingense, exhibiting high expression in buds. Population genomic analysis revealed that, compared with the widely distributed A. davidii, A. tsinglingense possesses lower genetic diversity, higher harmful mutation load, and signatures of a severe population bottleneck during the Late Pleistocene. Genome-environment association analysis further identified climate-adaptive genomic variations linked to five key environmental factors and projected potential genomic offsets under future climate scenarios. The southern lineage of A. tsinglingense exhibited greater climate sensitivity and genomic vulnerability under strong selective pressures, underscoring its importance as a conservation priority. Our research reveals that metabolic specializations in A. tsinglingense (such as the synthesis of nervonic acid) may confer competitive advantages in specific habitats. However, factors including its restricted distribution, historical population bottlenecks, and accumulated genetic load severely constrain its evolutionary potential to cope with rapid climate change. These findings emphasize the importance of elucidating the genomic basis and mechanisms of endangerment in metabolically specialized and threatened plant species to inform effective conservation strategies.

Genome, Plant↗
PubMed2025

Insights into salt adaptation from comparative genomics of Scirpus mariqueter and a related freshwater species.

The evolutionary mechanisms underlying ecological divergence between closely related species remain a central question in biology. Scirpus mariqueter is a coastal halophyte thriving in the saline intertidal zone and exhibits marked adaptive differences compared to its freshwater relative Bolboschoenus planiculmis. However, the genomic and physiological bases of its salt tolerance remain poorly understood. We generated high-quality genome assemblies for both species and investigated the anatomical and physiological innovations underpinning S. mariqueter's adaptation to extreme environments. Morphological analyses revealed that S. mariqueter evolved specialized traits-including denser leaf palisade tissues, enhanced stem aerenchyma, and compact root cortices-synergistically limiting salt intrusion. Using chromosome-level genomes, we identified lineage-specific expansions in S. mariqueter of gene families critical for salinity tolerance, including those regulating carbohydrate metabolism, photosynthetic fidelity, and reactive oxygen species (ROS) detoxification. Strikingly, germin-like protein (GLP) and wound-induced protein (WIP) families contain tandem repeats mediating ROS scavenging and cell wall integrity, underwent adaptive expansion, paralleling anatomical innovations. Physiological profiling under salt stress confirmed S. mariqueter's unique capacity to maintain photosynthetic activity and carbohydrate production, directly linking genomic adaptations to functional resilience. This study reveals an adaptive strategy whereby structural modifications, diversification of stress-responsive gene families, and metabolic stability collectively enable S. mariqueter to thrive in saline ecosystems.

Salt Tolerance↗
PubMed2026

Genetic (Genomic) and Morphological Evidence Suggest That the Korean Endemic Fat Minnow (Rhynchocypris kumgangensis) and the Deogyu Population Represent Distinct Species.

Geographically disconnected populations of freshwater fishes often show ecological and genetic divergence in response to opposing selection differentials in different habitat environments, sometimes leading to the formation of ecotypes and even speciation. Nevertheless, evidence for the speciation through allopatric processes in freshwater fish systems remains scarce. Kumkang fat minnow (Rhynchocypris kumgangensis), a Korean endemic coldwater fish, has recently been suggested to diverge into a separate species (Rhynchocypris deogyuensis). However, the level of their genetic and ecological divergence remains largely unknown. We analyzed population genetic structure of R. kumgangensis together with R. deogyuensis using mitochondrial DNA (mtDNA) and eight newly developed microsatellite markers. Genetic divergence at mitogenome level was further assessed between the presumed two species. Moreover, we examined morphology between two groups by analyzing morphometric traits and also conducted geometric morphometrics on body shape. We found distinct population structure between R. kumgangensis and R. deogyuensis at both mtDNA and microsatellites. One remnant population of R. deogyuensis harbored only a single haplotype and showed a very high level of inbreeding. Comparative analysis of the mitogenomes showed approximately 2.9% divergence between R. kumgangensis and R. deogyuensis, supporting the species-level divergence. The analyses of both morphometric traits and geometric morphometrics indicated significant morphological divergence between the two species. The observed low values of length-weight relationship and condition factor for R. deogyuensis are likely to be attributed to effects of the elevated level of inbreeding and depleted genetic diversity. Overall, our combined genetic/genomic and morphological analyses suggest the considerable divergence between R. kumgangensis and R. deogyuensis, supporting the hypothesis that they are distinct species. The mechanisms underpinning how they speciate still need to be studied further in detail.

Deogyu fat minnow↗
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↗
PubMed2025

The role of stochasticity in fungal community assembly: explaining apparent stochasticity with field experiments.

Stochasticity is a main process in community assembly. However, experimental studies rarely target stochasticity in natural communities, and hence experimental validation of stochasticity estimates in observational studies is lacking. Here, we combine experimental and observational data to unravel the role of stochasticity in the assembly of wood-inhabiting fungi. We carried out a replicated field experiment where the natural colonization of a focal fungal species was simulated through inoculation, and the local fungal communities were monitored through DNA metabarcoding before and after the inoculations. The amount of stochasticity in fungal colonization was less pronounced than expected from the amount of unpredictability in observational data, suggesting that stochasticity may play a smaller role in fungal occurrence than previously anticipated, or that it may be a stronger influence in the dispersal and establishment phases than in colonization per se. Stochasticity was more prominent in the initial phase of community succession, with the earliest successional stage involving a higher level of stochasticity than the later stage after 2 years. We conclude that experimentally measuring the role of stochasticity in community assembly is feasible for species-rich communities under natural conditions and highlight the importance of experimentally testing the accuracy of stochasticity estimates based on observational data.

Stochastic Processes↗
PubMed2026

A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae.

Saccharomyces cerevisiae occurs predominantly in the diploid state in nature, limiting genetic analyses of wild populations. Here, we establish a haploid collection from 32 Taiwanese S. cerevisiae isolates through targeted HO disruption. This resource spans predomesticated Asian wild lineages and enables the investigation of reproductive isolation and ecological trait variation. Although all pairwise hybridizations formed zygotes, many yielded reduced spore viability, revealing strong postzygotic barriers. Genome analyses associated reduced hybrid fertility with lineage-specific structural variation, including elevated levels of intra-chromosomal inversions in H413-8/TW1 and inter-chromosomal rearrangements in PD35A/CHN-V, rather than sequence divergence alone. Phenotyping revealed ecological differentiation, with TW1 favoring cooler growth and a natural hybrid exhibiting heterosis with expanded thermotolerance. Most wild strains grew poorly on maltose, whereas anthropogenic strains displayed enhanced utilization linked to MAL + regulatory alleles and maltose-specific transporters. Together, this haploid collection links structural variation and metabolic divergence to ecological and reproductive differentiation in wild S. cerevisiae.

Saccharomyces cerevisiae↗
PubMed2026

Crawling under the radar: Two novel Paulinella species expand knowledge about the ecology and evolution of a primary plastid-containing amoeba lineage.

The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes.

Paulinella↗
PubMed2026

GiantHost: a domain-adaptive and uncertainty-aware framework for giant virus host prediction.

MOTIVATION: Nucleocytoplasmic large DNA viruses (NCLDVs) play crucial roles in global ecosystems. Although metagenomics has vastly accelerated the discovery of novel NCLDVs, predicting their hosts from fragmented contigs remains a critical bottleneck, with no dedicated end-to-end computational tools currently available. Addressing this gap requires overcoming three fundamental challenges: the extreme scarcity of labeled reference genomes, the severe domain shift between laboratory isolates and diverse environmental metagenomes, and the inability of traditional deterministic models to quantify prediction uncertainty-a crucial requirement for reliable ecological profiling where novel, divergent viruses are prevalent. RESULTS: We present GiantHost, the first NCLDV host prediction tool with domain adaptation and uncertainlty awareness. GiantHost employs a dual-tower neural network to integrate dense genome traits and sparse GVOG profiles, allowing better integration of heterogeneous features. To overcome label scarcity and domain shift, we leverage 1400 environmental viral genomes (GVMAGs) via semi-supervised multi-task learning and Domain Adversarial Neural Networks (DANN), effectively bridging the distributional gap between RefSeq and environmental data. Additionally, GiantHost incorporates Conformal Prediction (CP) to output statistically guaranteed prediction sets rather than overconfident single labels. Evaluated under rigorous genome-level cross-validation, GiantHost demonstrates robust predictive power. Applied to the Tara Ocean dataset, GiantHost successfully captured the vertical stratification of NCLDV hosts-revealing a depth-dependent decline of phytoplankton-infecting viruses and a relative enrichment of Amoebozoa-infecting viruses in the mesopelagic zone. AVAILABILITY: The source code of GiantHost is available via: https://github.com/FuchuanQu/GiantHost.

Giant Viruses↗
PubMed2025

The distribution of fitness effects varies phylogenetically across animals.

The distribution of fitness effects (DFE) describes the selection coefficients () of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (), and the proportion of new beneficial mutations (). These findings align with Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGM's predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals.

Fisher’s geometric model↗
PubMed2026

The distribution of fitness effects of nonsynonymous mutations varies phylogenetically across animals.

The distribution of fitness effects (DFE) describes the selection coefficients of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of differences in the DFE for non-synonymous mutations have not been systematically investigated across species with divergent phylogenetic histories and ecologies. Here, we inferred the DFE in natural populations of 11 animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We found that mammals have a higher proportion of strongly deleterious mutations (defined as s≤-0.01; 22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Further, the DFE co-varies with phylogeny, such that the mean mutation effects are more similar in closely related species (Pagel's λ = 0.84, P = 0.01). Next, we investigated whether various summary statistics of the DFE were related to variation in life-history traits across these organisms. We found some support for genome size, body mass, and long-term effective population size being correlated with the DFE. Overall, our findings are consistent with predictions derived independently from the Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. FGM predicts that mutations are more deleterious in complex organisms, while strongly deleterious mutations occur more frequently in smaller populations. Our study demonstrates strong phylogenetic signal in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of epistasis, long-term population size and organismal complexity could be underlying variation in the DFE across animals.

Journal Article↗
PubMed2025

Rapid Divergence of Visual Systems and Signaling Traits to Contrasting Light Regimes During Early Speciation of African Crater Lake Cichlid Fish.

Sensory adaptation is widely hypothesized to drive ecological speciation, yet empirical evidence from natural populations undergoing early stage divergence remains limited. In Lake Masoko, a young crater lake in East Africa, the haplochromine cichlid Astatotilapia calliptera is undergoing early stage sympatric speciation into shallow-water littoral and deep-water benthic ecotypes that experience contrasting light environments. Here, we integrate retinal transcriptomics, phenotypic analyses, and visual modeling to uncover rapid sensory divergence associated with this ecological transition. We find striking shifts in cone opsin expression, with the benthic ecotype exhibiting a switch from short-wavelength sensitive SWS2B to SWS2A and an overall narrowing of cone sensitivity toward the center of the light spectrum, consistent with changes in deep-water light environment. In contrast, coding sequence variation in opsin genes was limited and no significant differences in allele frequencies were detected across nine polymorphic sites, pointing to expression regulation as the primary axis of early divergence in visual systems. In parallel, we observed divergence in male signaling traits, with benthic males displaying deeper red egg-spots, aligning with predictions from visual modeling of signal efficiency in different light environments. These results demonstrate rapid transcriptomic and phenotypic divergence in associated signaling traits-within ∼1,000 years-supporting a potential role for regulatory evolution in sensory adaptation during early ecological speciation.

Animals↗
PubMed2026

Divergent evolutionary strategies in spider venoms: A comparative proteomic profiling of four sympatric species from Yunnan.

Spider venoms comprise complex cocktails of bioactive molecules evolved for predation and defense, representing a valuable resource for biological research and pharmaceutical discovery. In this study, we performed a systematic analysis of venom gland extracts from four common spider species indigenous to Yunnan, China: Agelena limbata, Hippasa lycosina, Lycosa grahami, and Sinopoda pengi. Using an integrated transcriptomic and proteomic targeted profiling approach, we successfully annotated 141 distinct toxins. Comparative analysis revealed significant interspecific heterogeneity, suggesting distinct evolutionary trajectories and "weapon system economics." Both A. limbata and L. grahami exhibited a "peptide-dominant" profile anchored by neurotoxic peptides and isomerases, optimized for rapid chemical paralysis. In contrast, S. pengi displayed a distinct "protein-dominant" signature enriched with high-molecular-weight enzymes and CAP superfamily proteins, likely functioning to facilitate tissue degradation and toxin diffusion. Occupying an intermediate position, H. lycosina demonstrated a hybrid composition. These findings suggest that although these species share the same geographical range, their venom systems have undergone divergent evolutionary adaptations driven by specific ecological niches and hunting strategies. This study represents the first systematic proteomic characterization of these venom components, providing a valuable reservoir of molecular candidates while highlighting the bioinformatic nuances of analyzing whole-gland homogenates.

Animals↗
PubMed2025

A large-scale study across the avian clade identifies ecological drivers of neophobia.

Neophobia, or aversion to novelty, is important for adaptability and survival as it influences the ways in which animals navigate risk and interact with their environments. Across individuals, species and other taxonomic levels, neophobia is known to vary considerably, but our understanding of the wider ecological drivers of neophobia is hampered by a lack of comparative multispecies studies using standardized methods. Here, we utilized the ManyBirds Project, a Big Team Science large-scale collaborative open science framework, to pool efforts and resources of 129 collaborators at 77 institutions from 24 countries worldwide across six continents. We examined both difference scores (between novel object test and control conditions) and raw data of latency to touch familiar food in the presence (test) and absence (control) of a novel object among 1,439 subjects from 136 bird species across 25 taxonomic orders incorporating lab, field, and zoo sites. We first demonstrated that consistent differences in neophobia existed among individuals, among species, and among other taxonomic levels in our dataset, rejecting the null hypothesis that neophobia is highly plastic at all taxonomic levels with no evidence for evolutionary divergence. We then tested for effects of ecological factors on neophobia, including diet, sociality, habitat, and range, while accounting for phylogeny. We found that (i) species with more specialist diets were more neophobic than those with more generalist diets, providing support for the Neophobia Threshold Hypothesis; (ii) migratory species were also more neophobic than nonmigratory species, which supports the Dangerous Niche Hypothesis. Our study shows that the evolution of avian neophobia has been shaped by ecological drivers and demonstrates the potential of Big Team Science to advance our understanding of animal behavior.

Animals↗
PubMed2026

Landscape of retron diversity across the SPIRE microbial metagenome resource reveals candidate novel type XI-like lineages.

Retrons are bacterial genetic elements encoding a specialized reverse transcriptase (RT) that synthesizes multicopy single-stranded DNA and are increasingly recognized as components of bacterial anti-phage defense systems. However, their diversity and ecological distribution across large-scale genomic resources remain poorly characterized. Here, we surveyed retron RTs across the SPIRE representative metagenome collection, a non-redundant, species-level data set spanning diverse microbial habitats. Using a curated panel of type-specific hidden Markov models, we identified retrons representing all canonical types together with additional divergent lineages. Retron distribution showed strong taxonomic and ecological structuring, with some groups restricted to specific bacterial phyla, whereas others were broadly distributed across environmental categories. Systematic novelty assessment identified two candidate type XI-like lineages, TXI_C2like and TXI_noncan_h, characterized by protease-independent architectures and distinct accessory modules associated with WYL- and DnaB_C-containing proteins, respectively. De novo covariance-based analyses further identified candidate msr/msd-like non-coding RNA structures in both lineages, supporting conservation of the canonical RT-ncRNA organizational framework despite extensive sequence divergence. Together, these findings expand the known diversity of retron systems and identify type XI-like retrons as a dynamic and previously underexplored evolutionary group.IMPORTANCERetrons are bacterial genetic elements that are increasingly exploited as programmable tools for genome editing, molecular recording, and biosensing in addition to their natural role in anti-phage defense. Despite this growing biotechnological interest, the true diversity of retrons across the bacterial world has remained largely unmapped. By mining a resource of over 100,000 processed microbial metagenomes, we uncovered thousands of retron sequences spanning known types as well as previously unrecognized lineages and found that their distribution is strongly shaped by both bacterial taxonomy and ecological niche. Among these, we identified two candidate new lineages related to type XI retrons that lack the protease domain typical of this group but instead carry distinct accessory proteins, expanding the known architectural diversity of these systems. These findings broaden the catalog of retron diversity available for functional characterization and biotechnological engineering and provide a framework for prioritizing candidate lineages for future experimental validation.

effectors↗
PubMed2026

Phylogeographic epidemiology of Dabie bandavirus in East Asia: divergent transmission networks and genotype‑linked clinical severity.

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS), caused by Dabie bandavirus (SFTSV), exhibits geographically decoupled incidence and fatality patterns across East Asia. We aimed to elucidate the distinct ecological drivers and phylogeographic dynamics underlying this inland-coastal epidemiological divergence. METHODS: Integrating 1820 high-quality global genomes of SFTSV with well-characterized clinical cohorts (936 patients) and nationwide surveillance data (27,457 cases) from China, we constructed a comprehensive analytical framework. Ecological modeling, Bayesian phylogeography, and genotype-phenotype association analyses were employed to trace the evolutionary trajectories and clinical implications of the virus. RESULTS: A pronounced "inland-high-incidence vs. coastal-high-fatality" pattern of SFTS was identified. The incidence of SFTS exhibited divergent sensitivities to meteorological factors; inland transmission was sensitive to thermal fluctuations, whereas coastal dynamics were constrained by a sunshine threshold (>&#x2009;200&#xa0;h/month). In contrast, spatial divergence in clinical severity correlated with the distribution of regional viral genetic structures. Inland regions mainly co-circulated genotypes A, C, and D, while coastal regions were dominated by genotype B. Zhejiang province was identified as a genetic hub with significantly higher recombination frequencies than inland regions (11.0% vs. 3.5%, P < 0.001). Bayesian phylogeographic inference indicated frequent lineage exchange of Zhejiang province in China with the Republic of Korea and Japan. Clinically, genotypes B and D were associated with elevated mortality in coastal and inland regions, respectively, suggesting that the severe coastal phenotype is shaped by its genotype B-dominated structure. Additionally, the RdRp-N828S mutation emerged as a robust molecular correlate of fatal outcomes, warranting further functional validation. CONCLUSIONS: Divergent meteorological factors and plausible maritime transmission networks may underlie the geographically decoupled epidemiology of SFTS. These findings highlight that risk assessment must extend beyond incidence alone and provide a phylogeographically informed framework for targeted surveillance and genotype-specific interventions in high-risk hotspots.

Humans↗