Global population genomics of Salmonella enterica serotype Napoli, an emerging pathogen with an unusual epidemiologic pattern

Genomic signatures of local adaptation have been identified in many species but remain sparsely studied in amphibians. Here, we explored genome-wide divergence within the Asiatic toad, Bufo gargarizans, to study local adaptation and genomic offset (i.e., the mismatch between current and future genotype-environment relationships) under climate warming scenarios. We obtained high-quality SNP data for 94 Asiatic toads from 21 populations in China to study spatial patterns of genomic variation, local adaptation, and genomic offset to warming in this wide-ranging species. Population structure and genetic diversity analysis based on high-quality SNPs revealed three clusters of B. gargarizans in the western, central-eastern, and northeastern portions of the species' range in China. Populations generally dispersed along two migration routes, one from the west to the central-east and one from the central-east to the northeast. Both genetic diversity and pairwise F ST were climatically correlated, and pairwise F ST was also correlated with geographic distance. Spatial genomic patterns in B. gargarizans were determined by the local environment and geographic distance. Global warming will increase the extirpation risk of B. gargarizans.

Phalaris minor is a noxious weed that thrives in wet soils and swamps across various habitats in Iran. Inter Simple Sequence Repeat (ISSR) markers are effective tools for assessing both intra- and inter-species genetic variations. The relationship between geographical distribution and ecological adaptation in this genus has long been debated. This study aimed to investigate the genetic diversity of P. minor populations in Iran using ISSR and Start Codon Targeted (SCoT) markers to assess genetic variation within and between populations of this taxon. A total of 11 populations of P. minor were sampled. Genomic DNA was extracted from dried leaf samples using a modified Cetyl Trimethyl-Ammonium Bromide (CTAB) protocol. Seven ISSR and two SCoT primers, selected for their reliability and polymorphism, were employed. Genetic diversity indices, the correlation between genetic and geographical distances, and genetic differentiation within and among populations were analyzed. A high level of genetic diversity was observed in P. minor populations. The highest genetic diversity (61%) was found within populations, while genetic diversity between populations accounted for 39%. Genetic distance increased with geographical distance. The observed genetic diversity in P. minor may result from genetic drift, gene flow, and adaptation to environmental conditions.

Saussurea obvallata (DC.) Edgew., Asteraceae, is a traditional medicinal herbnative to the Qinghai-Tibet Plateau (QTP). Pharmacological investigationshave validated its pharmacological effects in anti-tumor, anti-inflammatory, heat-clearing, detoxifying, and analgesia. S. obv is presently facing habitat fragmentation and population decline. Therefore, we analyzed its genetic and chemical diversity to provide a scientific basis for the conservation and sustainable use of S. obv. Seven populations of S. obv were sampled from Xizang, China. The genetic diversity was analyzed using inter-simple sequence repeat (ISSR) markers, and metabolites were identified by ultra-high-performance liquid chromatography-tandem-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS). Correlation analysis among genetic diversity, differential metabolites, and climatic factors were performed by R. The genetic diversity among and within populations were both lowly and significantly correlated with geographical distance, showing a decreasing trend from east to west of the QTP. A total of 110 compounds were identified, including flavonoids, phenylpropanoids, lipids, fatty acids, terpenoids, alkaloids, etc. The metabolite contents among populations varied greatly and were related to environmental factors, mainly annual mean temperature and temperature fluctuation. The genetic diversity had little effect on the metabolic differences. These findings provided valuable baseline information for the conservation and pharmacological utilization of S. obv. Meanwhile, further research is necessary for the efficacy evaluation of anti-inflammatory, anti-tumor, radiation protection, and scar removal both in vitro and in vivo.

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.

Island ecosystems, serving as natural laboratories, facilitate geographical isolation, ecological specialization, and species divergence. The Sichuan Basin, surrounded by mountain ranges, represents a typical continental island due to its marked environmental spatial heterogeneity. This heterogeneity may contribute to geographical isolation and habitat heterogeneity, resulting in genetic divergence within populations. Therefore, we used the White-browed Laughingthrush (Garrulax sannio) as a model specimen to investigate the genetic divergence in the Sichuan Basin and its surrounding mountain ranges, given its presence in various habitats within and beyond this basin. Employing a RAD-seq dataset of 140 G. sannio individuals from 17 distinct ecological zones in the Sichuan Basin and its surrounding mountain ranges, we conducted PCA, population structure analysis, phylogenetic tree construction, and gene flow analysis to comprehensively analyze G. sannio groups. Additionally, in conjunction with geographical and ecological data, we performed isolation by distance, isolation by environment, PCA, and latent factor mixed model analysis to identify factors influencing the genetic divergence among these G. sannio groups. In summary, the 17 G. sannio groups were categorized into high-elevation, medium-elevation, and low-elevation groups. Genetic divergence in G. sannio may be attributed to both geographical distance and key ecological factors, particularly elevation and key climatic variables. Notably, the high-elevation group exhibited a greater number of SNPs and selected genes associated with the key ecological factors compared to the low-elevation group. The ADCY9 gene and several associated key pathways were identified as crucial elements driving ecological adaptation (elevation and key climatic variables) in the high-elevation group. Furthermore, climate changes during the glacial cycles may have facilitated gene flow among these groups residing in the Sichuan Basin and its surrounding mountain ranges. Our findings provide evidence of genetic divergence in G. sannio influenced by the geographical distance and key ecological factors between the Sichuan Basin and its surrounding mountain ranges. These results lay the groundwork for future research on the molecular systematics of continental islands.

We carried out a population genetic study of 14 populations (692 plants characterised at 23 microsatellite loci) of the plant species Antirrhinum majus L. (Plantaginaceae) across its geographic range. Our results showed that populations of A. majus are genetically differentiated and genetically diverse. We also found a small but statistically significant genetic differentiation between A. majus subspecies pseudomajus and striatum. Genetic diversity was higher in A. majus subspecies pseudomajus. Geographic distance and both latitudinal and longitudinal coordinates had no impact on genetic differentiation and diversity. We therefore did not find any signature of geographical range expansion. Mountains were found to play a role by affecting a small but statistically significant amount of genetic differentiation between populations. Our findings thereby suggest that most A. majus populations are reproductively isolated, and that the landscape and the evolutionary history of species affected their genetic variation.

Understanding the evolutionary processes that have shaped existing patterns of genetic diversity of reef-building corals over broad scales is required to inform long-term conservation planning. Genetic structure and diversity of the mass-spawning hard coral, Acropora tenuis, were assessed with seven DNA microsatellite loci from a series of isolated and discontinuous coastal and offshore reef systems in northwest Australia. Significant subdivision was detected among all sites (FST = 0.062, RST = 0.090), with the majority of this variation due to genetic differentiation among reef systems. In addition, genetic divergence was detected between the coastal and offshore zones that cannot be adequately explained by geographic distance, indicating that transport of larvae between these zones via large-scale oceanic currents is rare even over time frames that account for connectivity over multiple generations. Significant differences in the amount of genetic diversity at each system were also detected, with higher diversity observed on the lower latitude reefs. The implications are that these reef systems of northwest Australia are not only demographically independent, but that they will also have to rely on their own genetic diversity to adapt to environmental change over the next few decades to centuries.

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Consolida genetic diversity. Therefore, we collected and analyzed 19 species from 12 provinces of regions. Overall, one hundred and twenty-seven plant specimens were collected. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and principal component analysis (PCA) divided Consolida species into two groups. All primers produced polymorphic amplicons though the extent of polymorphism varied with each primer. The primer OPA-06 was found to be most powerful and efficient as it generated a total of 24 bands of which 24 were polymorphic. The Mantel test showed correlation (r = 0.34, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Consolida species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Consolida species. Our aims were 1) to assess genetic diversity among Consolida species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa.

The population genetic structure of invasive species can be strongly affected by environmental and landscape barriers to dispersal. Disentangling the relative contributions of these factors to genetic divergence among invading populations is a fundamental goal of landscape genetics with important implications for invasion management. Here, we relate patterns of genetic divergence in a global invasive agricultural pest, Colorado potato beetle (CPB; Leptinotarsa decemlineata), to environmental and landscape factors along an invasion front in Northwestern China. We first used microsatellite markers and spatial‐temporal samples to assess broad patterns of genetic diversity as well as fine‐scale changes in patterns of genetic divergence. We then distinguished the relative contributions of five factors to genetic divergence among front populations: geographic distance (isolation by distance), climate dissimilarity (isolation by environment), and least‐cost distances (isolation by resistance) modeled with three factors: climate suitability, cropland cover, and road networks. Genetic diversity broadly decreased from West to East, with the exception being Eastern China. Low levels of genetic diversity and varying degrees of divergence were observed in Northwestern China, reflecting the potential effect of landscape heterogeneity. Least‐cost distance across cropland cover was most positively correlated with genetic divergence, suggesting a role of croplands in facilitating gene flow. The contribution of climate to genetic divergence was secondary, whether modeled in terms of local adaptability or connectivity of the climatic landscape, suggesting that constraints to CPB gene flow imposed by a harsh climate may be ameliorated in agricultural landscapes. No evidence was found for an obvious effect of road networks on genetic divergence and population structuring. Our study provides an example of how agricultural landscape connectivity can facilitate the spread of invasive pests, even across a broad climatic gradient. More broadly, our findings can guide decisions about future land management for mitigating further spread.

Phenotypic and genetic divergence along environmental gradients often reflects local adaptation in broadly distributed species. The Fabaceae family is one of the largest and most ecologically important angiosperm groups; it has a centre of diversity in South America and shows high versatility in arid and disturbed environments. Here, we selected Vachelliacaven, a native tree with ecological breadth and taxonomic complexity, to investigate whether phenotypic trait variation among populations reflects adaptive divergence. We examined neutral genetic differentiation in six varieties among populations from Argentina, quantified the phenotypic differentiation of quantitative traits by an ANOVA, and performed PST-FST comparisons. We also assessed correlations between phenotypic variation, environmental variables, genotypic variation, and geographic distances. FST estimates revealed significant genetic divergence (0.329), in line with isolation by distance and environmental heterogeneity. PST-FST comparisons showed that all traits were under diversifying selection, supporting the hypothesis of adaptive phenotypic variation. We further detected that fruit width and length were significantly correlated with specific environmental variables like precipitation and temperature. These findings confirm that phenotypic divergence in V. caven is shaped by both geographic and environmental factors. This study offers a preliminary insight into the local adaptation of the examined traits, highlighting how morphological and genetic differentiation has enabled V. caven to thrive in diverse environments and contributing information as to how to face climate change scenarios.

The genetic structure and diversity of plants may change significantly in an elevational gradient because different elevations regulate different ecological conditions. Several factors may influence genetic variation, such as mutations, selection, genetic drift, and gene flow. The aim of the present study was to evaluate the genetic structure and diversity of populations of Tibouchina pulchra Cogn. (Melastomataceae) trees in two extremes of an elevational gradient experiencing different environmental conditions. Nine polymorphic microsatellite loci were used to measure the genetic diversity of 14 adult populations, whose structure was evaluated using frequentist and Bayesian analyses. We also carried out progeny structure and paternity analyses comparing the number of fathers of each progeny and the probability of the progeny genotypes to be the result of selfing in order to evaluate the possible current processes leading to such genetic structure. Genetic structure analyses indicated the existence of genetic differentiation between populations in adults and progenies, but with a contact interface between them. The population from the higher region showed smaller genetic diversity when compared to the population at the lower region. However, the pollen variability delivered to the stigmas at the higher region was not different from that of the lower region. These results may be explained by the dynamics of gene flow mediated by pollen, especially by the different amounts of pollination events in each region, as well as local adaptation, distribution, and reproduction characteristics of T. pulchra.

BackgroundPicea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. These populations are fragmented and can be classified into three geographically distinct clusters in the SMO. The total area covered by P. chihuahuana populations is less than 300 ha. A recent study suggested assisted migration as an alternative to the ex situ conservation of P. chihuahuana, taking into consideration the genetic structure and diversity of the populations and the predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The genetic diversity of populations, which affect vigor, evolution and adaptability of the species, must also be considered. In this study, we examined 14 populations of P. chihuahuana, with the overall aim of discriminating the populations and form clusters of this species.MethodsEach population was represented by one 50 × 50 m plot established in the center of its respective location. Climate, soil, dasometric, density variables and genetic and species diversities were assessed in these plots for further analyses. The putatively neutral and adaptive AFLP markers were used to calculate genetic diversity. Affinity Propagation (AP) clustering technique and k-means clustering algorithm were used to classify the populations in the optimal number of clusters. Later stepwise binomial logistic regression was applied to test for significant differences in variables of the southern and northern P. chihuahuana populations. Spearman’s correlation test was used to analyze the relationships among all variables studied.ResultsThe binomial logistic regression analysis revealed that seven climate variables, the geographical longitude and sand proportion in the soil separated the southern from northern populations. The northern populations grow in more arid and continental conditions and on soils with lower sand proportion. The mean genetic diversity using all AFLP studied of P. chihuahuana was significantly correlated with the mean temperature in the warmest month, where warmer temperatures are associated to larger genetic diversity. Genetic diversity of P. chihuahuana calculated with putatively adaptive AFLP was not statistically significantly correlated with any environmental factor.DiscussionFuture reforestation programs should take into account that at least two different groups (the northern and southern cluster) of P. chihuahuana exist, as local adaptation takes place because of different environmental conditions.

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

Cellulose is the most abundant renewable polymer on Earth which is extensively distributed in diverse ecosystems. It is present in higher plants, marine organisms, and also produced through microbial processes in organisms like algae, fungi, and bacteria. From an industrial perspective, the semicrystalline nature of cellulose present in different plant and microbial sources enables the fabrication of various types of nanocellulose, such as nanofibre and nanocrystals, through mechanical disintegration and chemical methods, respectively. Nanocellulose distinguishes itself as a sustainable, nonharmful, and biodegradable polymer. It will enable sustainable development for responsible consumption and production. Possessing a range of excellent properties, it can be seamlessly integrated into various materials. Research on nanocellulose is gaining momentum in response to current issues related to fossil fuels, including concerns about CO 2 emissions, plastic pollution, and the need for renewable energy sources. This review addresses nanocrystals production method from cellulose found in agricultural, microbial sources, and its applications in fields such as materials science, electronics, medicine, and environmental science.

The gut microbiome plays a fundamental role in host metabolism, immune regulation, and disease development. With the rapid accumulation of multi-omics and literature data, the microbiome field now faces the challenge of efficiently extracting scientific insights from massive, heterogeneous datasets. Artificial intelligence (AI) and large language models (LLMs) provide promising tools to address this complexity by enabling integrative analysis and knowledge synthesis across diverse biological sources. In this study, we developed METABOLISM, a microbiome-specialized LLM fine-tuned on 160,000 scientific abstracts to enhance literature-based contextual understanding of microbiome-liver interactions and related biological mechanisms. Using LoRA-based parameter-efficient training, METABOLISM was optimized for domain-specific reasoning and response generation. Model performance was evaluated through both automated Phi-4 scoring (a large language model-based evaluator for relevance, informativeness, and fluency) and structured human expert rubric assessments involving 20 domain specialists. The fine-tuned METABOLISM achieved superior relevance and clarity scores (mean > 7.5 ± 0.06) compared with general-purpose LLMs such as Gemma-3-12B-IT and ChatGPT-4o. Correlation analysis revealed weak to moderate negative relationships (R = -0.65, p < 0.0001) between traditional NLP metrics (BLEU, ROUGE) and human expert rubric scores, with a similar trend observed for correlations with Phi-4-based automated evaluation scores, indicating the limitations of surface-level similarity measures in biomedical contexts. Overall, our findings demonstrate that microbiome-adapted LLMs can effectively distill high-volume scientific data into biologically meaningful insights, supporting more efficient and interpretable research in microbiology and systems biology.