Understanding the genome-wide diversity of jute mallow (Corchorus olitorius L.) is crucial for unlocking the potential of global genebank collections, enabling the discovery and use of traits that support climate resilience, improve nutrition, and increase productivity. Using 23,471 high-quality diversity array technology sequencing single-nucleotide polymorphisms (SNPs), this study assessed the genetic diversity, population structure, and linkage disequilibrium (LD) of 607 accessions. Moderate genetic diversity was detected with a total gene diversity of 0.28, an expected heterozygosity of 0.26, and a Shannon index of 0.42. Four distinct genetic clusters were identified, reflecting geographic patterns, where Cluster 1 (n=62) and Cluster 4 (n=354) were predominantly composed of West African accessions. An analysis of molecular variance revealed significant genetic structuring (p<0.001), with most genetic variation occurring within countries (45.2%), followed by within individuals (32.5%), while differentiation among clusters accounted for 18.2% and variation among regions was minimal (2.9%). LD revealed low genome-wide r2 values (mean=0.028; r2 90=0.067) and a very rapid decay (LD50 ≈ 1bp), with only 4.2% of SNP pairs showing significant LD (r2>0.1, p<0.05), indicating extensive historical recombination. The findings suggest that a significant portion of the existing genetic variation remains untapped in breeding. Strategic conservation of the unique genetic variants through core and mini-core collections, coupled with targeted crosses among diverse regional accessions, can broaden the genetic base and support the development of resilient, high-yielding, and nutrient-rich dual-purpose varieties (i.e., leafy vegetables and industrial fibers) across diverse environments.

Genetic diversity and population structure analyses of banana (Musa species) germplasm collections from Ethiopia using ISSR markers

Genetic diversity and population structure within Kankrej Cattle: Insights from genome-wide SNP analysis

Hybrid zones are dynamic systems shaped by multidimensional ecological and evolutionary forces. When a hybrid zone is not entirely regulated by the environment or hybrid fitness, tracing the movement of populations and traits can provide further insights into the interplay between selective processes. Hybridization between two diverging plant lineages, Impatiens rosea and Impatiens balsamina, has formed a narrow hybrid zone in the Western Ghats of India that is not entirely environment-dependent nor regulated by hybrid fitness. To understand its maintenance, we studied the genetic structure of the hybrid zone using SNP markers. We assessed the role of inbreeding in maintaining population boundaries and investigated introgression, genetic composition, clinal patterns and the demographic history of the hybrid zone. The demographic analysis confirmed the origin of the hybrid zone in secondary contact. We found lower levels of heterozygosity and higher inbreeding in the hybrid zone than in parental populations. The hybrid zone is composed mainly of F2 or advanced-generation hybrids, suggesting minimal active hybridization, while inbred advanced-generation hybrids dominate the hybrid zone. Hybrids show asymmetric admixture with higher contribution from I. balsamina than I. rosea. Introgression is unidirectional from I. balsamina to I. rosea. I. balsamina is likely invading into I. rosea through a narrowly maintained hybrid zone. The narrow I. rosea-balsamina hybrid zone is a dynamic system that persists through inbreeding amongst hybrids and is regulated by a complex interplay of multiple ecological and evolutionary factors, offering insights into how such zones regulate landscape-level population dynamics.

A potential genetic link between inflammatory bowel disease (IBD) and educational attainment has been suggested. Understanding the underlying mechanisms of this genetic relationship is crucial for advancing the knowledge of their co-occurrence patterns. Using genome-wide association study data for both IBD and educational attainment, a multiphase analytical approach was applied to examine their genetic correlation. The study involved three phases: first, linkage disequilibrium score regression and high-definition likelihood models were used to assess genome-wide genetic correlation; second, SUPERGNOVA was employed to analyze the genetic structure across specific chromosomal regions; and third, conditional/conjunctional false discovery rate (cond/conjFDR) methods were applied to measure genetic overlap and identify shared genetic loci between the two traits. The genome-wide analysis revealed significant genetic correlations between IBD, especially Crohn's disease, and educational attainment, while the association with ulcerative colitis was weaker. Regional analyses identified localized genetic correlation signals across several chromosomal regions between these traits. The application of the conjFDR framework confirmed the presence of overlapping genetic components, leading to the identification of key genetic variants contributing to disease susceptibility and progression. This genetic study provides new theoretical insights into the association between IBD and educational attainment, contributing to a deeper understanding of the mechanisms underlying their co-occurrence.

Genetic diversity of Trichomonas vaginalis may reveal weak pathogenicity of predominant isolates.

This contribution describes and discusses the first fossil record of a male imago belonging to the genus Ecdyonurus Eaton, 1868 (Ephemeroptera, Heptageniidae). The features of the genitalia, with the characteristic structure of the not projected apical sclerite of the penis lobes curved laterally, undoubtedly indicate its belonging to the subgenus Helvetoraeticus Bauernfeind & Soldán, 2012. Ecdyonurus (Helvetoraeticus) hoffeinsorum sp. nov. is established for a single adult specimen from the Eocene Baltic amber, and its taxonomical relationships are analysed. Furthermore, based on the unique structure of the mesonotal lateroparapsidal suture, we raise Nestormeus stat. nov. (formerly a subgenus of Ecdyonurus comprising two Eocene species, i.e. Nestormeus leopoliensis (Godunko, 2004) comb. nov. and Nestormeus groehnorum (Godunko, 2007) comb. nov.) to the genus level. The extant species of the subgenus Helvetoraeticus are known from Western Palearctic only, based on adults and obligatory rheophilous larvae inhabiting water courses of different types in the mountainous and foothills regions of Europe, Minor Asia and the Caucasus. Well-grounded description of a fossil representative of the rheophilic subgenus Helvetoraeticus in the Cenozoic resin of Europe is significant for future precise reconstructions of the ecological and biogeographic patterns of the freshwater Eocene fauna, as well as a reliable calibration point for time scaled phylogeny reconstructions. Given the lack of knowledge on the molecular diversity of Ecdyonurus genus, significant morphological variability of all life stages, the presence of endemic and potentially cryptic species, and insufficient knowledge of the distributional pattern of most Helvetoraeticus representatives, we analyse the available data on the genetic structure of the Ecdyonurus genus revealing high diversity and putative misidentifications, underscoring the taxonomic challenges within this group.

Indigenous cattle are central to livestock production in Africa, valued for their adaptability to harsh tropical environments despite lower productivity than commercial breeds. Genome analyses offer critical insights into the genetic potential for enhancing both resilience and productive traits, supporting the advancement of worldwide cattle farming systems. Here, we generated whole-genome sequence data for 240 indigenous cattle representing breeds from distinct agro-climatic regions in Egypt, Uganda, and South Africa. The dataset comprises over ten terabytes of paired-end reads generated using the Illumina NovaSeq. 6000 platform, with an average genome coverage of approximately 10×. Post-filtering reads were mapped to the ARS-UCD1.2 reference genome with a mean mapping rate of 99.2% (range: 64.5-99.9%). Variant calling identified ~43 million SNPs and 6 million indels (≤50 bp) unevenly distributed across the genome. Functional annotation indicated that many variants were located within or near known genes. This comprehensive genomic resource provides a foundation for future studies of genetic diversity, breed identity, population structure, local adaptation, breed-specific traits, or strategies for global cattle conservation.

Understanding population structure is essential for conservation genetics, as it provides insights into population connectivity and supports the development of targeted strategies to preserve genetic diversity and adaptability. T-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) have proven effective for revealing population genetic structures in human and model organisms using hard-called genotypes, but their application in wild species using genotype likelihoods from low coverage sequencing (as a cost-saving measure) remains underexplored. Here, we present a Jupyter Notebook-based workflow that facilitates the use of UMAP and t-SNE on genotype likelihood-derived principal components. This workflow is demonstrated using medium to low-coverage whole-genome sequencing data from scimitar-horned oryx, which has been reintroduced into the wild and faces multiple conservation challenges. Detailed guidance on hyperparameter tuning and practical implementation is also provided, enhancing the application of these methods in wildlife genetics to potentially support biodiversity conservation. lcUMAPtSNE is designed as a complementary and exploratory dimensionality reduction tool, rather than a replacement or benchmarking framework, and its strengths are demonstrated here using empirical data.

Long-distance migrations across Eurasia have led to extensive admixture among ethnolinguistically diverse Altaic speakers and their Indo-European neighbors; however, the population histories of the Xibe and Daur in northern China remain poorly understood. We address this gap by analyzing genome-wide SNP data from 324 individuals to characterize genetic structure, admixture, and migration. Both groups cluster with East Asian populations, particularly Altaic-speaking groups, consistent with a shared origin of the geographically distinct Xibe and Daur populations. We identify divergent post-migration histories, in which northwestern Chinese Xibe show distinct profiles and stronger genetic ties to the Daur, while northeastern Xibe have substantial contributions from indigenous ancient Northeast Asian (ANA) and Sino-Tibetan speakers. Admixture modeling indicates that Daur and the majority of Xibe populations are best described as two-way mixtures with Han and ANA groups; a distinct West Eurasian/Steppe signal persists in specific Shandong subgroups, reflecting historical trans-Eurasian cultural interactions and gene flow. Notably, Xinjiang Xibe share a high-ANA genetic profile, whereas other Xibe groups possess additional Han-related ancestry. Shared-segment analyses support a northeastern origin for the Xinjiang Xibe, where subsequent westward migration served as a complementary event that preserved this ancestral diversity, whereas the Daur retains strong ties to ANA, especially those from Inner Mongolia. Together, these results clarify the layered demographic histories of Xibe and Daur, refine models of population structure in northern East Asia, and illustrate how repeated movements and regional interactions generate present-day genomic diversity at the crossroads between North China and Siberia.

Complex life would be impossible without cooperation at all levels of biological organization. However, Darwinian selection is commonly believed to favor selfish behavior, making societies of cooperators vulnerable to cheaters. A quintessential model of this behavior is the game of Prisoner's Dilemma in which cheaters always win, even though being cooperative results in greater rewards. Numerous scenarios have been proposed that allow for the evolution of cooperation in restrictive settings that postulate altruism between genetic relatives, explore mechanisms of direct and indirect reciprocity, focus on competition between groups, or impose spatial structure on the population. It is difficult to imagine how these scenarios would account for the evolution of cooperation in populations of organisms that lack sophisticated assessment mechanisms and have no spatial constraints. Here we demonstrate that it is possible to achieve high levels of cooperativity in the game of Prisoner's Dilemma without introducing any additional assumptions about genetic relatedness, population structure, or explicit reciprocal arrangements. The only requirement is that the willingness to cooperate varies depending on the opponent, for example in response to the opponent's physical appearance and patterns of behavior. This mechanism requires consistent opponent recognition during multiple encounters. Evolution of cooperativity due to opponent-specific responses may be the only available mechanism in many biological settings and may serve as a starting point for more sophisticated modes of cooperation observed in animal and human societies.

Global molecular diversity of the zoonotic tapeworm Spirometra mansoni (Cobbold, 1883) (Cestoda: Diphyllobothriidea).

The garden dormouse (Eliomys quercinus) is one of the fastest-declining mammals in Europe, and action is needed to prevent further population losses. The primary causes of declines are not well-understood, as the species experiences variable conditions and threats across its range, but likely include habitat fragmentation and loss. Previous genetic studies have provided evidence of highly structured garden dormouse populations in Western Europe, despite this region having been defined as a single clade with mitochondrial DNA analysis. Within Western Europe, the magnitude of declines has been recognized to be greater on the eastern edge of the species' range, which could explain differentiation within the clade as resulting from diversity loss and genetic drift for regions under greater risk of extirpation. Here, we focus on fine-scale genomic differentiation across the Western European clade to explore the consequences of genomic erosion on the eastern region and to help identify mechanisms driving genetic differentiation within this species. We found genetic differentiation both between and within major geographic regions. Populations located in the eastern edge of the species' range showed stronger signs of population isolation, including structure between spatially distant populations, lower genetic diversity, and greater rates of inbreeding. However, all populations exhibited signals of recent rapid population decline. Outlier analyses indicated that differentiation between regions was primarily due to genetic drift resulting from isolation-by-distance rather than adaptive differentiation. We also found genetic structuring between populations within the Rhine Valley, despite apparent lack of physical barriers preventing dispersal among groups within this region. Our findings indicate that population isolation following habitat loss and fragmentation has likely been a major contributor to garden dormouse declines. Dispersal among disparate garden dormouse sampling regions is restricted-even across local spatial scales-leading to loss of genetic diversity and potential erosion of evolutionary potential. With 21st century declines expected to continue across the species' range, even relatively common and well-connected populations are likely to follow the trajectory of the eastern populations, with increasing loss of diversity as populations contract and become more isolated.

The Chinese native Diqing Tibetan pig has a long history of domestication and is distributed in the southernmost region of China compared to other Tibetan breeds. In this study, we performed whole-genome sequencing of the Diqing Tibetan pigs. By integrating previously published data, we explored the genetic structure, population diversity, and genetic introgression from commercial European pigs and Southern Chinese domestic pigs into Diqing Tibetan pigs. We further examined the potential genetic influences of European pig introgression and inferred the historical events of admixture with Southern Chinese breeds. Our analysis revealed various instances of population admixture between Diqing Tibetan pigs and European pigs, as well as redundant introgression from South Chinese pigs when compared to other Tibetan pig populations. The introgression from European pigs significantly increased the population diversity in Diqing Tibetan pigs, which may influence fertility. Additionally, the introgression from European pigs affected the proportion of introgression from Southern Chinese pigs, with the most pronounced effect near the PSCK2 gene, which is associated with body size. Regarding ancestral genetic components from Southern Chinese pigs, we discovered a significant level of redundant proportion in Diqing Tibetan pigs compared to other Tibetan breeds. This admixture may have occurred at multiple time points from different breeds, with the Diannan small ear breed in Yunnan Province of China potentially serving as a recent primary contributor to the introgression into Diqing Tibetan breed. Our study reveals that the Diqing Tibetan breed has been shaped by admixture from European and multiple Southern Chinese sources, where European introgression increased diversity and reshaped Southern ancestry, while Southern introgression itself derives from distinct Southern Chinese pig breeds.

Clonality, management, and geography shape genetic structure in a perennial species with restricted distribution.

Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases. Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p < 0.05, |log2FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa. Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.

The Asian tiger mosquito, Aedes albopictus, is an aggressive invasive vector responsible for transmitting important arboviruses. Its global spread has been largely facilitated by human-mediated transport, especially through trade and road networks. Since its first detection in the Netherlands in 2005, repeated introductions have occurred via pathways such as lucky bamboo imports, used tires, aircraft, and ground traffic. Despite ongoing surveillance and elimination efforts, uncertainties remain about the origins, recurrence, and establishment potential of these introductions. We analyzed 200 Ae. albopictus specimens collected from 21 locations in the Netherlands from 2014 to 2023, including detections in residential areas and points of entry (PoEs). Samples were genotyped at 19 specific microsatellite loci. Genetic diversity and kinship were studied to better understand genetic structure, relatedness between and within locations, and local overwintering. We also determined the presence of Wolbachia endosymbiont strains in the specimens by sequencing Wolbachia markers. Genetic structure and kinship analyses revealed multiple independent introductions, genetic diversity among sites, and evidence of local overwintering at both residential and PoE locations, including used tire storage sites. Close-kin relationships were identified in 63 specimen dyads. Among these, one dyad confirmed overwintering at a used tire storage facility, four indicated kinship within a residential area, and two between two locations. Genetic assignment results also highlighted successful elimination of the species in one Dutch residential area. A total of 16 Dutch locations (76.19%) tested positive for the presence of Wolbachia. Overall, 48.86% specimens analyzed tested positive for at least one strain, and 35 close-kin dyads showed complete concordance in Wolbachia infection status. Our findings highlight the complex invasion dynamics of Ae. albopictus in the Netherlands. Our results demonstrate that microsatellite analysis, combined with kinship assessment, is an efficient approach for investigating kinship among individuals within and between urban areas and PoEs, providing evidence of local overwintering, and assessing the genetic structure of Ae. albopictus at introduction sites. The widespread presence of Wolbachia, which is known to reduce mitochondrial diversity, suggests that mitochondrial DNA (mtDNA)-based population analyses may be limited for the species.

Methods using environmental nucleic acids have become highly effective for monitoring aquatic biodiversity, with an array of suitable use cases, including metrics for fisheries assessment. Traditional methods for assessing fish populations often rely on invasive techniques with limited spatial and temporal coverage. Environmental DNA (eDNA) has revolutionised biomonitoring assessments by facilitating species detection and abundance estimation in a noninvasive and indirect manner. Environmental RNA (eRNA) offers a promising complement by capturing the transcriptional activity of organisms. In addition, the study of eDNA methylation may provide an avenue for detecting the regulation of the expression of genes of interest. This review highlights the opportunities to unlock the full potential of eDNA and eRNA in supporting sustainable fisheries assessment by offering noninvasive, alternative and complementary methods for age assessment, sex identification and reproductive stage, physiological and health status, genetic structure and stock identification. By integrating these innovative approaches with traditional methods, a more comprehensive understanding of aquatic ecosystems can be achieved, ultimately leading to improved fisheries conservation and management decision-making.

Genomic Characterization of an ST44 Escherichia coli Isolate Harboring an mcr-8.2-Bearing IncR Plasmid from a Pediatric Patient in China.

ABSTRACTThe Mesembryanthemoideae (Aizoaceae) are a diverse group of succulents in southern Africa, many of which are endemic to the Succulent Karoo and Cape Floristic Region of South Africa. This study investigated the population genetic structure and biogeography of two closely related species, Cryophytum crystallinum and C. guerichianum, and assessed whether abiotic factors, including temperature, precipitation and soil variables, contribute to their genetic differentiation. We also examined a putative hybrid from the Northern Cape Province, showing intermediate morphological traits. In C. crystallinum, populations at either end of the coastal range in the Western Cape Province were genetically similar, with distinct clusters occurring in between. We propose that repeated range shifts and the formation of refugia may explain this pattern and found little evidence that the abiotic variables considered here strongly shaped genetic structure. In C. guerichianum, we identified inland, intermediate and coastal genetic clusters, likely shaped by vicariance associated with the Cape Fold Belt. Across both species, genetic divergence showed some support for the Isolation by Environment hypothesis, with a correlation between genetic and environmental distances independent of geographic distance, although topography was likely the dominant driver. The suspected hybrids were genetically closer to C. guerichianum, suggesting asymmetric introgression and a possible mosaic pattern of hybridisation in areas of sympatry. As C. crystallinum is invasive in parts of the world, accounting for historical population structure and evolutionary history may help identify appropriate source populations for biological control, as genetically distinct populations can respond differently, and geographic distance alone may not reliably predict suitability.