Introduction Genetic diversity and population structure are critical for understanding species distribution, environmental adaptability, and responses to anthropogenic disturbances. Dendrocalamus longispathus , a commercially and ecologically important bamboo species in North East India, remains understudied in terms of its population genetics. This study aims to assess the genetic diversity and structure of this species across its natural range in Mizoram and Tripura. Methods Leaf samples were collected from 12 populations and analyzed using 13 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including number of alleles, allelic richness, heterozygosity, and inbreeding coefficients, were estimated. Population structure was examined using Bayesian analysis, Neighbor-Joining method based genetic clustering, and principal coordinate analysis (PCoA). Results The analysis revealed moderate genetic diversity, with mean number of alleles (Na = 2.84), effective alleles (Ne = 1.87), and expected heterozygosity (He = 0.362). Observed heterozygosity (Ho = 0.234) was lower than expected, indicating inbreeding, supported by a positive inbreeding coefficient (F IS = 0.306). Populations from Mizoram exhibited higher allelic richness compared to those from Tripura. AMOVA showed that 70% of genetic variation occurred within populations and 30% among populations (F ST = 0.297), indicating very high levels of genetic differentiation with low gene flow (Nm = 0.86). Bayesian analysis identified three genetic clusters (K = 3), with most populations clearly structured except one admixed population. Overall, pattern of genetic clustering between population was largely aligned with geographic proximity. Discussion The findings indicate moderate genetic diversity, very high genetic differentiation, and robust genetic structure in D. longispathus populations, with evidence of limited gene flow and inbreeding. These results highlight the need for targeted conservation strategies and the use of genetically diverse populations for plantation and sustainable management programs.

Comparison of genetic structure of multiple Betula species across China reveals ploidy variation, latitudinal diversity patterns and interspecific hybridization and admixture.

Genetic architecture of two novel chicken breeds from Xinjiang: A whole-genome sequencing study on Ili gamecock and Yemili Chicken.

Genetic diversity, population structure and multiple introductions of invasive blackchin tilapia Sarotherodon melanotheron in Thailand

Whole genome resequencing reveals grass carp candidate sex chromosome and sex determination system

Phylogeography and genetic structure of avian isospora based on mitochondrial COI gene sequences from 17 countries.

The hypertensive disorders of pregnancy (HDPs), that is, preeclampsia and gestational hypertension, are characterized by endothelial dysfunction in pregnancy and are epidemiologically and genetically associated with risk for coronary artery disease (CAD). A recent study suggested that endothelial cell (EC)-acting CAD risk variants may identify individuals who benefit from more intensive lipid-lowering treatment. The present study evaluated whether the same EC CAD genetic risk score is also associated with HDPs using comprehensive statistical genetic approaches. We examined 35 previously identified EC-acting and 205 non-EC-acting risk variants associated with CAD. First, using the nuMoM2b (Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-Be), a prospective, multicenter US pregnancy cohort, we calculated polygenic risk scores (PRS) comprised of either EC-acting or non-EC-acting CAD risk variants in genotyped, unrelated participants across multiple ancestry groups. Scores were adjusted for population genetic structure using 10 principal components, then tested for associations with HDPs using logistic regression models adjusted for age. Second, we tested the genetic association of EC-acting and non-EC-acting CAD variants with preeclampsia and gestational hypertension using 2-sample Mendelian randomization. Among 6782 unrelated nuMoM2b participants (mean [SD] age, 27.0 [5.5] years, 1040 [15.3%] with HDPs in the index pregnancy), participants with higher EC-acting PRS had a higher incidence of HDPs. Each SD of higher EC-acting PRS was associated with 1.09-fold increased odds of HDP (95% CI, 1.02-1.17; P=0.008); by contrast, the non-EC-acting PRS was not significantly associated with HDP risk (odds ratio, 1.05 [95% CI, 0.98-1.12]; P=0.14). In 2-sample Mendelian randomization, EC-acting CAD variants were strongly associated with both preeclampsia (odds ratio, 1.55 [95% CI, 1.30-1.86]; P<0.001) and gestational hypertension (odds ratio, 1.54 [95% CI, 1.29-1.85]; P<0.001). PRS and 2-sample Mendelian randomization approaches suggest enrichment for EC-acting CAD genetic risk variants in women with HDPs. These findings support a shared genetic architecture between HDPs and CAD through endothelial dysfunction.

Genetic polymorphism and natural selection of merozoite surface protein 1 C-terminal 42 kDa in Vietnamese Plasmodium vivax isolates.

Genetic structuring associated with Ganoderma boninense resistance in oil palm revealed by multivariate marker analysis of the EgLCC24 gene

The aurochs, the wild ancestor of domestic cattle, was a keystone herbivore in Late Pleistocene Eurasian ecosystems and a major prey species for Palaeolithic hunter-gatherers. Despite its significance, the genetic structure of aurochs populations that survived the Last Glacial Maximum (LGM) remains poorly understood, especially in southeastern Europe. Here, we present the first directly dated ancient genomes of aurochs from the eastern Adriatic region, recovered from the Upper Palaeolithic site of Šandalja (Istria, Croatia). Two female individuals, dated to approximately 14,800-14,200 and 11,800-11,400 calibrated years before present, were sequenced for low-coverage whole genomes and near-complete mitochondrial genomes. Bayesian phylogenetic analyses and median-joining network reconstruction place both specimens within mitochondrial haplogroup P, the dominant European aurochs lineage. However, they do not cluster within the main P sub-haplogroup observed in most ancient aurochs samples and in modern cattle carrying P-type mitochondrial lineages. Instead, one specimen is placed within an 'alternative' P sub-haplogroup, whereas the position of the other appears more isolated and should be interpreted cautiously, as it may be influenced by limited sequence coverage and the resulting uncertainty in phylogenetic placement. At the nuclear genomic level, the two Šandalja aurochs show affinity to Late Pleistocene and Early Holocene aurochs from Italy. Although based on a limited number of specimens, this pattern is consistent with possible genetic connectivity across the Adriatic region, potentially associated with the now-submerged Great Adriatic Plain (GAP). Overall, our results suggest regional structure among Late Pleistocene aurochs, potentially associated with the exposed Adriatic Plain as a refugium and dispersal corridor between the Apennine and Balkan Peninsulas. By filling a major geographic and temporal gap in the aurochs genomic record, this study highlights the Adriatic Basin as a potentially overlooked centre of Pleistocene megafaunal diversity and refines models of postglacial recolonization and cattle evolutionary history.

Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.

Brown trout (Salmo trutta) has adapted to a wide range of habitats and displays a variety of life-history strategies. Being facultatively anadromous, populations without migration barriers to the sea consist of both resident and anadromous individuals in different proportions. This affects genetic drift and the level of gene flow between populations, and therefore shapes the metapopulation structure. Here, utilizing genetic variation at 95 SNP markers, we describe the genetic structure and effective size of a brown trout population inhabiting the Fremstad catchment that supports both anadromous and freshwater resident life histories. Compared to other sea trout populations in the region, the Fremstad population is genetically divergent with a unique genetic signal. A weak and significant genetic structure was observed in the Fremstad catchment, and anadromous individuals were not assigned to a specific lake or stream. The effective population size of brown trout in the Fremstad catchment is large compared to the average annual entry of sea trout into the catchment; hence, a large proportion of non-anadromous spawners likely contribute to the population. Approximately 2% of sea trout entering the catchment were strays from other populations. Because of a large proportion of non-anadromous spawners, the proportion of strays into the overall spawning population is likely to be lower than observed among the sea trout, and contribute to the genetic divergence of the Fremstad population from other populations. This study adds to our understanding of the evolutionary drivers that affect the genetic structure of anadromous brown trout populations and demonstrates how small spawning streams can be evolutionarily important in supporting a large and genetically unique population.

Endangered woody plants are threatened by habitat degradation, demographic instability, and genetic erosion. Ormosia microphylla (small-leaved Ormosia) is an endangered tree, but how genetic, demographic, and environmental factors jointly contribute to its decline remains insufficiently resolved. We investigated the age structure of seven wild O. microphylla populations and resequenced 62 adult individuals to assess genetic variation, population structure, linkage disequilibrium, gene flow and demographic history. In three representative populations, we further quantified seed production, germination, logging traces, soil properties and bird diversity, and integrated these variables using exploratory Spearman correlations, standardized multi-factor indices and principal component analysis (PCA). Overall, 71% of the surveyed populations exhibited unstable age structures. All populations showed low genome-wide nucleotide diversity (π < 0.005) and were grouped into three geographically interpretable genetic clusters: GX, HG and HN. TreeMix detected limited gene flow among clusters, and smc + + inferred historical declines in effective population size, with a slower decline in HN than in GX and HG. Rapid LD decay indicated that low diversity was not accompanied by extensive genome-wide linkage. Selective sweep analyses identified cluster-specific enriched pathways, including cutin, suberin and wax biosynthesis in HG and phenylpropanoid biosynthesis in HN. Among representative populations, all produced viable seeds, but seed production declined annually and germination was constrained by the seed coat. Spearman correlations among bird diversity, stump counts, seed output and recruitment were weak and non-significant. PCA indicated that regeneration status, mature-tree availability and reproductive output defined the primary population-performance gradient, whereas disturbance pressure and biotic support formed a secondary external-context gradient. O. microphylla vulnerability is associated with interacting genetic risks, demographic imbalance, reproductive limitation and external pressures, supporting targeted in situ protection, within-cluster genetic management and cluster-representative ex situ conservation.

Enterobius vermicularis (pinworm) is a globally distributed intestinal nematode that primarily infects children. Despite its high prevalence, information on the molecular diversity of human-derived E. vermicularis populations remains limited, particularly in geographically diverse regions such as Türkiye. This study aimed to characterize genotype and haplotype diversity based on the mitochondrial cytochrome c oxidase subunit 1 (COI) gene in E. vermicularis egg isolates collected from humans in different regions of Türkiye. A total of 71 microscopy-positive samples were analyzed by nested PCR, and 40 COI amplicons (397 bp) yielded high-quality sequences for further evaluation. Sequence analysis revealed 16 distinct haplotypes defined by 20 polymorphic sites. Overall haplotype diversity was high (Hd = 0.871), whereas nucleotide diversity was low (π = 0.00714). Among the regional populations, the highest haplotype diversity was observed in Kars (Hd = 0.895), while the highest nucleotide diversity was detected in Balıkesir/Edremit (π = 0.00927). Maximum-likelihood phylogenetic analysis demonstrated that all Türkiye haplotypes belonged to Genotype B and formed three subclusters together with previously reported human-derived reference sequences from Europe and the Middle East. Seven haplotypes showed no 100% match in GenBank and were therefore considered novel, whereas the remaining haplotypes were identical to genotype B sequences previously reported from Greece, Bulgaria, Iran, Iraq, and Türkiye. To our knowledge, this study presents the first COI-based haplotype dataset of E. vermicularis egg isolates from multiple regions of Türkiye and demonstrates substantial intraspecific genetic diversity despite the predominance of a single mitochondrial genotype. These findings expand current knowledge of the genetic structure of human-derived E. vermicularis in Türkiye and provide a basis for future large-scale molecular epidemiological studies. Further studies including larger sample sizes and additional genetic markers are needed.

Heterogeneity of plasmids containing OXA-48-like and NDM-5 carbapenemases and emergence of OXA-181 and NDM-5 co-carrying strains and plasmids in Escherichia coli from veterinary settings.

A high-resolution molecular tool for tracking and differentiating closely-related Plasmodium vivax populations is critically needed. This study aimed to develop and validate a novel single nucleotide polymorphism (SNP) barcode to monitor the progress of malaria elimination in the Great Mekong Subregion (GMS). A total of 210 P. vivax clinical samples were collected across four time points in three international border areas: China-Myanmar border, Thailand-Myanmar border, and Bangladesh-Myanmar border. Parasites were genotyped at 36 SNPs using MassARRAY technology (Sequenom), with Sanger sequencing validation for low-efficiency loci. The complexity of infection (COI) was estimated via a maximum likelihood approach implemented in COIL, while genetic diversity metrics were computed in GenAIEx version 6.5. Population differentiation was assessed through molecular variance analysis, Mantel rank test, and pairwise FST estimation. Genetic structure was resolved using principal component analysis, phylogenetic analysis, and ADMIXTURE. 198 samples were successfully genotyped at 22 validated SNPs, revealing 37.9% polyclonal infections. The proportion of polyclonal infections differed significantly among the five P. vivax populations (P = 0.0001, Pearson Chi-square test, χ2 = 23.15), with 2020 CMB samples having the highest proportion (56.1%). The average COI was highest in BMB parasites (1.109 ± 0.007). The TMB 2018 samples exhibited the maximal nucleotide diversity (π = 0.342 ± 0.033) and expected heterozygosity (He = 0.325 ± 0.04). The P. vivax populations from the western GMS showed significantly reduced genetic diversity in recent years compared to earlier timepoints (0.372 ± 0.009 vs. 0.426 ± 0.009; P < 0.0001, Student's t-test). Pairwise FST values indicated moderate to high genetic differentiation (0.165 - 0.417) across nine population pairs, except for the temporally proximal CMB populations, which showed low differentiation. Structure analysis consistently resolved three discrete genetic clusters corresponding to CMB, TMB, and BMB parasite populations. This 22-SNP barcode provides a high-resolution genotyping tool capable of differentiating P. vivax parasite infections from the western GMS. Our data demonstrate that sustained malaria control interventions drive the fragmentation of P. vivax populations into genetically distinct transmission foci, creating opportunities for elimination strategies in border hotspots.

Reproduction traits constitute the primary objective of porcine genetic improvement programs, with litter size being the principal determinant of herd reproduction output. Relative to the intensively selected Large White line, as a breed derived from Large White (LW) and Beijing Black (BJB) pigs, Jishen Black (JSB) pigs exhibit markedly lower litter size, indicating substantial potential for genetic improvement. Whole-genome resequencing data were obtained from 110 individuals of six pig populations differed in litter size: a Large White line with high litter size (> 16, LWH), cryopreserved Large White samples from 1977 (LW1977), dam-selected (LWD) and sire-selected (LWS) lines derived from LW1977, Berkshire (BKS), and Jishen Black pigs (JSB). Principal component analysis (PCA) captured clear population genetic structure along PC2, with the observed distribution pattern descriptively coinciding with litter size variation across populations, though such an association was not statistically verified. A composite selection-signature scan that integrated Fst, π-ratio, and XP-EHH was performed between multiple population groups. Candidate signals were filtered by excluding those also detected in a control comparison (Jishen Black vs. Berkshire) that showed minimal litter‑size difference, to screen selection signatures with potential relevance to reproductive trait differentiation at the population level. Twelve genes were identified as putative candidate genes for litter size, including PEX14, CDK15, KCNQ1, SPAG17, TTF2, CD101, CASQ2, VANGL1, ARID5B, KLHL32, EML1, and NAV1. Functional enrichment analysis indicated that these genes significantly over-represented in microtubule-related biological processes. Among them, KCNQ1 was consistently detected by all methods and comparison groups. Further analysis of KCNQ1 revealed multiple SNPs with significant allele-frequency differentiation among populations; notably, two intronic variants (chr2:A1,861,604G and chr2:A1,867,076G) showed population-specific allele frequency patterns that descriptively aligned with the stratification of litter size performance. By comprehensively dissecting population genomic differentiation among multi-breed populations divergent in litter-size performance, this study implemented established a feasible framework for screening candidate loci associated with porcine prolificacy at the population level, expanded the gene list with suggestive selection signatures, and provided potential molecular markers requiring further independent cohort validation and functional verification to support future genetic improvement in swine reproduction efficiency.

Blister-forming eriophyoid mites of the genus Eriophyes are important pests of rosaceous plants and have traditionally been regarded as polyphagous species with broad host ranges. However, increasing evidence suggests that many eriophyoids represent complexes of cryptic species or host-associated lineages. In this study, we applied an integrative taxonomic approach to investigate the taxonomic status of Eriophyes populations associated with Malus domestica, Pyrus spp., and Sorbus aucuparia. We analyzed mitochondrial COI and nuclear D2 region of 28S rDNA sequences from multiple populations, together with multivariate morphometric analyses based on 28 quantitative morphological characters. Phylogenetic reconstruction and species delimitation analyses (bPTP) revealed strong host-associated genetic structuring and identified up to seven deeply divergent evolutionary lineages. Mitochondrial COI data resolved multiple host-specific clades with high inter-lineage divergence, while the more conserved nuclear D2 marker supported major host-associated groupings but recovered fewer lineages, indicating mito-nuclear discordance consistent with recent or ongoing divergence. Morphometric analyses detected statistically significant differentiation among host-associated populations; however, extensive overlap in diagnostic characters was observed, particularly between pear- and rowan-associated mites, indicating cryptic speciation. In contrast, mites associated with apple exhibited clearer morphological differentiation consistent with molecular clustering. Our results demonstrate that leaf blister mites associated with rosaceous hosts represent a complex of distinct, host-specialized species. These findings highlight the limitations of morphology-based taxonomy in Eriophyoidea and underscore the need for integrative approaches to accurate species delimitation, with important implications for vector identification and improved pest management.

ABSTRACT Eucalyptus bosistoana (Myrtaceae) is a breeding species of NZDFI (New Zealand Dryland Forests Innovation), which aims to establish forestry plantations of ground-durable, high-value hardwoods in New Zealand. For this purpose, plants from E. bosistoana seeds collected from natural source locations in Australia between 2008–2012 have been used since 2009 to establish breeding trials in New Zealand. To inform the NZDFI breeding programme, leaf samples of 177 E. bosistoana breeding families were genotyped using a Eucalyptus 72K single nucleotide polymorphism (SNP) Axiom array. This was done to identify patterns of genetic structure among E. bosistoana breeding families and to assess the genetic structure and diversity of the natural source populations from which their seeds were obtained. PCoA and STRUCTURE analyses indicated that the E. bosistoana seeds were obtained from three natural source populations with similar levels of genetic diversity. Weak genetic structure among most natural source locations of E. bosistoana within these populations was observed, and families from nearby source locations were generally genetically more similar to each other than to those established from more distant locations. We also found that some families in the E. bosistoana breeding programme represent E. melliodora. These combined genetic patterns provide the genetic basis for establishing, maintaining, or improving NZDFI’s E. bosistoana breeding populations.

Ficus carica L. is an economically important fruit crop widely cultivated in the Mediterranean region. In this study, genetic diversity and population structure were investigated in 72 F. carica genotypes collected from the Derecik and Çukurca regions of Hakkâri province, Türkiye, using 15 highly polymorphic Start Codon Targeted (SCoT) markers. A total of 481 amplification bands were obtained, of which 475 were polymorphic, resulting in a high average polymorphism rate of 98.60%. Genetic diversity indices indicated substantial variation among the genotypes, with a mean effective number of alleles of 1.53, gene diversity of 0.31, and Shannon information index of 0.47. The average genetic distance among genotypes was 0.37, with the highest pairwise distance (0.721) observed between genotypes HC4 and HD7. Analysis of molecular variance (AMOVA) revealed that most genetic variation was distributed within populations (93%), whereas only 7% was among populations. Bayesian STRUCTURE analysis identified two distinct genetic clusters corresponding largely to geographic origin, with 22 genotypes (30.56%) classified as admixed based on a membership coefficient threshold of < 0.70. Principal coordinate analysis (PcoA) clearly separated genotypes according to their sampling locations, where Axis 1 and Axis 2 explained 24.31% and 15.07% of the total genetic variation, respectively. Overall, these findings demonstrate the effectiveness of SCoT markers in assessing genetic diversity and population structure in F. carica germplasm from southeastern Türkiye. Future studies should use codominant markers (SSRs and SNPs) expand geographic sampling, and adopt open data repositories to enhance conservation and breeding strategies.