Search Results (935)

The accurate characterization of human immunodeficiency virus (HIV) genetic diversity and drug resistance is critical for effective surveillance and treatment, yet current sequencing technologies face limitations in sensitivity and scalability for community-level implementation. We present G-HIV, an integrated platform combining long-read sequencing (G-seq500) with an automated bioinformatics pipeline. G-HIV processes raw FastQ data to generate automated reports on point mutations, drug resistance predictions, viral quasispecies diversity, and haplotype networks via a two-step analytical approach. Applied to 44 HIV-1 plasma samples (42 used in the final comparison after excluding 2 samples with low-quality Sanger chromatograms), G-HIV detected 3–48 candidate minority variants per sample that were not observed by Sanger sequencing, identifying drug-resistant quasispecies in two samples with undetectable Sanger signals, and revealed mixed infection cases (e.g., inter-subtype CRF07_BC/CRF08_BC) through phylogenetic analysis. G-HIV addresses an integration of long-read sequencing with a fully automated, one-stop bioinformatics pipeline designed for frontline laboratories without specialized bioinformatics expertise—providing a scalable solution for community-based resistance surveillance and personalized therapy optimization in resource-limited settings. This research addresses an integrated long-read sequencing and automated bioinformatics platform for rapid and precise HIV-1 surveillance. G-HIV surpasses conventional approaches like Sanger sequencing in resolution, efficiency, and accessibility for community-level surveillance. By integrating long-read sequencing, streamlining workflows and eliminating the need for specialized bioinformatics expertise, G-HIV is positioned to become a new solution, providing more effective one-stop services for HIV-1 prevention and control. Full article

Understanding how historical climatic oscillations and contemporary dispersal interact to shape genetic diversity is central to interpreting population structure in long-distance migratory birds. The White Stork (Ciconia ciconia) has a broad trans-Eurasian distribution, yet populations from the Caucasus region remain underrepresented in population genetic studies. Here, we investigate mitochondrial and nuclear genetic variation in breeding populations from Armenia, a region located at the junction of Europe and Southwest Asia. We analyzed sequence variation in the mitochondrial control region and COI gene together with a nuclear intron (SPIN) from 102 individuals sampled across northern, central, and southern Armenia and integrated these data with publicly available Eurasian sequences. Genetic diversity indices, haplotype networks, mismatch distributions, and hierarchical analyses of molecular variance were used to evaluate spatial genetic structure and demographic history. Armenian populations exhibited high mitochondrial haplotype diversity but heterogeneous nucleotide diversity, consistent with complex demographic histories. AMOVA revealed no significant genetic differentiation among Armenian populations (FST = 0.019, p = 0.226) or between Armenia and Europe (FCT = −0.021, p = 0.754), indicating that Armenian breeding populations form part of a single, well-connected Western Palearctic mitochondrial gene pool. Mismatch distributions revealed a consistent secondary peak across all three populations, suggesting demographic complexity that may reflect the retention of older mitochondrial lineage diversity, though this interpretation remains tentative given the limited discriminatory power of mismatch analyses alone and requires confirmation through expanded sampling and complete mitogenome sequencing. These results indicate that Armenian White Stork populations are genetically diverse and well-connected to the broader Western Palearctic population, while also carrying signatures of a complex demographic history potentially shaped by Pleistocene lineage divergence and post-glacial admixture. Our findings provide a regional genetic baseline for an understudied part of the species’ range and highlight the South Caucasus as a candidate area for future genomic studies integrating complete mitogenomes and genome-wide nuclear markers. Full article

Understanding population dynamics and genetics can be critical to understanding distribution, spread, and vectorial capacity of disease vectors. One well-studied disease vector, Aedes aegypti, has been the focus of research due to the wide range of diseases it vectors and the high transmission capabilities. We examined the genetic diversity of A. aegypti utilizing a large number of individual samples from a small geographic range, as opposed to previous studies that focus on a large range and small collection. Using the COI locus, we examined 107 mosquitoes from South Texas, with multiple haplotypes identified. We observed that the samples from South Texas have a unique distribution of haplotypes relative to several invasive global locations from North America, Central America, South America, and Asia. Population measurements suggest a recent population expansion in South Texas, with multiple rare alleles identified. Our intensive sampling strategy using a small geographic scale revealed high levels of diversity not found in non-East African countries and unique haplotypes. We hypothesize that expanding sampling size when studying genetic diversity could help inform movement of mosquitoes. In addition, increased haplotype diversity may be correlated with increased insecticide resistance and differing vector competence. Full article

The population genetic diversity and demographic history of Hypomeces pulviger in Thailand were examined based on mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S ribosomal DNA (16S rDNA) sequence data. A total of 171 and 104 individuals from multiple populations were analyzed using CO1 and 16S rDNA sequences, respectively. The CO1 sequence dataset revealed high haplotype diversity (Hd = 0.999) and moderate nucleotide diversity (Nd = 0.0323), whereas the 16S rDNA showed lower diversity (Hd = 0.750, Nd = 0.0026). Population structure analyses showed low to moderate differentiation in CO1 sequences with a significant isolation-by-distance pattern, suggesting distance-limited gene flow, while 16S rDNA sequences showed weaker structure. Neutrality tests and mismatch distribution analyses supported a recent population expansion, as indicated by significantly negative Fu’s Fs and a unimodal distribution. Haplotype network and phylogenetic analyses further demonstrated greater resolution in the CO1 gene compared to the 16S rRNA gene. Collectively, H. pulviger populations in Thailand are genetically diverse, connected, and expanding, likely facilitated by both natural dispersal and agricultural activities. These findings provide important insights for understanding pest dynamics and developing effective management strategies. Full article

We investigated mitochondrial diversity and phylogeographic structure across all subspecies of the barn swallow (Hirundo rustica) to clarify evolutionary relationships, identify novel haplogroups, and assess the extent of hybridisation and maternal introgression. We analysed 580 complete H. rustica mitochondrial genomes together with twelve additional Hirundo species, three of which were newly obtained. We identified 553 unique haplotypes, including 166 previously undescribed ones, revealing high nucleotide diversity among subspecies. Phylogenetic analyses found five major haplogroups. Of these, a novel haplogroup (E) was discovered and ascribed to H.r. tytleri, previously considered part of H.r. erythrogaster. Comparative analyses with other Hirundo species support a southern African origin of H. rustica at the end of the Pliocene, followed by diversification and northward expansion. Our comprehensive dataset substantially refines the phylogeographic resolution of the species. We identify a novel haplogroup, clarify subspecies-level relationships, and reveal pervasive hybridisation and maternal introgression. These findings revise the evolutionary history of H. rustica and underscore the complexity of its population structure and gene flow. Beyond reconstructing lineage history, our study provides an evolutionary framework crucial for predicting environmental change responses and guiding migratory species conservation strategies. Full article

Tick-borne pathogens remain insufficiently investigated in donkeys, particularly in southeastern Europe. This study investigated the occurrence of piroplasms, Anaplasmataceae, and hemotropic Mycoplasma spp. in donkeys from Croatia and assessed the genetic diversity of detected Theileria equi. Blood samples from 135 apparently healthy donkeys originating from 15 herds in six Croatian counties were examined using PCR. Positive T. equi samples were further characterized by sequencing, haplotype determination, and phylogenetic analysis. Theileria equi DNA was detected in 31/135 animals (22.96%; 95% CI: 15.99–29.94%), whereas no Anaplasmataceae or hemotropic Mycoplasma spp. DNA was detected. Infection showed marked geographical and herd-level variation. The highest prevalence was recorded in Šibensko-Kninska County (17/34; 50.0%), while all positive animals originated from three herds in the Croatian littoral region. Prevalence differed significantly among herd-size categories (p = 0.012), with no positive animals detected in small herds. Sequence analysis identified three T. equi haplotypes: D was predominant (22/31; 70.97%), followed by A (8/31; 25.81%) and E (1/31; 3.23%). Phylogenetic analysis confirmed all Croatian sequences as T. equi and indicated the presence of multiple genetic lineages within the sampled donkey population. These findings provide new molecular epidemiological data on T. equi in Croatian donkeys and demonstrate a heterogeneous distribution of infection among the investigated regions and herds. Among the selected tick-borne pathogens investigated, T. equi was the only pathogen detected. Further studies integrating larger and longitudinal datasets with detailed management, environmental, and tick-vector data are needed to better understand the factors underlying the observed epidemiological patterns. Full article

The native Mozambique tilapia (Oreochromis mossambicus) serves as a cornerstone for aquaculture development in Limpopo Province, South Africa. Its adaptability to diverse culture systems, including backyard farming, highlights its potential to address food insecurity and poverty in rural communities. However, the long-term sustainability of this initiative depends on the genetic health and management of the cultured populations. This study investigated the evolutionary history, genetic diversity, and differentiation of O. mossambicus across five localities in Limpopo Province (Cordier reservoir, Nandoni reservoir, Mall of the North pond, University of Limpopo pond, and Polokwane Farm) using the combined mitochondrial DNA (COI + D-loop) dataset. Phylogenetic analysis revealed monophyly, with three well-supported clades. There was evidence of genetic affinities among some individuals within the five localities, supported by low genetic variation among populations and a common haplotype shared across all five localities. The Mall of the North population showed no genetic variation (Hd = 0.00; π = 0.00), indicating high homogeneity, whereas Nandoni exhibited the highest diversity (Hd = 0.83; π = 0.01), suggesting its potential as a primary broodstock source. These findings provide an important genetic baseline for farmed O. mossambicus, offering essential information for sustainable aquaculture management and conservation planning in the province. Full article

Understanding how co-occurring freshwater species respond to the same hydrological landscape is important for interpreting genetic diversity and population connectivity. We compared the population genetic structure of two widespread freshwater fishes, Rutilus rutilus (Linnaeus, 1758) and Perca fluviatilis Linnaeus, 1758, across major Lithuanian river basins using mitochondrial ATP6 and D-loop sequences. Both species exhibited high haplotype diversity but differed markedly in genetic structure. R. rutilus showed weak differentiation, widespread haplotype sharing among basins, and demographic signals compatible with population expansion. By contrast, P. fluviatilis exhibited stronger, more spatially heterogeneous structuring, with less consistent demographic signals and more localized differentiation. Contrary to expectations, genetic variation was not consistently associated with major drainage-basin boundaries in either species. Instead, the observed patterns suggest that species-specific ecological traits, particularly differences in dispersal capacity and habitat use, may play a greater role in shaping population structure than contemporary hydrological boundaries alone. These findings demonstrate that co-occurring freshwater fishes can exhibit contrasting patterns of genetic diversity even within shared hydrological systems. Although nuclear or genome-wide markers would strengthen these mitochondrial inferences, the study highlights the value of comparative approaches for understanding population connectivity and informing freshwater biodiversity conservation and management. Full article

Genetic background strongly influences the penetrance and phenotypic expression of SMAD4-associated intestinal tumorigenesis, yet the underlying modifier loci remain poorly defined. To investigate the genetic architecture of tumor susceptibility and systemic physiology, we analyzed 260 Smad4⁺/⁻ × Collaborative Cross (CC)-F1 mice derived from 14 CC lines using 11 quantitative traits, including longitudinal body weight, adjusted organ weights, and intestinal polyp counts across anatomical regions. Principal component analysis reduced these traits to seven components explaining more than 85% of total phenotypic variance. PC1 represented a tumor burden–metabolic axis, whereas PC2 captured systemic organ-physiology variation. Genome-wide QTL mapping of principal component scores identified significant loci for PC1 on chromosomes 1 and 4 and a female-specific locus for PC5 on chromosome 10, with additional suggestive loci supporting a polygenic architecture. Founder-effect analysis revealed strong contributions from CAST/EiJ, 129S1/SvImJ, and WSB/EiJ haplotypes. Candidate gene annotation identified biologically relevant coding and noncoding loci, including Galnt7 and Galntl6, as well as regulatory regions with potential enhancer activity. Together, these findings indicate that intestinal tumor susceptibility in Smad4⁺/⁻ × CC-F1 mice is influenced by multiple coding and regulatory genetic modifiers with sex-dependent effects. This study demonstrates that integrating multivariate phenotyping with systems genetics analyses provides an effective framework for identifying the complex genetic networks underlying intestinal tumorigenesis and associated systemic physiological variation in genetically diverse mouse populations. Full article

Ticks are hematophagous ectoparasites of major veterinary and public health importance, acting as vectors of numerous pathogens affecting wildlife, domestic animals, and humans. Data on tick species infesting lagomorphs in Croatia remain scarce. This study investigated the species composition and genetic diversity of ticks collected from European brown hares (Lepus europaeus) in Croatia during 2024–2025 using morphological and molecular methods. A total of 158 hares from 18 localities were examined, and ticks were detected on 145 individuals, resulting in an infestation prevalence of 91.8%. Morphological identification and molecular analyses revealed nine tick species. The tick community was dominated by Ixodes ricinus (59.1%; n = 821), followed by Ixodes festai (26.8%; n = 372) and Rhipicephalus bursa (9.6%; n = 133), together accounting for more than 95% of all collected ticks. Molecular analyses confirmed species identification and revealed 10 haplotypes of I. ricinus, eight of I. festai, two of I. ventalloi, and one in I. inopinatus. The results demonstrate that European brown hares are important hosts for diverse tick species in Croatia and provide baseline data for future studies on tick ecology, tick-borne pathogens, and wildlife health management. Full article

Low-coverage whole-genome resequencing (lcWGS) is emerging as a powerful population-scale genomic strategy for livestock and poultry research. By integrating sparse sequencing reads with genotype likelihoods, haplotype information and imputation models, lcWGS enables genome-wide variant discovery and genetic inference across large animal cohorts. This feature is particularly valuable for breeding populations, indigenous breeds and conservation resources, where broad sampling is essential for capturing population-specific variation and linking genomic diversity with economically and adaptively important traits. In this review, we synthesize the statistical foundations, analytical workflows and major applications of lcWGS in livestock and poultry genomics. We discuss how lcWGS supports genetic diversity assessment, population structure analysis, genome-wide association studies, genomic selection, selection-signature detection, environmental adaptation research and genetic resource conservation. We further highlight the importance of coordinated study design, including sequencing depth, sample size, reference-panel construction, imputation strategy, phenotype quality and downstream analytical models. Beyond its role as a cost-efficient genotyping approach, lcWGS provides a flexible framework for integrating population genomics with functional annotation, multi-omics resources, long-read assemblies, graph pan-genomes and interpretable prediction models. These developments are expanding the potential of lcWGS from variant discovery toward biological interpretation, precision breeding, climate-resilient animal production and the sustainable management of livestock and poultry genetic resources. Full article

Mimusops zeyheri Sond. is an underutilized indigenous fruit tree with significant nutritional, ecological, and socio-economic value in southern Africa. However, its domestication potential remains constrained by a limited understanding of intraspecific variation across geographically distinct populations. This study integrated morphological, sensory, and chloroplast genetic analyses to assess the diversity and population structuring of M. zeyheri in two regions of South Africa (Limpopo and Mpumalanga). A total of 40 trees (20 per region) were evaluated for fruit, nut, and leaf traits, while sensory attributes were assessed by 100 participants using a 9-point hedonic scale. Genetic diversity was examined using the chloroplast markers matK and trnH–psbA. Significant regional differences were observed in reproductive morphology, with Mpumalanga populations producing larger fruits (29.41 ± 0.61 mm) and nuts (2.11 ± 0.36 cm) than those from Limpopo. In contrast, sensory evaluation revealed consistently higher preference scores for Limpopo fruits across all attributes, particularly taste, aroma, and overall acceptability (mean scores 7.7–8.0 vs. 5.0–5.4). Genetic analyses identified two major chloroplast lineages corresponding broadly to geographic origin, alongside rare haplotypes indicating localized divergence. Leaf morphology remained largely conserved across regions. The combined evidence demonstrates strong regional structuring driven by both environmental gradients and historical genetic divergence. Importantly, the decoupling of fruit size and sensory preference highlights the need to prioritize quality traits in domestication strategies. These findings point to a promising domestication direction, through crossbreeding superior-tasting Limpopo genotypes with larger-fruited Mpumalanga genotypes to combine consumer-preferred sensory quality with an improved fruit size. These findings provide a foundation for conservation planning and the selection of superior genotypes for the development of M. zeyheri as a high-value indigenous fruit crop. Full article

Background/Objectives: The White-tailed Sea-eagle, Haliaeetus albicilla, experienced severe population declines throughout Europe during the nineteenth and twentieth centuries, followed by a remarkable recovery in recent decades. Although the genetic structure of northern and central European populations has been extensively investigated, the phylogeographic history and contribution of the lower Danube population to the mitochondrial genetic diversity of the species remain poorly understood. Methods: We analyzed mitochondrial control region (MT-CR HVR1) sequences from White-tailed Sea-eagles breeding in the Danube Delta Biosphere Reserve (DDBR) and integrated these data with previously published sequences covering the species’ distribution across Europe and Asia; a total of 480 samples were examined. Results: The analysis revealed 47 haplotypes, including 11 haplotypes unique to the DDBR population. Phylogeographic analyses support the Scandinavian Peninsula as the ancestral source area of the species, followed by an early colonization of Central Europe and subsequent expansion into the Balkan Peninsula through the Danube corridor. The Romanian population exhibited the highest haplotype diversity among the investigated regions (Hd = 0.9367) and was characterized by numerous private haplotypes and a predominance of haplogroup C (approximately 76% of individuals), which was rare or absent in most northern and central European populations. Demographic analyses revealed significant evidence of recent population expansion following historical bottlenecks (Fu’s Fs = −5.736, p = 0.006), whereas gene-flow estimates indicated only moderate connectivity with neighbouring Balkan and Central European populations. Conclusions: The high frequency of private haplotypes, the absence of significant isolation-by-distance patterns, and the distinct distribution of mitochondrial haplogroups, characterized by the predominance of haplogroup C, suggest that the current DDBR population may have originated primarily through local demographic recovery rather than recent large-scale recolonization. Our results indicate that the lower Danube region represents an important reservoir of genetic diversity and support the hypothesis that the Danube Delta may have acted as a potential secondary refugium and center of diversification for H. a. in southeastern Europe. Full article

The β-casein gene (CSN2) encodes one of the major milk proteins involved in calcium and phosphorus transport and combines a highly conserved genomic organization with extensive genetic diversity, making it an informative model for investigating mammalian genome evolution. Although numerous studies have described CSN2 polymorphisms, particularly in domestic species, the broader evolutionary history of the locus remains poorly understood. Here, we investigated the evolutionary architecture of CSN2 across Bovidae and related Cetartiodactyla by integrating coding variation, non-coding polymorphisms, retroposon insertions and recombination analyses. Comparative genomic analyses identified previously undescribed caprine haplotypes, expanded the known spectrum of β-casein variation in domestic and wild Caprinae, and revealed multiple structural configurations of the locus, including distinct retroposon architectures and intronic insertion/deletion polymorphisms. Retroposon mapping and comparative analyses supported a hierarchical accumulation of structural variants, while also indicating ancestral polymorphism and lineage-specific retention in rapidly radiating caprine lineages. A locus-level phylogenetic analysis revealed two deeply divergent allelic lineages and provided evidence of ancient interallelic recombination predating the divergence of Capra and Ovis. Comparative analyses further showed that a two-amino-acid deletion previously associated mainly with Caprinae is more widely distributed across Bovidae than previously recognized. Overall, the CSN2 locus emerges as a multilayered evolutionary system shaped by structural variation, ancestral polymorphism, incomplete lineage sorting and ancient recombination, illustrating how the integration of coding, structural and retroposon variation can improve locus-level evolutionary reconstruction in Bovidae. Full article

Y-chromosomal Short Tandem Repeats (Y-STRs) provide insight into forensic evidence interpretation and male population history. Romania’s position at the crossroads of Europe and Western Asia makes it a key reference population for both domains, yet existing Romanian Y-STR databases are limited in geographic coverage and marker number. We genotyped 928 unrelated Romanian males across all 41 counties and Bucharest at 27 Y-STR loci using the Investigator Argus Y-28 Kit, and modeled haplotype frequencies using the Discrete Laplace (DL) distribution (disclapmix v1.7.5, 17-locus panel; disclapmix2 v0.6.1, 27-locus panel). Discrete Laplace modeling revealed 12 and 14 optimal mixture components for the 17- and 27-locus models, respectively, with median match probabilities of 1 in 1.25 × 10⁷ and 1 in 5.8 × 10¹², reflecting nearly six order-of-magnitude gain in evidential weight. Haplogroup analysis identified 16 Y-lineages; R1a, I2a, E1b1b, J2a, and R1b collectively represent ~80% of the population, and reflect Romania’s layered Steppe, Balkan, and Near Eastern ancestry, with subtle regional gradients between Moldavia, Transylvania, and Muntenia. This dataset provides validated forensic reference data and new insights into the patrilineal genetic structure of the Romanian population. Full article