Search Results (285)

Simulated (or measured) photoabsorption spectra often provide the first indication of how matter interacts with light when irradiated by some radiation source. In addition to the direct, often slowly varying photoabsorption cross-section as a function of the incident photon frequency, such spectra typically exhibit numerous resonances and edges arising from the interaction of the radiation field with the subvalence or even inner-shell electrons. Broadly speaking, these resonances reflect photoexcitation, with its subsequent fluorescence, or the autoionization of bound electrons. Here, a (relativistic) cascade model is developed for estimating the photoabsorption of (many) atoms and multiply charged ions with a complex shell structure across the periodic table. This model helps distinguish between level- and shell-resolved, as well as total photoabsorption, cross-sections, starting from admixtures of selected initial-level populations. Examples are shown for the photoabsorption of C${}^{+}$ ions near the $1s-2p$ excitation threshold and for Xe${}^{2+}$ ions in the photon energy range from 10 to 200 eV. While the accuracy and resolution of the predicted photoabsortion spectra remain limited due to the additive treatment of resonances and because of missing electronic correlations in the representation of the levels involved, the present implementation is suitable for ions with quite different open-shell structures and may support smart surveys of resonances along different isoelectronic sequences. Full article

Background/Objectives: Y-chromosomal short tandem repeats (Y-STR) are genetic markers widely used in forensic and population genetics. However, despite their importance, many populations remain under-represented in published studies and genetic databases. One such population is the Cape Verdean, which, despite its unique history of admixture between European and sub-Saharan African populations, continues to be under-represented in global Y-STR reference databases. This study aims to characterize the Y-STR haplotype diversity and paternal lineage composition of the Cape Verdean population using a high-resolution STR panel. Methods: A total of 143 unrelated Cape Verdean men were analyzed using a set of 26 Y-STR loci, including rapidly mutating markers. Allele and haplotype frequencies were calculated, along with standard forensic parameters such as gene and haplotype diversity. Paternal lineages were inferred, and genetic relationships with other populations were evaluated using distance-based and graphical methods. Results: A total of 135 haplotypes were detected, with 88.8% being unique, yielding a haplotype diversity of 0.999. The most common haplogroups reflected both West African and European ancestry. Genetic distance analysis positioned the Cape Verdean population between African and European groups, supporting its intermediate and admixed genetic background. Conclusions: This study provides the first high-resolution Y-STR dataset for Cape Verdeans, contributing valuable reference data for forensic casework and population genetic studies. The results highlight the utility of extended Y-STR panels in admixed populations and underscore the need to enhance the representation of admixed populations in international forensic reference databases. Full article

Global trade facilitates multiple introductions of alien species, yet the role of genetic admixture between divergent lineages in driving invasion success remains debated. Here, we address this question by analyzing dynamic genetic changes across invasion stages in the dioecious weed Amaranthus palmeri, introduced to China from North and South America. Combining chloroplast phylogeography with nuclear genetic analyses, we systematically investigated genetic changes in populations at casual, naturalized, invasive, and dispersal stages. Initial casual populations originated from distinct North and South American lineages, but all established populations (naturalized, invasive, dispersal) retained only North American haplotypes. South American genetic introgression decreased progressively during invasion (from 34% in naturalized to 3% in dispersal populations), accompanied by declining inbreeding coefficients. Established populations exhibited high inter-population crosses within the North American lineage (54–60%), maintaining genetic diversity and overcoming bottlenecks. Our findings demonstrate that invasion success in A. palmeri may be driven by gene flow within the North American lineage, rather than admixture between divergent lineages. These findings enhance our understanding of the genetic mechanisms underpinning plant invasions, highlighting lineage-specific management as a critical strategy for controlling invasive populations. Full article

Objectives: Sillago japonica is a commercially important marine fish species in the Northwestern Pacific, and understanding its genetic diversity and population structure is crucial for germplasm resource conservation and elucidating population evolution mechanisms. This study specifically aimed to systematically explore the genetic diversity and population structure of S. japonica across five geographic regions (DJW, YSW, ST, ZS, and RS) in its distribution range. Methods: A total of 50 S. japonica individuals from the five geographic regions were analyzed using high-throughput mitochondrial genome sequencing data. We identified single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) loci, followed by comprehensive population genetic analyses including phylogenetic tree construction, principal component analysis (PCA), ADMIXTURE analysis, and calculation of genetic differentiation indices (Fst) and genetic diversity parameters. Results: A total of 2966 SNPs and 414 insertion-deletion loci were identified. Phylogenetic tree topology, PCA, and ADMIXTURE 1.3.0 analysis consistently showed low genetic differentiation among the five populations, a pattern supported by low pairwise Fst values ranging from 0.00047 to 0.05589, indicating extensive gene flow across regions. Genetic diversity parameters varied slightly among populations: observed heterozygosity (0.00001–0.00528), expected heterozygosity (0.04552–0.07311), percentages of polymorphic loci (19.41–30.36%), and nucleotide diversity (0.04792–0.07697). Conclusions: The low genetic differentiation and diversity observed in S. japonica populations may result from the combined effects of historical bottleneck-induced gene pool reduction and extensive gene flow. These findings provide essential theoretical support for formulating targeted conservation strategies for S. japonica germplasm resources and further studies on its population evolution mechanisms. Full article

The Shagya Arabian horse breed was created to address the need of Imperial Hussars (Hungarian light horsemen) for a horse with the intelligence, essential characteristics, and endurance of the Arabian breed, but also of a bigger size and having a better weight-carrying capacity and jumping ability. The present study aimed to explore the genetic variability and population structure of the uninvestigated Shagya Arabian horse population in Bulgaria based on genotyping at 15 equine microsatellite markers. A total of 140 horses belonging to six genealogical lines (Dahoman, Gazal, Ibrahim, Kuhailan Zaid, O’Bajan, and Shagya) were included in the survey. Genetic distances, analysis of molecular variance, principal coordinates analysis, and a Bayesian method were applied. The mean number of alleles in the individual subpopulations ranged from 3.67 in the Shagya to 5.13 in the Ibrahim sire line. The F_IS index was negative or close to 0 for the entire population and was −0.202. The overall F_ST was 0.014, indicating a low level of genetic differentiation between the subpopulations. The results of the principal components and the STRUCTURE analysis showed some level of admixture among the subpopulations in almost all genealogical lines. However, structural analysis also indicated a genetic similarity between the Ibrahim, Kuhailan Zaid, and Shagya lineages, while it showed a completely different genetic profile regarding the other three sire lines. Due to the higher admixture and the discovery of more distinct genetic clusters, it can be assumed that there is a higher gene flow from one lineage to another in the Shagya Arabian horse population in Bulgaria and that there is sufficient genetic variability and diversity to suggest adequate measures for preserving this rare breed. In addition, this study may highlight the risk of the loss of gene diversity in this population and help to implement suitable breeding programs to preserve genetic diversity. Full article

The Yucatán Black Hairless Pig (YBHP) is a native Mexican breed with cultural and agricultural importance in the Yucatán Peninsula. This study explored the genetic diversity and population structure of YBHP using a genome-wide single-nucleotide polymorphism (SNP) from the porcine GGP 50K chip, comparing it with native and cosmopolitan breeds worldwide. Genetic diversity analyses revealed an observed heterozygosity (HO) of 0.3602 ± 0.032 and an inbreeding coefficient (F_IS) of 0.1517 ± 0.076, indicating moderate diversity and a relatively low level of inbreeding for an endangered native breed. ADMIXTURE analyses revealed a predominant and distinctive ancestry component exclusive to YBHP, along with shared ancestry with European breeds, particularly those of presumed Iberian origin. Principal Component Analysis (PCA) and phylogenetic network clustering supported its genomic singularity while confirming ancestral proximity to traditional European pigs. These findings highlight the dual nature of the YBHP: a genetically distinct native breed shaped by local adaptation yet retaining ancestral signals from Old World lineages. This genomic insight provides a scientific basis for conservation planning, supports the breed’s recognition as a unique genetic resource, and promotes its sustainable use in regional production systems. Full article

Background/Objectives: The gene pool of the Apennine wolf is affected by admixture with domestic variants due to anthropogenic hybridisation with dogs. Genetic monitoring at the population level involves assessing the extent of admixture in single individuals, ranging from pure wolves to recent hybrids or wolf backcrosses, through the analysis of nuclear and mitochondrial DNA (mtDNA) markers. Although individually non-diagnostic, mtDNA is nevertheless essential for completing the final diagnosis of genetic admixture. Typically, the identification of wolf mtDNA haplotypes is carried out via sequencing of coding genes and non-coding DNA stretches. Our objective was to develop a fast real-time PCR assay to detect the mtDNA haplotypes that occur exclusively in the Apennine wolf population, as a valuable alternative to the demanding sequence-based typing. Methods: We validated a qualitative duplex real-time PCR that exploits the combined presence of diagnostic point mutations in two mtDNA segments, the NDH-4 gene and the control region, and is performed in a single-tube step through TaqMan-MGB chemistry. The aim was to detect mtDNA multi-fragment haplotypes that are exclusive to the Apennine wolf, bypassing sequencing. Results: Basic validation of 149 field samples, consisting of pure Apennine wolves, dogs, wolf × dog hybrids, and Dinaric wolves, showed that the assay is highly specific and sensitive, with genomic DNA amounts as low as 10⁻⁵ ng still producing positive results. It also proved high repeatability and reproducibility, thereby enabling reliable high-throughput testing. Conclusions: The results indicate that the assay presented here provides a valuable alternative method to the time- and cost-consuming sequencing procedure to reliably diagnose the maternal lineage of the still-threatened Apennine wolf, and it covers a wide range of applications, from scientific research to conservation, diagnostics, and forensics. Full article

Durum wheat, the world’s second most cultivated wheat species, is a staple crop, critical for global food security, including in Ethiopia where it serves as a center of diversity. However, climate change and genetic erosion threaten its genetic resources, necessitating genomic studies to support conservation and breeding efforts. This study characterized genome-wide diversity, population structure (STRUCTURE, principal coordinate analysis (PCoA), neighbor-joining trees, analysis of molecular variance (AMOVA)), and selection signatures (F_ST, Hardy–Weinberg deviations) in Ethiopian durum wheat by analyzing 376 genotypes (148 accessions) using an Illumina Infinium 25K single nucleotide polymorphism (SNP) array. A set of 7842 high-quality SNPs enabled the assessments, comparing landraces with cultivars and breeding populations. Results revealed moderate genetic diversity (mean polymorphism information content (PIC) = 0.17; gene diversity = 0.20) and identified 26 loci under selection, associated with key traits like grain yield, stress tolerance, and disease resistance. AMOVA revealed 80.1% variation among accessions, with no significant differentiation by altitude, region, or spike density. Landraces formed distinct clusters, harboring unique alleles, while admixture suggested gene flow via informal seed exchange. The findings highlight Ethiopia’s rich durum wheat diversity, emphasizing landraces as reservoirs of adaptive alleles for breeding. This study provides genomic insights to guide conservation and the development of climate-resilient cultivars, supporting sustainable wheat production globally. Full article

Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the F_IS inbreeding coefficient, and runs of homozygosity (ROH). The genetic differentiation of breeds was assessed using the F_ST index, whereas their population structure was analyzed using admixture and principal components analysis (PCA). Historical recombination patterns and genetic drift were evaluated based on linkage disequilibrium, effective population sizes, and gene flow analysis to reveal migration patterns. PCA revealed distinct clusters mostly separating mountainous, insular, and lowland breeds. The F_ST value was the lowest between Serres and Karagouniko breeds (0.050). Admixture analysis revealed a genetic substructure for Serres and Kalarritiko breeds, while Chios, followed by Katsika, demonstrated the highest within-breed genetic uniformity. ROH analysis revealed low levels of inbreeding for all breeds. Genetic introgression from both Anatolia and Eastern Europe has been evidenced for Greek sheep breeds. The results also revealed that Greek sheep breeds maintain adequate levels of genetic diversity, without signs of excessive inbreeding, and can serve as valuable resources for the conservation of local biodiversity. Full article

Growing environmental concerns have led to the search for alternative biological repellents against the large pine weevil Hylobius abietis L., Europe’s most important coniferous forest regeneration pest. A laboratory study was carried out to assess the effectiveness (damage intensity) of six combinations of a novel biological repellent, consisting of plant-based oils, beeswax, calcium carbonate, vanillin, pine bark extractives, terpentine, abrasive particles, solvent, and a viscosity agent, in comparison with commercially available repellent Norfort LDW 115. The application complexity of the repellents, their persistence on seedlings, and the extent of H. abietis damage were evaluated. The five alternative repellents had higher protection compared to the control repellent, highlighting the potential for new alternative repellents. The base (without additives) repellent provided the highest protection, indicating a redundancy of admixtures. A mixed cumulative link model, employed to estimate differences between the repellents, estimated 85% undamaged and none significantly damaged saplings in the case of the base repellent. However, the consistency and hence persistence of certain repellents on plantlets would benefit from improvements; further field studies are needed to upscale the test of the stability and efficiency of high levels in real environments under different H. abietis population pressures. Full article

Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality worldwide, but its molecular drivers remain underexplored in Latin American populations. This study investigated the prevalence, co-occurrence, and tissue distribution of somatic mutations in the TERT promoter (C228T/C250T) and CTNNB1 exon 3, as well as TERT gene expression, in liver tissues from Brazilian patients. A total of 85 samples (42 HCC, 21 cirrhosis, and 22 hepatitis) were analysed using Sanger sequencing and RT-qPCR. TERT promoter mutations were detected in 47.6% of HCC tissues, including C228T (45.2%) and C250T (2.4%), and were also present in 19% of cirrhotic tissues but absent in hepatitis samples, supporting their emergence in early hepatocarcinogenesis. CTNNB1 exon 3 mutations occurred in 17.2% of HCCs and significantly co-occurred with TERTp mutations (66.7%, p = 0.0485), although the number of CTNNB1-mutated cases was limited. TERT expression was significantly upregulated in HCC tissues regardless of mutation status (p < 0.001). This is the first study to characterise these mutations in Brazilian HCC patients, highlighting the C228T mutation as a promising biomarker for early detection and molecular surveillance in cirrhotic individuals. Despite the genetic admixture of the studied population, the mutational patterns were comparable to those reported in more homogeneous populations, reinforcing the global relevance of these molecular alterations. Full article

This study investigates the taxonomic status, phylogenetic relationships, and genetic diversity of Japanese chestnut (Castanea crenata Siebold & Zucc.) in Liaodong, China, and across East Asia. Additionally, it evaluates core germplasm resources through cluster and population structure analyses using simple sequence repeat (SSR) marker data from 13 Castanea henryi, 18 Castanea seguinii, and 27 Castanea mollissima, and 142 Japanese chestnut resources. The results show that the East Asian Castanea genus forms a monophyletic group with distinct interspecific boundaries. Japanese chestnut and two varieties/lines of C. seguinii (187 and 170) form a sister clade, indicating a close phylogenetic relationship. All Japanese chestnut resources are divided into two branches, with considerable admixture. The genetic diversity analysis revealed that the 142 Japanese chestnut varieties/lines collectively possessed 141 allelic loci, with genetic distances (GDs) ranging from 0.429 to 0.880 with an average of 0.740. Based on unique characteristics, seven resources with distinctive features were selected as mandatory. A total of 41 core germplasm resources were finally determined using the simulated annealing method. The comparative analysis revealed that, aside from a notable difference in polymorphic information loci, the core germplasm and original germplasm showed no significant differences in other genetic diversity parameters. This indicates that the 41 core germplasm resources effectively preserve the genetic diversity of the original germplasm and have been influenced by artificial selection. This study provides a scientific basis for conserving and using C. crenata germplasm resources. Full article

Camels have been essential to human survival and development across the arid Central Asian steppes, particularly in Kazakhstan, where the breeding of one-humped and two-humped camels is a longstanding tradition supporting the nomadic lifestyle. This study aimed to assess the genetic diversity and population structure of these camels across their distribution range in Kazakhstan. Blood samples from 100 individuals were collected from five locations, Almaty (ALA), Atyrau (ATR), Shymkent (SHK), Kyzylorda (KZL), and Taraz (TRZ), and genotyped using 17 microsatellite markers. All loci were polymorphic, with a mean observed heterozygosity of 0.707 in C. dromedarius and 0.643 in C. bactrianus. The highest expected heterozygosity (He = 0.939) was observed at VOLP67 in C. bactrianus and at VOLP03 in C. dromedarius. Genetic differentiation was low (FST = 0.021), indicating a weak population structure between the two species with substantial gene flow (Nm = 19.972). The hybrid analysis identified 31% hybrids, including F1, F2, and backcrosses, with the highest frequencies in KZL and TRZ, moderate frequencies in ATR, and lowest frequencies in SHK and ALA. These patterns, consistent with STRUCTURE clustering, reflect widespread but regionally variable hybridization. The phylogenetic analysis revealed three clades, separating Bactrian camels (ALA), dromedaries (SHK), and a hybrid group (ATR, KZL, and TRZ). These findings enhance our understanding of the genetic diversity of Kazakhstan’s camels and support effective conservation, breeding strategies, and genotyping applications in camel husbandry. Full article

Edge populations can harbor unique genetic diversity shaped by historical isolation and play a key role in species’ resilience and range expansion under ongoing climate warming. The Aesculapian snake (Zamenis longissimus) reaches the northern limit of its range in Central Europe, where isolated populations may provide key insights into the species’ evolutionary potential and conservation priorities. In Bohemia (the western Czech Republic), only one reproducing population, in the vicinity of Stráž nad Ohří (SO), had previously been confirmed north of the species’ continuous distribution. Here, we report two additional reproducing populations recently discovered through long-term monitoring: one at the Želinský meander (ZM) and another in Central Bohemia (CB). The ZM population is autochthonous, viable, and genetically remarkable, harboring two divergent mitochondrial haplotypes: the widespread Eastern phylogeographical clade haplotype E1 and a novel haplotype, W10, belonging to the Western clade. This represents the first confirmed record of a Western clade haplotype in the Czech Republic, and only the second known locality within the species’ entire range where both clades coexist. In contrast, the CB population—founded by human-mediated translocation from SO—is expanding dynamically and is represented solely by E1, the only haplotype previously recorded in the country. Our study highlights the importance of incorporating genetic data into conservation planning and understanding species’ evolutionary potential. The mitochondrial diversity uncovered at the ZM exemplifies how historical processes, isolation, and lineage mixing shape contemporary genetic structure. Preserving such populations, which retain unique evolutionary diversity, will be critical for maintaining the resilience of Z. longissimus in Central Europe. More broadly, disjunct northern populations may serve as reservoirs of genetic diversity, enhancing adaptive potential and supporting future range expansion under climate change. Recognizing and conserving this diversity is essential not only for local persistence but also for species-level resilience in a rapidly changing environment. Full article

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP) is the only freshwater cetacean species that remains in the Yangtze River, China. Poyang Lake is connected to the main stream of the Yangtze River, and the number of YFPs in Poyang Lake constitutes approximately half of the total species population. To implement effective conservation measures and formulate scientific genetic management strategies for the YFPs in Poyang Lake, we conducted population genetic analyses on 125 blood samples from the Poyang population and 46 tissue samples from the Anqing population, utilizing mitochondrial DNA D-loop and microsatellite loci. The genetic diversity analysis revealed two haplotypes in the Poyang population, with mitochondrial genetic diversity indices of Hd = 0.481 ± 0.020 and Pi = 0.00078 ± 0.00030. Microsatellite markers further demonstrated indices of Ho = 0.610 and He = 0.655. The genetic differentiation analysis indicated that the two populations exhibited moderate genetic differentiation (0.05 < Fst < 0.15). Upon excluding the dead samples from the Anqing population, the genetic differentiation between the two populations increased and the gene flow diminished. This indicated that certain dead samples from the Anqing population might have originated from Poyang Lake or had a background of Poyang Lake–Yangtze River migration and gene exchange. This finding was further corroborated by STRUCTURE analysis, which revealed genetic admixture between the two populations. We assessed the current genetic diversity of the Poyang population and its genetic differentiation from the Anqing population. This study provides fundamental data for formulating a conservation program for YFPs in Poyang Lake. Full article