Search Results (90)

(1) Background: Rubus geoides Sm., a native species of southern Patagonia, faces increasing threats due to climate change and anthropogenic land-use changes. Historically widespread, its distribution has become restricted by overgrazing, urban expansion, extractive industries, and direct harvesting from natural populations driven by interest in its nutraceutical potential since the first European settlements. (2) Methods: To assess its resilience and conservation prospects, we analyzed the morphological variability, genetic diversity, and population structure, complemented by species distribution modeling under past and future climate scenarios. (3) Results: Our findings reveal moderate genetic differentiation and private alleles in specific populations, alongside significant variation in flowering phenology. Paternity analysis indicates a tendency toward self-pollination, although this conclusion is constrained by the limited number of microsatellite markers employed. These results suggest post-glacial dispersal patterns and highlight the species’ potential for expansion under certain climate scenarios. (4) Conclusions: This study provides critical insights for biodiversity conservation and sustainable land management, directly aligned with the UN Sustainable Development Goals SDG 15 (Life on Land). Indirectly, this study contributes to SDG 2 (Zero Hunger) by highlighting the importance of threatened species that hold value for human consumption and food security. Land-use changes, particularly mining and green hydrogen industry settlements, may represent stronger limitations to species expansion than climate change itself. Full article

Rumex crispus L. is a globally distributed invasive species that has naturalized in South Korea, where its use as a medicinal, edible, and ecological restoration resource continues to expand. However, its genetic background remains insufficiently understood, underscoring the need for species-specific molecular markers to enable accurate assessments of intraspecific genetic diversity and population structure. Using 19 newly developed microsatellite markers, we analyzed 120 plants from 6 populations in the riparian zone. A total of 166 alleles were detected, with a mean polymorphism information content of 0.637. Across the six populations, genetic diversity analysis showed mean observed (Ho = 0.304) and expected (He = 0.588) heterozygosity values indicative of heterozygote deficiency (inbreeding coefficient F_IS = 0.456–0.559). Genetic differentiation was low in AMOVA (10%) and F_ST (0.048–0.120) but higher in Jost’s D (0.096–0.342). STRUCTURE analysis identified two major genetic clusters (ΔK = 2), and spatial Bayesian clustering revealed six distinct genetic units (K = 6), suggesting that partial barriers to gene flow may have influenced population structure. These findings provide essential genetic insights that can support the effective control of R. crispus spread and its potential use as a valuable plant resource. Full article

The complex life cycle, high reproductive potential and ability to quickly develop resistance to insecticides are key factors contributing to the destructiveness of the peach–potato aphid (Myzus persicae Sulzer) among pest species. Monitoring its population dynamics at a large scale allows us to better understand M. persicae biology and take relevant measures for pest management. For this purpose, reliable molecular tools are needed. Based on the analysis of 128,362 microsatellite loci, we developed four multiplex assays including 49 comprehensively characterised SSR markers. Internal validation confirmed the species specificity and low genotyping error (e_a = 0.8%, e_l = 0.99%, e_obs = 22.7%) of the assays. A total of 194 alleles were identified (mean = 4 alleles per locus, range = 2–8 alleles per locus) within a group of 365 aphid accessions collected in the Vysočina region (Czechia). The studied aphid population showed the typical characteristics expected of the species with clonal or partially clonal reproduction (heterozygote excess, negative F_IS, moderate-to-high linkage disequilibrium (LD), and distortion of the H-W equilibrium for most of the loci), and did not exhibit any stratification on a spatiotemporal level. Owing to the high discriminatory power of the markers, we discovered that the population sample was founded upon a small number of fundatrices, as only five dominating lineages comprising over 70% of all accessions were identified. In conclusion, this study identified a significant number of new high-quality markers with the high discriminatory power necessary for revealing the population structure and dynamics of M. persicae, which holds considerable potential in both general biological and agricultural research. Full article

Genetic variability in terrestrial mammals is essential for understanding population and evolutionary dynamics, as well as for establishing effective strategies in conservation biology. This comprehensive review aimed to critically analyze invasive and non-invasive techniques used to assess genetic variability in wild terrestrial mammals. Using the PICO (Population, Intervention, Comparison, Outcome) format and following PRISMA guidelines, a comprehensive literature search was conducted in Web of Science, Scopus and Science Direct databases, including articles published in English from January 2015 to April 2025. Thirty-one experimental studies were selected that met specific criteria related to genetic evaluation using invasive (direct blood or tissue collection) and non-invasive (stool, hair and saliva collection) techniques. The results indicate that invasive techniques provide samples of high genetic quality, albeit with important ethical and animal welfare considerations. In contrast, non-invasive techniques offer less disruptive methods, although they present significant challenges in terms of quantity and purity of DNA obtained, potentially affecting the accuracy and confidence of genetic analysis. Detailed analysis of selected studies showed diverse patterns of heterozygosity and inbreeding coefficients between different taxonomic orders (Carnivora, Artiodactyla, Proboscidea, Primates and Rodentia). In addition, the main anthropogenic threats and current conservation strategies implemented in different species were identified. An overall genetic variability ranging from high to moderate was observed, with large species being more vulnerable to genetic reduction due to changes in habitat and human activities. Rather than a static comparison, our synthesis traces a clear methodological arc from small short tandem repeats (STR, or microsatellites) panels towards SNP-based approaches enabled by next-generation sequencing, including reduced representation (ddRAD), amplicon panels (GT-seq), and hybridisation capture tailored to degraded DNA from hair, faeces, and environmental substrates. Over 2015–2025, study designs shifted from presence/absence and coarse diversity estimates to robust inference of relatedness, assignment, effective population size, and gene flow using hundreds–thousands of SNPs and genotype-likelihood frameworks tolerant of allelic dropout and low coverage. Laboratory practice converged on multi-tube replication, synthetic blocking oligos, and capture-based enrichment; bioinformatics adopted probabilistic genotype calling, error-aware filtering, and replication-based consensus. This review provides a solid basis for optimizing genetic sampling methods, allowing for more ethical and efficient studies. Furthermore, it contributes to strengthening conservation strategies by underlining the importance of adapting the sampling method to the biological and ecological particularities of each species studied. Ultimately, these findings can significantly improve genetic conservation decision-making, benefiting the sustainability and resilience of wild land mammal populations. Full article

Background/Objectives: The mutational dynamics of microsatellites over deep evolutionary timescales are poorly understood. This study aims to elucidate the life history of trinucleotide microsatellites by tracing orthologous loci across divergent vertebrate lineages and characterizing their mutational pathways. Methods: We developed a bioinformatic framework for identifying orthologous microsatellite loci using conserved flanking sequences. This approach was applied to three trinucleotide microsatellites located in exonic, intronic, and intergenic regions, respectively. These loci were amplified and sequenced across 126 individuals representing 64 vertebrate species, whose divergence times range from 6 to 150 million years ago (MYA). Results: Flanking sequences proved essential for reliable orthology assignment, while repeat motifs revealed distinct mutational pathways. Microsatellite decay occurs through two primary mechanisms: the complete loss of dominant repeats or their progressive reduction to solitary units (≤1 repeat). This degeneration process is facilitated by cryptic simple sequences (CSS), which act as genomic catalysts promoting birth–death transitions. Large intra-motif deletions were identified as the key mutational event driving contractions and eventual locus degeneration. Furthermore, mutational patterns were highly locus-specific, influenced by genomic context. Conclusions: Although the study focused on only three loci, limiting broader generalizations, our findings provide mechanistic insights into microsatellite evolution. These results establish a foundation for modeling complex microsatellite life histories and highlight the role of CSS in facilitating evolutionary turnover. Full article

The population size of black poplar (Populus nigra L.), once an important part of floodplain forests in the Czech Republic, has greatly declined due to human activity. In this study, we applied microsatellite (SSR) markers to identify species and assess genetic diversity, with the aim of supporting conservation of this endangered species. A total of 378 poplar trees were analyzed following field surveys. Five diagnostic SSR markers with species-specific alleles for P. deltoides Bartr. ex Marsh. enabled the identification of 39 interspecific hybrids, which were distinguished from native P. nigra. Thirteen SSR loci were used to evaluate genetic diversity among confirmed P. nigra individuals. The results revealed high genetic variation, with 66% of pairwise genotype comparisons differing at all loci. After excluding 45 genetically similar individuals, 292 genetically verified and polymorphic P. nigra trees were selected as potential sources of reproductive material. Genetic differentiation (Fst) was highest between P. nigra and P. deltoides (0.27), and lowest between reference Populus ×euroamericana clones and detected hybrid poplars (0.05) from natural localities. Distinct genetic structures were identified among P. nigra, P. deltoides, and hybrid individuals. These findings provide essential data for the protection, reproduction, and planting of black poplar. Full article

Bats are great models for studying repetitive DNAs due to their compact genomes and extensive chromosomal rearrangements. Here, we investigated the repetitive DNA content of two phyllostomid bat species, Artibeus lituratus (2nn = 30♀/31♂) and Carollia perspicillata (2n = 20♀/21♂), both harboring a multiple XY₁Y₂ sex chromosome system. Satellite DNA (satDNA) libraries were isolated and characterized, revealing four and ten satDNA families in A. lituratus and C. perspicillata, respectively. These sequences, along with selected microsatellites, were in situ mapped onto chromosomes in both species and phylogenetically related taxa. SatDNAs showed strong accumulation in centromeric and subtelomeric regions, especially pericentromeric areas. Cross-species mapping with C. perspicillata-derived probes indicated terminal localization patterns in other bat species, suggesting conserved distribution. Microsatellites co-localized with 45S rDNA clusters on the neo-sex chromosomes. Additionally, genomic hybridization revealed a male-specific signal on the Y₁ chromosome, pointing to potential sex-linked repetitive regions. These findings confirm that bat genomes display relatively low amounts of repetitive DNA compared to other mammals and underscore the role of these elements in genome organization and sex chromosome evolution in phyllostomid bats. Full article

This study investigates the genetic diversity and population structure of Castanopsis tribuloides, a vital tree species in Asian forest ecosystems. Understanding the genetic patterns of keystone forest species provides critical insights into forest resilience and ecosystem function and informs conservation strategies. We analyzed population samples collected from three distinct locations within Doi Suthep Mountain in northern Thailand using Short Tandem Repeat (STR) markers to assess both intra- and inter-population genetic relationships. DNA was extracted from leaf samples and analyzed using a panel of polymorphic microsatellite loci specifically optimized for Castanopsis species. Statistical analyses included the assessment of forensic parameters (number of alleles, observed and expected heterozygosity, gene diversity, polymorphic information content), population differentiation metrics (G_ST), inbreeding coefficients (F_IS), and gene flow estimates (N_m). We further examined population history through bottleneck analysis using three models (IAM, SMM, and TPM) and visualized genetic relationships through principal coordinate analysis and cluster analysis. Our results revealed significant patterns of genetic structuring across the sampled populations, with genetic distance metrics showing statistically significant differentiation between certain population pairs. The PCA and cluster analyses confirmed distinct population groupings that correspond to geographic distribution patterns. These findings provide the first comprehensive assessment of C. tribuloides population genetics in this region, establishing baseline data for monitoring genetic diversity and informing conservation strategies. This research contributes to our understanding of how landscape features and ecological factors shape genetic diversity patterns in essential forest tree species, with implications for managing forest genetic resources in the face of environmental change. Full article

Background: Sedum, with the largest number of species in the family Crassulaceae, is a taxonomically complex genus and an important group of horticultural plants within this family. Despite extensive historical research using diverse datasets, the branching patterns within this genus and the family remain debatable. Methods: In this study, we conducted sequencing and comparative analyses of plastomes from eight Sedum species, focusing on the diversities in nucleotide, microsatellite repeats, putative RNA editing, and gene content at IR junctions. The phylogenetic inferences were further conducted at the order level—Saxifragales. Results: Our IR junction analyses of the eight investigated Sedum species detected a unique 110 bp IR extension into rps19, a feature highly conserved across Crassulaceae species, indicating a remarkably family-specific pattern. Additionally, we obtained 79 PCGs from 148 Saxifragales species and constructed a phylogenetic tree using a larger set of plastomes than in previous studies. Our results confirm the polyphyly of Sedum and reveal that S. emarginatum is more closely related to S. makinoi than to S. alfredii, which is sister to S. plumbizincicola. Furthermore, we also performed analyses of codon usage, putative RNA editing sites, and microsatellite repeats. Conclusions: These findings and the generated sequence data will enrich plastid resources and improve understanding of the evolution of Sedum, Crassulaceae, and Saxifragales. Full article

Oncomelania hupensis quadrasi is the intermediate host of S. japonicum, the causative species of schistosomiasis in the Philippines. Conventionally, risk areas are identified by procedures requiring highly skilled personnel and constant surveillance efforts. Recent developments in disease diagnostics explore the utilization of environmental DNA as targets for polymerase chain reactions in disease surveillance. In this study, a low-cost, specific, and efficient SYBR Green-based real-time PCR assay to detect O. h. quadrasi DNA from water samples was developed, optimized, and validated. Primers were designed based on the A18 microsatellite region of O. h. quadrasi. The assay exhibited a detection limit of one copy number per microliter at 99.4% efficiency and R² = 0.999, which specifically amplified O. h. quadrasi DNA only. Validation of this assay in environmental water samples demonstrated 100% PPV and NPV values, suggesting its potential as a tool for identifying risk areas, pathogen-directed surveillance, policy making, and disease control. Full article

Artificial gynogenesis is an effective means of producing pure lines and is widely used for genetic analysis of fish and for sex control. In this study, inactivated sperm from heterogenous blunt snout bream (Megalobrama amblycephala, MA) were used to activate Kohaku koi (Cyprinus carpio var. koi, CK) and produce high-quality female offspring. To determine whether the offspring were gynogenetic fish, the karyotype and DNA content of the CK, MA and the induced offspring (IO) were first compared and it was found that the IO were diploid with 100 chromosomes and their karyotype was 22m + 34sm + 22st + 22t. The DNA content of the IO was not significantly different from that of the CK. Subsequently, the amplified band profiles of CK, MA and IO were analyzed with species-specific microsatellite markers. The results showed that there were no amplified MA microsatellite bands in IO. The size of the amplified bands and the sequence of the 5S rDNA in CK, MA and IO were also analyzed. It was found that the amplified 5S rDNA gene fragments in IO contained two fragments that were both the same size as those of CK and matched more than 90% with those of CK. Finally, the sex of IO was verified using gonadal tissue sections. The result showed that IO was not an all-female population; males were also present (36.7%). In summary, a series of validation methods confirmed that the induced offspring were gynogenetic fish, which is the basis for the subsequent genetic improvement of pure lines of high-quality koi. Full article

Snakes are cytogenetically dynamic, characterized by largely conserved diploid chromosome numbers although displaying varied variable evolutionary stages of their sex chromosomes. This study examined four snakes, with a special focus on the genus Ptyas, to provide evolutionary insights into the evolution of ZW sex chromosomes. We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches, described for the first time the karyotype of Ptyas korros, and revisited the karyotype descriptions of P. mucosa, Chrysopelea ornata, and Fowlea flavipunctatus. We found that all species except F. flavipunctatus have highly heterochromatic W chromosomes enriched in satDNAs or microsatellite repeats. Repetitive sequences accumulate with the heterochromatinization of the W chromosome but are not necessarily associated with this process, demonstrating the dynamic makeup of snake sex chromosomes. Autosomal locus-specific and sex chromosome probes from Pogona vitticeps and Varanus acanthurus did not show hybridization signals in Ptyas snakes, suggesting divergent evolutionary pathways. This finding highlighted the dynamic nature of sex chromosome evolution in snakes, which occurred independently in lizards. Full article

In this study, we compared the genetic diversity and structure of small yellow croaker (Larimichthys polyactis, LP), large yellow croaker (Larimichthys crocea, LC), and their reciprocal hybrids (LP ♀ × LC ♂ (LCP) and LC ♀ × LP ♂ (LPC)) using 14 microsatellite loci. Our results revealed that genetic diversity was highest in LCP, followed by LP and LPC, with LC exhibiting the lowest level. Additionally, among the two hybrid progenies, the number of loci in LCP deviating from Hardy–Weinberg equilibrium was lower. This suggests that LCP is a more appropriate choice as breeding material and has the potential to enhance germplasm resources. Based on the analysis of 14 microsatellite loci, we observed that both hybrid species clustered with their respective maternal parents. Specifically, LPC exhibited a closer genetic relationship to its maternal parent than LCP did. Furthermore, the majority of genes in LPC were inherited from its maternal parent (LP). In the LCP population, approximately 63% of individuals possessed gene profiles similar to those observed in LPC, while the remaining individuals displayed a mix from both parents. This study provides a strategic direction for the efficient utilization and management of novel germplasm resources in hybrid yellow croaker. Hybrid yellow croaker serves as an intermediate breeding material, playing a significant role in the genetic improvement of Larimichthys crocea and Larimichthys polyactis. Full article

Anseriformes represent a basal order in the phylogeny of neognath birds and are of particular interest in cytogenetic research due to their distinctive chromosomal features. However, aspects of their chromosomal evolution, such as the distribution and organization of microsatellite sequences, remain poorly understood. Given the role of these dynamic repetitive sequences in chromosome organization, differentiation, and evolution, we analyzed microsatellite distribution in three Anatidae species, each representing a different subfamily: Amazonetta brasiliensis-Brazilian Teal (Anatinae), Coscoroba coscoroba-Coscoroba Swan (Anserinae), and Dendrocygna viduata-White-faced Whistling Duck (Dendrocygninae). This is the first karyotypic description for White-faced Whistling Duck (2n = 78) and Brazilian Teal (2n = 80), whereas Coscoroba Swan, previously analyzed, exhibits a notably high diploid number (2n = 98). Despite sharing a similar macrochromosome morphology, the three showed differences in diploid numbers and microsatellite distribution. Extensive microsatellite accumulation was found in both autosomal and sex chromosomes (Z and W) of Brazilian Teal and Coscoroba Swan, while White-faced Whistling Duck displays minimal hybridization signals and an absence of microsatellites on the sex chromosomes. The accumulation of specific microsatellites, such as (CAC)₁₀ and (GAG)₁₀, in centromeric and pericentromeric regions suggests an association with transposable elements, potentially driving chromosomal evolution. Notably, the substantial accumulation of these sequences on the Z and W chromosomes of Brazilian Teal and Coscoroba Swan, but not White-faced Whistling Duck, supports the hypothesis that repetitive sequence expansion occurs in a species-specific manner, contributing to sex chromosome differentiation. These findings highlight microsatellite mapping as a valuable tool for understanding chromosomal evolution and genomic differentiation in Anseriformes. Full article

Background/Objectives: The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important species in freshwater aquaculture. Genetic admixture and degradation due to rapid industry expansion threaten sustainable development. This study aims to assess the genetic diversity and structure of six P. sinensis populations for better management. Methods: We combined morphological analysis and microsatellite markers to evaluate the genetic diversity of six populations. A discriminant function based on morphology was developed, achieving 71.4% classification accuracy. Two SSR markers were identified to specifically distinguish the HS population. Results: The six populations were classified into three subgroups. Frequent gene flow was observed among the CY, W, and DT populations, with most genetic variation occurring within individuals. However, significant genetic differentiation was detected between populations. While gene flow enhanced diversity, it suppressed differentiation. Conclusions: This study provides insights into the genetic structure and diversity of six P. sinensis populations. The discriminant function and SSR markers offer a basis for germplasm conservation and management, supporting sustainable aquaculture development. Full article