Search Results (508)

Understanding genetic diversity and population structure is essential for the sustainable management of freshwater fish, particularly in systems influenced by long-term stocking. In this context, the genetic status of Albanian common carp (Cyprinus carpio) remains poorly understood. Here, 125 individuals from five populations representing natural lakes (Ohrid and Shkodra), semi-managed freshwater systems (Prespa and Belshi), and a hatchery stock (Tapiza) were genotyped at 12 polymorphic microsatellite loci. High genetic diversity was detected across all populations, with low genetic differentiation and relevant estimates of gene flow. Bayesian clustering identified two main genetic groups, with natural lake populations predominantly represented by a single genetic lineage and managed systems showing higher admixture. Multivariate and phylogenetic analyses supported a close genetic relationship between Ohrid and Shkodra natural lake populations. These patterns may reflect historical stocking and translocation programmes, potentially involving genetically similar or shared broodstock sources, which may have contributed to the observed genetic similarity among populations while maintaining high levels of within-population genetic diversity. The more homogeneous genetic composition of natural lake populations may also reflect local environmental conditions that influenced the distribution of allelic variants among populations. Overall, this study provides a comprehensive genetic assessment of Albanian common carp and establishes a baseline for future sustainable management plans. Full article

In post-mortem genetic identification, teeth represent one of the most reliable sources of nuclear DNA when other biological samples are unavailable, owing to their ability to protect genetic material from autolysis, microbial degradation, and environmental insults. The present study describes a forensic veterinary case report involving a Staffordshire Bull Terrier litter in which the appearance of blue-coated offspring from a phenotypically black sire and a blue dam prompted parentage verification. The sire died before formal ante-mortem sampling could be carried out. In accordance with Regulation (EC) No. 1069/2009, Article 15, the carcass was interred in the owner’s garden. Before burial, two teeth were collected as the sole biological material available for identification by the official veterinarian, ensuring an unambiguous chain of custody from death certification to laboratory analysis. DNA extraction was performed using two independent protocols: Method A, a silica-membrane-based purification (QIAamp DNA Kit, Qiagen), applied to dental pulp, and Method B, a decalcification-based workflow (T-Bone Ex Kit) followed by DNA extraction using EZ2 Connect Instruments (Qiagen). Quantification of the DNA samples obtained were done by fluorometry. Short Tandem Repeat (STR) genotyping was performed using the Canine Genotypes™ Panel 1.1 by Applied Biosystems (Thermo Fisher Scientific, Waltham, MA, USA) targeting the 18 autosomal ISAG-recommended microsatellite loci. Parentage assignments were carried out against reference STR profiles obtained from peripheral blood of the dam and offspring. The two methods, considering a different biological matrix and different operating conditions, allowed us to obtain the STR profile, but Method B showed quality electropherograms, improving the confidence and interpretation of all the markers analyzed. The differences observed between the two approaches may reflect a combination of factors, including the different dental matrices analysed, the quantity and quality of the starting material, tooth identity and tissue preservation, and differences inherent to the extraction procedures themselves; therefore, in this case, the more complete and clearer STR profile obtained with Method B should be considered a case-specific observation rather than evidence of a direct effect of the extraction method. Overall, regardless of the DNA extraction method used, the results did not exclude the biological paternity of the blue-mantled offspring. Furthermore, this case report provides practical methodological guidance for DNA recovery from canine teeth and supports their use as a reliable source of post-mortem DNA for STR-based parentage testing. Full article

Freshwater ecosystems are increasingly affected by habitat alteration and reduced connectivity, which can influence the genetic structure of aquatic organisms. This study investigated the population genetic structure of Eurasian perch (Perca fluviatilis L.) in major river systems of Latvia (Daugava River) and Lithuania (Nemunas and Neris rivers) using nine microsatellite loci. The quantitative parameters of genetic diversity were assessed using standard population genetic analyses. The evaluation of population genetic structure was also based on Bayesian clustering and phylogenetic reconstruction. All of the studied populations exhibited relatively high genetic diversity, with the number of alleles per locus ranging from 4 to 24 and observed heterozygosity ranging from 0.536 to 0.716. Genetic differentiation among populations was low to moderate but significant, with F_ST values ranging from 0.021 to 0.079 within the Daugava River basin and reaching 0.034 between the Nemunas and Neris rivers. Bayesian clustering and Neighbor-Joining analyses revealed genetic structuring at both regional and local scales, including pronounced substructuring within the Daugava River, which is divided into a few fragments due to three hydroelectric plants. The observed patterns indicate that population connectivity is not uniform across the study area and likely reflects the combined influence of historical and contemporary processes. These findings improve our understanding of perch population structure in Baltic river systems and provide relevant information relevant for the conservation and management of freshwater fish genetic resources. Full article

Alpacas (Vicugna pacos) are of increasing economic importance, mainly due to their high-quality fiber. This study aimed to develop and validate molecular tools for sex identification, individual identification and parentage testing, and to characterize genetic diversity and population structure in Huacaya alpacas bred in Poland. Forty-five previously described microsatellites and one newly developed SRY-based marker were organized into three multiplex panels containing sixteen, seventeen and thirteen markers. The SRY marker was validated in 17 reference animals of known sex (5 males, 12 females) and subsequently in 239 study animals, showing complete concordance with recorded sex. The 44 microsatellites, excluding SRY and the monomorphic YWLL02, showed a mean of 11.45 alleles per locus, observed heterozygosity (Ho) of 0.708, expected heterozygosity (He) of 0.755 and mean polymorphism information content (PIC) of 0.727. Combined non-exclusion probabilities were 1.58 × 10⁻¹¹ for a first parent and 1.08 × 10⁻³⁰ for a parent pair. Seven loci showing elevated null allele frequencies were excluded from population structure analyses. Multivariate, phylogenetic and Bayesian analyses revealed no strong genetic subdivision. The developed tools provide practical support for genetic management of alpacas in Poland. Full article

Background/Objectives: The black grouse (Lyrurus tetrix) is experiencing a rapid decline across much of Europe. In Poland, the Carpathians and Sudetes constitute two of the last important strongholds of this endangered species; however, the genetic relationships between populations inhabiting these mountain systems remain poorly understood. Methods: A total of 579 non-invasive samples were collected in the Jizera Mountains and Giant Mountains (Sudetes), as well as in the Tatra Mountains and the Orava–Nowy Targ Basin (Carpathians). Microsatellite genotyping at nine loci identified 122 individuals. Genetic diversity and population genetic structure were assessed using F-statistics, AMOVA, STRUCTURE, PCoA and DAPC. Results: Significant genetic differentiation was detected among populations, with substantially lower differentiation within the mountain regions than between the Sudetes and Carpathians. Analyses consistently identified two major genetic groups corresponding to the Sudetes and Carpathians. The highest genetic diversity was recorded in the Tatra Mountains. Some individuals from this population displayed genetic signatures consistent with possible connectivity to neighbouring populations outside the study area, although this hypothesis requires testing with additional reference samples from these populations. Conclusions: The results demonstrate strong genetic structuring of black grouse populations in southern Poland and suggest limited contemporary gene flow between the Sudetes and Carpathians mountain ranges. The observed differentiation supports treating the Sudeten and Carpathian populations as separate Management Units. The Tatra Mountains constitute an important reservoir of genetic diversity and may play a key role in maintaining genetic connectivity within the Carpathian population. Full article

Widespread species complexes often contain hidden evolutionary diversity shaped by dispersal, isolation and climatic change. Here, we aimed to characterize geographic genetic structure within the Rhinolophus pusillus species complex, assess the concordance among genetic, morphological and acoustic patterns and the evolutionary distinctiveness of the Taiwan-endemic R. monoceros, and determine whether Quaternary changes in habitat suitability were geographically consistent with the inferred phylogeographic and demographic history. To address these objectives, we analyzed 378 individuals from 70 localities and integrated mitochondrial sequences, nuclear loci, microsatellite genotypes, external phenotypic traits comprising forearm length, body mass, forearm mass index and echolocation resting frequency, demographic inference, ancestral-area reconstruction and ecological niche modelling. Mitochondrial analyses identified five geographically structured lineages within R. pusillus, corresponding broadly to South China, East China, Central China, Hainan Island and Southwest China, while R. monoceros formed a closely related but distinctive Taiwan lineage. South China showed the highest mitochondrial diversity, occupied a central position in haplotype networks and was repeatedly inferred as an important ancestral and refugial region. Divergence-time estimates placed the early diversification of the complex in the Middle Pleistocene, followed by demographic expansion in several lineages during the Late Pleistocene. In contrast, nuclear loci and microsatellites revealed extensive allele sharing and weaker geographic subdivision, suggesting incomplete lineage sorting and historical connectivity. Our results indicate that the R. pusillus complex represents an ongoing diversification system shaped by Quaternary climatic fluctuations, sea-level changes and regional isolation, highlighting the value of integrative phylogeography for conserving hidden evolutionary diversity in widespread bats. Full article

The green peach aphid, M. persicae (Sulzer), is one of the most important pests of horticultural crops worldwide. In Chile, M. persicae causes severe losses in peach and herbaceous crops. Understanding aphid population dynamics across its primary (peach) and secondary (weed) hosts is fundamental to developing a more effective pest control strategy. To investigate the spatial genetic connectivity of M. persicae populations between cultivated and non-cultivated hosts, we conducted a longitudinal survey in three commercial peach orchards in central Chile. Apterous aphid colonies were repeatedly sampled from peach trees and weed hosts located both within and outside orchards, and population genetic structure and clonal diversity were characterized using six polymorphic microsatellite loci. Genetic differentiation was low between weed populations inside and outside orchards, whereas greater differentiation was observed between peach trees and weeds outside orchards. Three recurrent multilocus genotypes persisted across multiple seasons, orchards, and host plants, indicating substantial spatiotemporal persistence of particular clonal lineages. Comparison with insecticide-resistance profiles further showed that neutral population structure and resistance-associated variation were not necessarily concordant. These findings support an important role for non-cultivated hosts in maintaining recurrent M. persicae lineages within peach agroecosystems and highlight the value of considering surrounding vegetation in integrated pest management. Full article

The scallops of the genus Argopecten hold a significant position in the international shellfish aquaculture industry. However, due to their hermaphroditic nature, selfing reproduction has led to an increasingly severe phenomenon of germplasm degradation. The development of interspecific hybridization can effectively address this issue, but the fertility of interspecific hybrid offspring is greatly affected. Backcrossing appears to be a more practical and feasible solution, yet current research in this regard remains extremely scarce. In this study, the F1 generation of bay–Peruvian hybrid scallops (Aip derived from Ai ♀ × Ap ♂) and Peruvian–bay hybrid scallops (Api derived from Ap ♀ × Ai ♂) were successfully backcrossed with Peruvian scallops (Argopecten purpuratus, Ap) and bay scallops (Argopecten irradians, Ai) to produce F2 backcrossed population (Aipi derived from Aip ♀ × Ai ♂; Aipp derived from Aip ♀ × Ap ♂; Apii derived from Api ♀ × Ai ♂ and Apip derived from Api ♀ × Ap ♂). These F2 populations were comprehensively analyzed in terms of heterozygosity, gonadal development and differentiation, fertility, genetic diversity, and offspring identification. The results revealed that the fertilization and hatching rates of the F2 generation were significantly lower than those of the parental generations. However, they exhibited normal development through larval, juvenile, and adult stages, albeit with prolonged larval development periods. Notably, the juvenile and adult stages demonstrated significant hybrid vigor. The F2 generation retained hermaphroditic characteristics but also included individuals with exclusively female gonads. Cloning of Dmrt1 and Foxl2 genes in these scallops showed high similarity with the bay scallop’s corresponding genes, and Dmrt1 is specifically expressed in the testis, while Foxl2 is specifically expressed in the ovary, as is the case in the bay scallop. Eleven pairs of polymorphic loci were selected from developed microsatellite markers for bay scallops, and the analysis revealed that the polymorphism levels in the F2 backcrossed population were higher than those in purebred parental self-crosses. Additionally, the reliability of parental genetic information in the backcrossed population has also been corroborated according to the scallop descent identification experiments. The findings of this study enhance the understanding of Aipi, Aipp, Apii, and Apip, providing a theoretical foundation for the selection and breeding of scallop species with superior traits and addressing inbreeding decline in scallop culture. Full article

The FMD is an endangered species under first-class national protection in China. Comparative genomic investigation of microsatellite (SSR) in CDS may provide insights into adaptive evolutionary mechanisms and may inform conservation management strategies for captive populations. Here, we analyzed the FMD genome alongside five closely related ruminants: cattle (Bos taurus), red deer (Cervus elaphus), white-tailed deer (Odocoileus virginianus), sheep (Ovis aries), and goat (Capra hircus). Through genome-wide bioinformatic identification, we systematically compared the abundance, density, structural categories, repeat motifs, chromosomal distribution, and pathway enrichment analysis of SSR-containing genes in CDS. Furthermore, we performed synteny analysis and evaluated population genetic diversity. A total of 2509 SSRs in CDS were identified in the FMD, with a relative density of 62.61 loci/Mb. Trinucleotide SSRs were overwhelmingly dominant (88.46%) in the FMD. Notably, the FMD exhibited the highest relative abundances of both tetranucleotide and pentanucleotide repeats among the six species (2.37 and 2.18 loci/Mb, respectively), with pentanucleotide abundance approximately 5.6- to 9.1-fold higher than that of the other species. Chromosomal mapping revealed the highest SSR density in CDS regions on chromosome 27, while SSR-containing genes exhibited a heterogeneous pattern characterized by localized clustering. Synteny analysis demonstrated relatively conserved syntenic relationships between the FMD and goat, sheep, and cattle, with moderate conservation also observed with red deer and white-tailed deer, suggesting that SSR-containing genes in ruminants may remain highly conserved during chromosomal rearrangements. GO and KEGG analyses indicated that SSR-containing genes across all species were predominantly enriched in transcriptional regulation, RNA processing, and signal transduction pathways. Specifically, the FMD showed enrichment patterns associated with hypoxia response, mRNA processing, and epigenetic regulation, which may reflect lineage-specific transcriptional patterns, though the functional involvement of these SSRs remains to be experimentally validated. In addition, the five primer pairs screened in this study exhibited high polymorphism, with a mean polymorphism information content (PIC) of 0.93. The observed heterozygosity (Ho) was significantly lower than the expected heterozygosity (He), and the mean inbreeding coefficient (FIS) was 0.57, indicating heterozygote deficiency and an elevated risk of inbreeding in this captive FMD population. Collectively, our findings provide preliminary insights into the conserved patterns of microsatellite evolution and lineage-specific divergence in ruminants, offering a reference framework for comparative genomics and adaptive evolution research, as well as practical molecular markers for genetic management of captive populations. Full article

Maintaining genetic diversity is essential for the long-term conservation of migratory freshwater fishes facing increasing anthropogenic pressures. Prochilodus magdalenae (bocachico), one of Colombia’s most economically and ecologically important freshwater fish species, supports artisanal fisheries, regional food security, and the livelihoods of local communities but has experienced population declines associated with overfishing, habitat degradation, and hydrological alteration. This study evaluated the genetic diversity and population structure of wild and hatchery-associated P. magdalenae from northern Colombia using sequence-based microsatellite genotyping (SSR-GBS). Sixty individuals (48 wild adults from three localities in the Department of Sucre and 12 hatchery-associated fingerlings from Cereté) were genotyped at seven polymorphic microsatellite loci. Wild populations retained high genetic diversity and exhibited weak but significant genetic differentiation (FST = 0.017, p = 0.003), with only 2% of the molecular variation distributed among populations and high estimated gene flow (Nm = 14.899). Hatchery-associated fingerlings consistently exhibited lower allelic richness while maintaining relatively high heterozygosity. Rarefied allelic richness did not differ significantly among populations (Kruskal–Wallis, p = 0.400); however, hatchery-associated fish consistently showed lower values, highlighting the value of allelic richness as a complementary indicator for evaluating hatchery-produced stocks. These findings provide a genetic baseline for the conservation of P. magdalenae and support incorporating routine genetic monitoring into supportive breeding and restocking programs. Full article

Background/Objectives: African swine fever (ASF) has caused substantial wild boar (Sus scrofa) mortality across Europe and prompted intensive density-reduction measures, yet its long-term effects on population genetics remain poorly understood. To our knowledge, this is the first study to compare genetic diversity, population structure, demographic signatures, and wildlife forensic identification parameters in the same wild boar population before ASF emergence and after several years of ASF-related management. Methods: Wild boar samples collected before ASF emergence in Hungary (n = 67) were compared with samples collected after several years of ASF-related management from the same geographic area (n = 65). All 132 individuals were genotyped at 13 tetrameric microsatellite loci. Diversity was assessed using allelic richness, allele number, and heterozygosity; differentiation using F-statistics, analysis of molecular variance, and discriminant analysis of principal components; demographic history using a two-phase mutation model; and forensic performance using probability of identity and probability of identity among siblings. Results: The post-ASF population showed lower genetic diversity and significant temporal differentiation. Paired Wilcoxon tests indicated a significant reduction in the number of alleles, whereas changes in heterozygosity were not significant. Bottleneck analyses provided no robust evidence of a recent genetic bottleneck. Forensic discrimination power declined modestly while remaining sufficient for individual identification. Conclusions: Because no contemporaneous unaffected reference population was available, these changes cannot be attributed specifically to ASF or management rather than to genetic drift or natural turnover, although they are consistent with sustained demographic disturbance. Nevertheless, this study provides the first temporal genetic comparison of a European wild boar population before ASF emergence and after several years of ASF-related management and demonstrates that a routinely used STR marker panel remains suitable for wildlife forensic individual identification despite these genetic changes. Full article

This study compared the genetic diversity and structure of Salvelinus fontinalis (SF), Salvelinus malma (SM), and their hybrids (♂ SM × ♀ SF, FM) using 10 microsatellite loci. Our results showed that the three groups of populations had moderate-to-high diversity, with an average polymorphism information content (PIC) ranging from 0.4534 to 0.5400, and the genetic diversity was the highest in FM. This indicates that FM is a suitable breeding material and has the potential to enhance germplasm resources. Based on STRUCTURE analysis (optimal K = 3), we observed that the hybrid population was between the two parental populations, and UPGMA clustering showed that the hybrid population had a closer relationship with the maternal parent. This study can provide a theoretical basis and strategic reference for the efficient development, conservation and utilization of new hybrid Salvelinus germplasm resources; the hybrid Salvelinus can serve as an excellent breeding material and has important application value in the germplasm genetic improvement and variety selection of S. fontinalis and S. malma. Full article

Reintroduction programmes are increasingly used to restore threatened freshwater fishes, yet evaluating their success remains challenging during the early stages of population establishment. Genetic monitoring is commonly used to assess diversity but rarely provides direct evidence of natural reproduction. Here, we investigated natural reproduction following reintroduction in the endangered Zingel asper, a benthic fish endemic to the Rhône River basin. Between 2006 and 2015, more than 25,000 captive-bred individuals from two source populations were released into the Drôme River (France). Using 54 microsatellite loci, we assessed genetic diversity, effective population size, relatedness and inbreeding, reconstructed parentage relationships, and evaluated admixture among source lineages through hybrid assignment analyses. Wild source populations differed markedly in genetic diversity and effective population size, whereas captive propagation reduced genetic diversity and increased relatedness and inbreeding. Despite these effects, the reintroduced population exhibited higher allelic richness than any captive cohort. Parentage analyses provided direct genetic evidence of natural reproduction by identifying individuals whose genetic origin could not be explained by the captive breeding pedigree. Hybrid assignment analyses independently confirmed admixture between source lineages. These results show how complementary genetic approaches can provide early evidence of reintroduction success and support adaptive management of threatened fish populations. Full article

To evaluate the effectiveness of microsatellite (SSR) markers for verifying the authenticity of walnut controlled-cross offspring, seven controlled-cross combinations were established using improved and widely cultivated walnut varieties from Guizhou Province, China, generating a total of 108 candidate offspring. Among 60 previously reported SSR primer pairs, 15 loci exhibiting stable amplification and clear genotyping profiles were selected for analysis. Parentage identification was conducted using the genotype exclusion and maximum likelihood methods, and the applicability of each method was assessed through genetic diversity and cluster analyses. The 15 SSR loci detected a total of 68 alleles, with an average of 4.53 alleles per locus. The polymorphism information content (PIC) ranged from 0.017 to 0.608, with a mean value of 0.396. The genotype exclusion method confirmed 76 offspring as genetically consistent with their recorded parental combination, corresponding to an overall identification rate of 70.37%. In the maximum likelihood analysis, 27 offspring were assigned to their most likely parent pairs when both parents were unknown, with an identification rate of 25.00%. When the maternal parent was known and only the paternal parent was unknown, 47 offspring were successfully assigned, increasing the identification rate to 43.52%. Cluster analysis showed that most offspring clustered near their corresponding parents, although some individuals deviated from their original cross combinations, suggesting allele sharing or complex genetic origins among the parental materials. The shared maternal parent structure, closely related paternal backgrounds, high-frequency alleles, and null alleles may jointly influence the efficiency of SSR-based parentage assignment. Compared with the maximum likelihood method, the genotype exclusion method showed greater practical stability for verifying recorded cross combinations in a structured walnut breeding population characterized by a shared maternal parent, multiple closely related paternal parents, and moderate SSR polymorphism. These findings indicate that likelihood-based parentage assignment should be interpreted cautiously when candidate parents are genetically similar and marker informativeness is limited. This study provides a technical reference for authenticity verification of walnut controlled-cross offspring, pedigree management, and marker-assisted breeding. Full article

Urban-driven landscape fragmentation is a major factor contributing to amphibian population decline yet its genetic consequences remain incompletely understood. We examined the genetic structure and variability of the common toad (Bufo bufo) in Warsaw, Poland, using seven nuclear microsatellite loci and mitochondrial cytochrome b sequences (800 bp). Samples (N = 97) were collected from six breeding sites representing contrasting urban habitats on both banks of the Vistula River. Genetic analyses revealed low but significant population differentiation, elevated inbreeding coefficients, and a heterozygosity deficit despite relatively high effective population sizes. This pattern is consistent with post-fragmentation genetic inertia, in which demographic buffering temporarily maintains genetic diversity despite reduced connectivity. Consequently, contemporary genetic patterns may underestimate the extent of ecological isolation imposed by urban infrastructure. Mitochondrial analyses identified seven haplotypes, including six previously unreported, forming a star-like network topology indicative of a single postglacial colonization event. The Vistula River did not constitute a significant barrier to gene flow, based on pairwise F_ST and hierarchical AMOVA. Supervised feature selection (MCFS-ID) identified specific alleles and body mass as key discriminants among sites, suggesting emerging responses to local urban conditions. Our results indicate that urban common toad populations can retain substantial genetic variation despite fragmentation, although continued isolation may ultimately increase inbreeding and genetic drift. Full article