Search Results (459)

European black pine (Pinus nigra Arn. subsp. nigra) persists in scattered montane stands across Greece, where isolated populations harbour genetic variation shaped by local environments and demographic history. In this study, we assessed the genetic diversity and population structure of P. nigra using nuclear microsatellite markers (nSSRs) across four populations: Mt. Athos, Sithonia, Thassos, and Perama. A total of 67 individuals were genotyped, and seven high-quality polymorphic loci were retained after rigorous filtering. The Mt. Athos population exhibited the highest allelic richness and heterozygosity, with all loci being polymorphic and a low inbreeding coefficient after null allele correction. In contrast, the Perama population displayed reduced diversity, fewer polymorphic loci, and persistent heterozygote deficits. Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) revealed weak overall population structure, with Perama genetically distinct from the other sites. Spatial Principal Component Analysis (sPCA) further uncovered an east–west cline within Athos and localized structure potentially shaped by both natural isolation and human influence. These findings highlight regional variation in genetic diversity within P. nigra and identify Athos as a genetically rich population of particular interest. The results provide a foundation for long-term monitoring and support informed strategies for the management and conservation of P. nigra in Greece. 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

Myriophyllum heterophyllum is an aquatic macrophyte that is invasive to the northeastern United States and several western European countries. Spreading by vegetative clonal propagation, especially fragmentation, extensive resources are devoted to limiting its growth and spread; however, genetic assessments are not typically included in management strategies. Reduction in genetic (clonal) diversity should accompany biomass reduction, yet without genetic assessment, the efficacy of plant removal remains unclear. This paper is the first to describe a microsatellite marker library and its use in the characterization of Myriophyllum heterophyllum. Eighty-seven tissue samples were collected across the invasive distribution of Myriophyllum heterophyllum in Maine, USA. DNA was extracted, and PCR amplification was employed to screen 13 published microsatellites. Sequencing of the amplified loci was performed to characterize repeat motifs and confirm primer binding sites. Fragment sizing of PCR amplicons was employed to determine microsatellite lengths across the 87 samples. A total of 7 of the 13 tested markers were amplified, with six of those seven found to be variable. Polyploidy was evident from allelic diversity within individuals, although precise ploidy could not be determined. Observed heterozygosity ranged from 0.16 to 1.00 across variable markers. This seven-marker library was effective in characterizing the genetic diversity of both newly discovered (<5 years) and older (>50 years) infestations and is expected to be suitable for assessment of genetic diversity in populations within the native range of M. heterophyllum. The marker library also shows potential for use in several other Myriophyllum species. Full article

Background/Objectives: Loss and fragmentation of habitat from agricultural conversion led to the near extirpation of the pygmy rabbit (Brachylagus idahoensis Merriam, 1891) population in the Columbia Basin (CB) of Washington, USA. Recovery efforts began in 2002 and included captive breeding, translocations from other regions for genetic rescue, and reintroduction into native habitat in three sites: Sagebrush Flat (SBF), Beezley Hills (BH), and Chester Butte (CHB). Methods: We used noninvasive and invasive genetic sampling to evaluate demographic and population genetic parameters on three translocated populations of pygmy rabbits over eight years (2011–2020). For each population, our goal was to use fecal DNA sampling and 19 microsatellite loci to monitor spatial distribution, apparent survival rates, genetic diversity, reproduction, effective population size, and the persistence of CB ancestry. Over the course of this study, 1978 rabbits were reintroduced as part of a cooperative conservation effort between state and federal agencies. Results: Through winter and summer monitoring surveys, we detected 168 released rabbits and 420 wild-born rabbits in SBF, 13 released rabbits and 2 wild-born in BH, and 16 released rabbits in CHB. Observed heterozygosity (H_o) values ranged from 0.62–0.84 (SBF), 0.59–0.80 (BH), and 0.73–0.77 (CHB). Allelic richness (AR) ranged from 4.67–5.35 (SBF), 3.71–5.41 (BH), and 3.69–4.65 (CHB). Effective population (N_e) within SBF varied from 12.3 (2012) to 44.3 (2017). CB ancestry persisted in all three wild populations, ranging from 15 to 27%. CB ancestry persisted in 99% of wild-born juveniles identified in SBF. Apparent survival of juvenile rabbits differed across years (1–39%) and was positively associated with release date, release weight, and genetic diversity. Survival of adults (0–43%) was positively influenced by release day, with some evidence that genetic diversity also positively influenced adult apparent survival. Conclusions: Noninvasive genetic sampling has proven to be an effective and efficient tool in monitoring this reintroduced population, assessing both demographic and genetic factors. This data has helped managers address the goals of the Columbia Basin recovery program of establishing multiple sustainable wild populations within the sagebrush steppe habitat of Washington. 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

In recent decades, fishery stock enhancement has been increasingly utilized as a restoration tool to mitigate population declines and enhance the resilience of marine fisheries. Nevertheless, persistent enhancement efforts risk eroding the evolutionary potential of wild populations via genetic homogenization and maladaptive gene flow. Using long-term monitoring data (2017–2023), we quantified the effects of large-scale Penaeus penicillatus stock enhancement (~10⁸ juveniles/yr) on wild population dynamics and genetic integrity in the Beibu Gulf ecosystem. Temporal genetic changes were assessed using eight highly polymorphic microsatellite loci, comparing founder (2017) and enhanced (2024) populations to quantify stocking impacts. Insignificantly lower expected heterozygosity was observed in the stocked population (He = 0.60, 2024) relative to natural populations (He = 0.62–0.66; p > 0.1), indicating genetic dilution effects from enhancement activities. No significant erosion of genetic diversity was detected post-enhancement, suggesting current stocking practices maintain short-term population genetic integrity. Despite conserved heterozygosity, pairwise Fst analysis detected significant genetic shifts between temporal cohorts (pre-enhancement—2017 vs. post-enhancement—2024; Fst = 0.25, p < 0.05), demonstrating stocking-induced population restructuring. Genetic connectivity analysis revealed that while the enhanced Beihai population (A-BH) maintained predominant self-recruitment (>90%), it experienced substantial stocking-derived gene flow (17% SW → A-BH). The post-stocking period showed both reduced genetic exchange with adjacent populations and increased asymmetric dispersal from A-BH (e.g., 5% to YJ), indicating that hatchery releases simultaneously enhanced population isolation while altering regional genetic structure. Our findings revealed the paradoxical dual effects of stock enhancement and allelic diversity while disrupting natural genetic architecture. This underscores the need for evolutionary-impact assessments in marine resource management. 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

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

Macrobrachium rosenbergii, commonly known as giant freshwater prawns (GFPs), is an economically and nutritionally important decapod crustacean species in China. Understanding the genetic diversity of selective breeding populations is crucial in breeding plans for selecting genetically diverse broodstocks and maintaining genetic diversity. The genetic structure of six breeding populations (Hefu (HF), Nantaihu No.2 (NTH), Jiaxin (JX), Shufeng (SF), Taiwan (TW), and Guangxi (GX)) of GFP in China was examined using 16 newly developed microsatellite loci and the mitochondrial control region (D-loop). The microsatellite data revealed that all 16 loci have high diversity, with all values of polymorphism information content (PIC) more than 0.5. The average expected heterozygosity (He, 0.89) and the number of alleles (Na, 18.25) of SF were the highest, followed by He (0.89) and Na (14.75) of the JX, and GX has the lowest He (0.83) and Na (11.31). The average PIC value for the six stocks ranged from 0.80 to 0.87. Pairwise comparisons revealed that Fst ranged from 0.03541 to 0.09637 and was significant (p < 0.05) between most populations, indicating from low to moderate genetic differentiation among the six populations. The D-loop analysis identified 114 variable sites and 29 haplotypes, with an average haplotype diversity (Hd) and nucleotide diversity (π) of 0.640 and 0.01247, respectively. Genetic differentiation among the six populations based on the D-loop was from moderate to high, with Fst values of 0.05603–0.80788, and all p < 0.05. This study demonstrates that selective breeding stocks of M. rosenbergii in China show moderate to high genetic diversity and have the potential for further selective breeding, providing a theoretical basis for conserving and utilizing M. rosenbergii genetic resources. Full article

Anopheles darlingi is a major malaria vector in South America. Understanding its population dynamics is critical for designing effective vector control strategies. While various Anopheles collection methods exist, they may sample distinct populations. Microsatellite genotyping across nine loci was performed to characterize An. darlingi populations, which were collected in French Guiana between 6:30 p.m. and 7:00 a.m. using human landing catch (HLC) or Mosquito Magnet^® (MM) traps. Traps were arranged in a 3 × 3 Latin square design to minimize possible effects of geographical position. Pairwise F_ST index and discriminant analyses of principal components (DAPC) were used to make comparisons. A total of 431 An. darlingi were analyzed. No significant genetic differentiation was observed between collection methods or time slots (F_ST values non-significant, p > 0.25), with DAPC revealing a single genetic cluster. Despite documented phenotypic variations, no significant population structure was detected among An. darlingi sampled in a rural village in French Guiana via collection methods or time slots. These findings confirm that mosquitoes collected with these various methods or time slots are suitable for the molecular studies of An. darlingi in French Guiana. In this context, Mosquito Magnet^® traps could also represent an alternative to the now controversial human landing catch. Full article

Dikili Tash is a Neolithic settlement that lies next to the ruins of the ancient city of Philippi on the north-eastern part of Greece. A recent archaeological excavation has unearthed charred grapevine pips and pressings together with two-handed clay cups, jugs, and jars that date to 4300 BC. The majority of the pips were found to be Vitis vinifera ssp. sylvestris. Natural populations of this species have been localized in the valley surrounding Dikili Tash and also on Mt Pangaion and Mt Lekani, which flank the valley. Fifty-one samples from these modern populations have been analyzed using microsatellites on twenty microsatellite loci, and a dendrogram has been constructed showing the genetic closeness of the samples analyzed. Cuttings from all the vines analyzed are currently rooted and grown in the Hellenic Agricultural Organization—DIMITRA (ELGO-DIMITRA) greenhouse facilities in Lykovryssi (Athens) with the aim to, eventually, be transplanted in the grapevine, thus establishing the first V. sylvestris ex situ conservation site in Greece. Full article

Vertebrate molecular genetic research methods typically employ single genetic loci (monolocus markers) and those involving a variable number of loci (multilocus markers). The former often employ microsatellites that ensure accuracy in establishing inbreeding, tracking pan-generational dynamics of genetic parameters, assessing genetic purity, and facilitating genotype/phenotype correlations. They also enable the determination and identification of unique alleles by studying and managing marker-assisted breeding regimes to control the artificial selection of agriculturally important traits. Microsatellites consist of 2–6 nucleotides that repeat numerous times and are widely distributed throughout genomes. Their main advantages lie in their ease of use for PCR amplification, their known genome localization, and their incredible polymorphism (variability) levels. Robust lab-based molecular technologies are supplemented by high-quality statistics and bioinformatics and have been widely employed, especially in those instances when more costly, high throughput techniques are not available. Here, we consider that human and livestock microsatellite studies have been a “roadmap” for the genetics, breeding, and conservation of wildlife and rare animal breeds. In this context, we examine humans and other primates, cattle and other artiodactyls, chickens and other birds, carnivores (cats and dogs), elephants, reptiles, amphibians, and fish. Studies originally designed for mass animal production have thus been adapted to save less abundant species, highlighting the need for molecular scientists to consider where research may be applied in different disciplines. Full article

Background/Objectives: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding. Methods: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties. Results: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine–cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers. Conclusions: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera. Full article

The Himalayan griffon (Gyps himalayensis), an obligate scavenging bird in the Qinghai–Tibet Plateau, provides significant ecological services but is currently listed as near threatened. Despite their importance for conservation, genome-wide screening for microsatellites (or SSRs) in G. himalayensis and the development of corresponding molecular markers have been lacking. This study presents the first in-depth characterization of genome-wide microsatellites in G. himalayensis and the successful development of polymorphic SSR markers. A total of 240,741 microsatellite loci were detected in the G. himalayensis genome, with an average density of 202.2 SSRs per Mb, accounting for 0.44% of the genome. Mononucleotide repeats (53.2%) were the most prevalent among the different microsatellite motif types. Additionally, 100 primer pairs were initially identified, with 17 found to be polymorphic markers. These loci hold significant potential for revealing genotypic diversity in G. himalayensis, thereby laying a foundation for the conservation of this species. Full article

The Atacama Desert, the driest and oldest desert on Earth, hosts a unique floral phenomenon known as the Desierto Florido (Flowering Desert), which occurs sporadically in response to rare rainfall events. Bomarea ovallei (Phil.) Ravenna is an endemic and endangered species of the Atacama Desert. However, its populations are geographically restricted and potentially vulnerable to genetic erosion due to isolation and extreme environmental conditions. This study aims to assess the genetic diversity of B. ovallei populations and develop microsatellite markers using next-generation sequencing (NGS) technology. A total of 268 microsatellite loci were identified, and 34 co-dominant markers were successfully developed for the first time in B. ovallei. Genetic diversity analysis using eight fluorescently labeled SSR markers revealed low genetic diversity across four populations, with the highest diversity observed in the QCA population, located within Llanos de Challe National Park, and the lowest in the TOTO population, which is highly exposed to anthropogenic activities. UPGMA and STRUCTURE analyses revealed three genetic clusters and high admixture among populations, suggesting historical or ongoing gene flow despite geographical separation. The presence of non-polymorphic loci and low PIC values in some markers further supports limited genetic variation. The newly developed microsatellite markers offer a valuable tool for future genetic studies, enabling the monitoring of genetic diversity and informing strategies for the preservation of this rare and ecologically significant species. Full article