Search Results (19)

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

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 adaptive capacity of tree species is crucial for their survival under environmental change. Liushan (Cryptomeria japonica var. sinensis), an allogamous conifer species, is widely distributed across southern China. However, despite its broad distribution, there have been few investigations on the geographical variation and environmental adaptability of this species. Here, we combined the phenotypic (eight needle traits) and genetic data (14 nSSR loci) to fill this gap by assessing the genetic variation of geographical populations and exploring environmental adaptations of this species. Both phenotypic and molecular genetic analyses indicated a strong genetic differentiation among geographic populations. All populations could be clustered into three groups that were consistent with their geography. Most of the needle traits showed significantly correlated with geography and environmental factors. Geographical isolation and environmental differences are the main factors that have shaped current morphological traits and patterns of genetic variation. We suggest conservation measures to be implemented on a population level with existing populations, especially those with rare phenotypes as the main goal. Our findings shed light on the geographic variation in Liushan and expanded the knowledge of its putative adaptive mechanisms, ultimately benefiting the conservation of this species. Full article

Scot pine (Pinus sylvestris L.) is one the main forest-forming tree species in Russia, and is of great ecological, economic and social value. In order to manage the genetic resources of this important forest tree species efficiently, knowledge of its genetic diversity and structure is needed. Here, we assessed the genetic variation of 17 populations representing different parts of Scots pine range in Russia by using nuclear microsatellite markers (nSSR). Specifically, 14 populations were chosen within the natural distribution range of the species in Middle Siberia and three distant populations were sampled from the European part of Russia, the West Siberia and the Russian Far East. All populations showed high values of genetic diversity (H_E = 0.514) and A_R = 4.150. However, the easternmost population has shown the lowest level of genetic diversity (H_E = 0.433) and allelic richness (A_R = 3.505). Five genetic groups could be detected that correspond to: the European part of Russia, the south of Middle Siberia, the northwest of Middle Siberia, West and Middle Siberia, and the Russian Far East. However, the European population was the most genetically distinct one. The variation among Scots pine populations accounted for only 5% of the total variance. The highest level of genetic differentiation was found only between westernmost and easternmost populations (F_ST = 0.097). Our genetic data may contribute to a better understanding of the pattern of genetic diversity of Scots pine populations in Middle Siberia and help the conservation efforts of these genetic resources. Full article

Ecuador is considered one of the most biodiverse countries in the world but currently has one of the highest deforestation rates in South America. However, genetic knowledge needed to sustain conservation actions is generally absent in most species. In this study, we developed eight nuclear microsatellites (nSSR) to study the patterns of genetic diversity, population structure, and level of inbreeding of Ocotea rotundata van der Werff (Lauraceae), an endemic tree from South Ecuador occurring in five populations, and with a very low number of mature individuals. This study focused on these five populations where 140 adult trees were collected (populations: LOJ n = 25; CER n = 30; YAN n = 30; CAT n = 25; ZAM n = 30). We also included 40 individuals from two populations described in the North of Ecuador as O. rotundata (populations: MAQ n = 20, PAC n = 20). Our results show high levels of genetic diversity across populations (Ho: LOJ = 0.72; CER = 0.73; YAN: 0.69; CAT = 0.67; ZAM = 0.43; MAQ: 0.72; PAC: 0.77) although much lower than the expected ones (He = LOJ = 0.86; CER = 0.81; YAN: 0.73; CAT = 0.80; ZAM = 0.72; MAQ: 0.85; PAC: 0.86) and overall higher levels in the North and South populations. The number of alleles was also high (LOJ = 11; CER = 9; YAN: 10; CAT = 12; ZAM = 6; MAQ: 12; PAC: 11). The Bayesian clustering program STRUCTURE found the highest LnP(D) and ΔK values for K = 2, dividing North and South populations. A similar pattern was found in the principal coordinate analysis. Allelic fixation was always significantly greater than zero (F = 0.17 ± 0.06) in all populations (p < 0.05) indicating a heterozygosity deficit across loci probably due to inbreeding. Conserving the genetic diversity of O. rotundata through future in and ex situ actions and the processes that determine it, would be crucial for increasing the resilience of Ecuador’s forests. Altogether, these results indicate a low frequency of gene flow and connectivity between the North and South regions, being enough to promote differentiation. In fact, samples collected in the North had, generally, smaller leaves than the ones from South Ecuador, and some branches had pubescent flowers. The morphological differences in the Ecuadorian populations together with the genomic results found here could imply the existence of different species, a hypothesis that needs future taxonomic studies. Full article

Sassafras tzumu (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of S. tzumu are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of S. tzumu via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of S. tzumu. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean PIC = 0.356), and the transferability of these markers in other Sassafras species was high (85.19%). A moderately low level of genetic diversity and a high variation (F_ST = 0.286) of six wild populations of S. tzumu were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (H_E) of 0.430 at the species level and H_E ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six S. tzumu populations into two clusters, and the further strong population subdivision appeared from K = 2 to K = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (r = 0.742, p = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (N_m = 0.625), a relatively high degree of inbreeding (F_IS = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of S. tzumu and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of S. tzumu and other Sassafras (Lauraceae) species. Full article

We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots pine individuals of mature age from 23 natural Scots pine stands in Lithuania and used the AMOVA and a set of genetic-clustering methods. The among-population differentiation was weak for nuclear microsatellite loci (nSSRs) (F_ST = 0.005) but much stronger for cpSSRs (PhiST = 0.240). The populations were structured into highland and lowland populations based on cpSSRs and eastern highland versus the rest for nSSRs. We detected two mtDNA mitotypes—the universal type A and northeastern type B, and the latter occurred at a markedly higher frequency in eastern Lithuania. Within-population genetic diversity was higher in large pine-dominated forest tracts in the eastern highlands than in fragmented forests in the western highlands. We concluded that phenology-based genetic networks following the temperature climate gradients have a strong effect on shaping the genetic structure of otherwise rather homogeneous gene pools of Scots pine populations in Lithuania. The possible effects of human interference with forests on genetic diversity of Scots pine populations in Lithuania are discussed. Full article

Background and objectives—Podocarpus latifolius (synonym of P. milanjianus) is a key tree representative of Afromontane forests where it is highly threatened by climate and land-use changes. While large populations occur in East Africa, only a few isolated and usually small populations remain in western Central Africa (Cameroon to Angola). Studying the evolutionary history of such relictual populations can thus be relevant to understand their resilience under changing environments. Materials and Methods—we developed nine polymorphic nuclear microsatellites (nSSRs) to estimate genetic variability, (historical) gene flow, and demographic changes among natural populations from Central to East Africa. Results—despite the extended distribution range of P. latifolius, a strong isolation-by-distance pattern emerges at the intra-population scale, indicating low seed and pollen dispersal capacities. Central African populations display a lower genetic diversity (He = 0.34 to 0.61) and are more differentiated from each other (F_ST = 0.28) than are East African populations (He = 0.65 to 0.71; F_ST = 0.10), suggesting high genetic drift in the Central African populations. Spatial genetic structure reveals past connections between East and West Africa but also a gene flow barrier across the equator in western Central Africa. Demographic modelling anchors the history of current lineages in the Pleistocene and supports a strong demographic decline in most western populations during the last glacial period. By contrast, no signature of demographic change was detected in East African populations. Conclusions—in Cameroon, our results exclude a recent (re)colonization from one source population of all mountain ranges, but rather indicate long-term persistence of populations in each mountain with fluctuating sizes. A higher impact of genetic drift and further loss of diversity can be expected by survival through climatically unfavorable periods in such small refugial populations. Tracking the Quaternary legacy of podocarp populations is thus essential for their conservation since there is a temporal gap between environment crises and an ecological/genetic answer at the population level. Full article

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima. Full article

Two alder species (Alnus glutinosa and A. incana) have overlapping distribution, naturally occur in Lithuania, and are considered ecologically and economically important forest tree species. The objective of our study was to estimate the likelihood of spontaneous hybridizations between native alders in natural stands of Lithuania based on leaf morphology and nuclear microsatellite markers. The sampled trees were assigned to the three taxonomic groups of A. glutinosa, A. incana, and potential hybrids based on the leaf and bark morphological traits. The genetic differentiation and potential hybridization between these three groups was tested based on 15 nSSR markers. We identified studied Alnus spp. individuals as pure species and hybrids. Two microsatellite loci were reported as discriminating well between these species. We concluded that our results showed the highest likelihood of two genetic group structures, a clear genetic differentiation between the morphology-based groups of A. glutinosa and A. incana, and rather variable likelihood values in the putative hybrid group. The results provide important implications for genetic conservation and management of Alnus spp. Full article

The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, N. pectoralis is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in N. pectoralis. The haploid genome size estimated using a k-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in N. pectoralis consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic N. pectoralis. Full article

Beech (Fagus sylvatica L.) is one of the most important forest trees in Europe and its current broad expanse over the continent is believed to be the outcome of the Holocene postglacial expansion of lineages originating from different glacial refugia. Studies using gene markers, pollen profiles and fossils suggest the main locations of glacial refugia in Southern Europe. In this study, we conduct a fine-scale genetic study on the beech populations surrounding the Almopia basin, an area that is said to have hosted one of the main European glacial refugia for several plant and animal species during the Pleistocene Epoch. We test the hypothesis of the existence of a local refugium in the study area for beech to understand the spatial genetic pattern of the putative refugial beech populations in the area and to investigate possible genetic connections between the local beech populations and the European expansion of the species. The genetic diversity of 100 sampled trees in 20 plots representing the expansion of beech in the area was studied using chloroplast and nuclear DNA microsatellites (cpSSR and nSSR, respectively). All three cpSSR regions were polymorphic, resulting in eight haplotypes, separated spatially in two distinct groups (one on the western and the other on the eastern part of the Almopia basin) that correspond to two different postglacial beech lineages. Furthermore, the cpSSR sequences of the eastern lineage are genetically identical to those of beech populations extending over central and northern Europe. The nSSR markers were highly polymorphic, and the trees studied were separated into two genetic groups that coincided with the cpSSR ones in locations where the topography is more pronounced. These results indicated that the Almopia region was indeed a major refugium for beech that possibly produced two main postglacial lineages for Europe, one of which is connected with the majority of beech populations growing on the continent. These southern refugial populations are important diversity centers that need to be the subject of special management and conservation. Full article

Large old trees are extraordinary organisms. They not only represent a historical, landscape and environmental heritage of inestimable value, but they also witness a long history of environmental changes and human interventions, and constitute an as yet poorly known reserve of genetic variability which can be considered a great resource for management programs of forest species. This is the first genetic study on Italian, large, old chestnut trees (Castanea sativa Mill.). Ninety-nine trees were surveyed and analysed. For each tree, more than one sample from canopy and root suckers was collected to test for the genetic integrity of the individuals. All samples were genotyped using nine nuclear microsatellite markers (nSSRs) and 106 unique genetic profiles were identified. A Bayesian analysis performed with the software STRUCTURE revealed the occurrence of two main gene pools and unveiled the genetic relationships existing among the genotyped individuals, and with the natural chestnut populations living in proximity. A phylogeographic structure of the plastid diversity was also obtained by the use of DNA sequence variation at two marker regions, revealing different origins and probable connections of the old trees with different glacial refugia. Our results contribute to an improved evaluation of the European chestnut genetic resources and provide useful insights into the species’ history and domestication in Italy. The importance of carefully targeted conservation strategies for these invaluable organisms is reaffirmed. Full article

Small, isolated populations are more vulnerable to natural disturbances and loss of genetic diversity. Scots pine, an abundant tree species in the boreal forest of Eurasia, has a scattered natural distribution across Eastern and Southern Carpathian Mountains, where only a few relict populations still exist. We estimated genetic diversity and spatial genetic structure in Scots pine on the basis of microsatellite nuclear markers (nSSR) data. We found a relatively high level of genetic diversity (He = 0.697) within populations and no evidence of recent bottlenecks. Genetic diversity was lower in peat bog populations, as compared to populations that grow on rocky slopes or acidic soils and nutrient-poor sites. Population genetic structure was weak, and genetic discontinuities among populations were detected. Spatial genetic structure (SGS) was observed in nearly all Scots pine populations. The strength of SGS, quantified by Sp statistics, varied greatly among populations, ranging from 0.0011 to 0.0207, with an average of 0.01. Our study highlights that Eastern and Southern Carpathian populations still possess high within-population diversity in spite of the recent fragmentation and reduction of the Scots pine natural distribution range. We discuss the importance of spatial patterns of genetic diversity for developing strategies of conservation and sustainable use of Scots pine genetic resources in the Carpathian region. Full article

The cosmopolitan genus Fraxinus comprises about 40 species occupying several habitats in the Northern Hemisphere. With some species hybridizing and sharing genetic variants, questions remain on the species assignment of germplasm within the genus Fraxinus despite numerous species-specific assessments. A multidisciplinary approach was employed to provide a definitive insight into the genetics of an endangered Fraxinus “manna ash” collection, located in a rich plant biodiversity hotspot of the Madonie Mountains (Sicily). Although the collection size was small, genetic diversity, assessed by chloroplast (cpSSR) and nuclear (nSSR) microsatellites (SSR—Simple Sequence Repeats), allowed identifying three different chloroplast haplotypes, with one (H5) dominant, and several polymorphic loci, able to discriminate most of the local accessions studied. Molecular data were linked to cytofluorimetric and phenotypic evaluations and, contrary to popular belief that manna ash is Fraxinus ornus L., the germplasm currently used for manna production belongs to Fraxinus angustifolia Vahl. Interestingly, joint analysis of our genetic panel with a large European dataset of Fraxinus spp. suggested the presence of a possible glacial refuge in Sicily, confirming its importance as biodiversity source. Our results will be helpful for the design of long-term conservation programs for genetic resources, such as in situ and ex situ conservation, seed collection and tree reintroduction. Full article