Characterization of genetic variance within and among five populations of Sperata seenghala (Skyes, 1839) revealed by random amplified polymorphic DNA markers

This study reports on 156 specimens of the amphibian Eupemphix nattereri, a widely distributed leiuperid, obtained from 11 municipalities of central Brazil. The extent of genetic variation was quantified by determining the mean number of alleles per locus and the proportion of polymorphic loci. An analysis of molecular variance (AMOVA) was performed on the random amplified polymorphic DNA (RAPD) haplotypes. The genetic distances obtained by calculating pairwise phist among local samples were used to determine population relationships using the unweighted pair-group method (UPGMA) and non-metric multidimensional scaling (NMDS). The cophenetic correlation was calculated to confirm agreement between the genetic matrix and the unweighted pair group method with averages (UPGMA) dendrogram. To determine if genetic distances were correlated to geographical distances we constructed pairwise genetic distance and geographical distance matrices and compared them using the Mantel test. The AMOVA results indicated significant genetic differences (p < 0.001) between E. nattereri populations, representing 69.5% of the within population genetic diversity. The Mantel test showed no significant correlation (r = 0.03; p = 0.45) between the genetic and geographical distance matrices. Our findings indicate that the genetic variation of E. nattereri populations was randomly distributed in geographic space and that gene flow for this species is probably structured at spatial scales smaller than those between our samples

According to the distribution of Phrynocephalus vlangalii hongyuanensis in Zoige Wetland，three geographic units: Zoige Xiaman (XM)，Hongyuan (HY)，both in Sichuan Province and Maqu (MQ) in Gansu Province were defined. We used molecular methods to reveal these unit’s genetic variation and diversity. A 785bp fragment of the mtDNA ND4-tRNAleu was determined from 72 samp1es in seven populations of P. vlangalii hongyuanensis. Seven variable nucleotide sites and nine haplotypes were identified in the 785bp fragments. As a whole，the haplotype diversity was high (0.806±0.024)，but the nucleotide diversity was low (0.00231±0.00016). In a single population，MQa，MQb and XMb had very low genetic diversities，and XMc had a much higher one. The Kimura 2-parameter distances among all the populations were small (0.001-0.005)，and the distance between MQa and XMa was the greatest. Analysis of molecular variance (AMOVA) showed that the three units were distinctly different (P<0.01)，and 62.61% of the total genetic diversity was attributable to variation among units. There were 3 haplotypes shared among XM and HY，and no geographic clustering was observed except MQ from the TCS network. The results from the mismatch distribution analysis and Fu’s Fs test (Fs=－2.21937) implied that there might be a recent population expansion in the XM unit，and this may be the reason why XM had a high haplotype diversity but a low nucleotide diversity. We estimate that the MQ and XMb have lower diversities because of some very recent geographic events，such as the formation of the Yellow river’s upriver and the Zoige Wetland. Although they are distinctly different，not enough time has passed for them to have diverged a great genetic distance.

We examined the genetic diversity, population structure and gene flow in a dominant mangrove tree (Rhizophora stylosa) at its northern biogeographical limit in Sakishima islands of the Japanese archipelago. Simple sequence repeat (SSR) markers from chloroplast (cpSSR) and nuclear DNA were used to analyze 16 populations recovered from various river basins across the chain of three Sakishima islands—Iriomote, Ishigaki and Miyako. The average number of alleles (1.7–2.7) and observed heterozygosities (0.031–0.216) at nuclear SSR and haploid diversity (0.000–0.489) at cpSSR across the populations suggested low genetic diversity in R. stylosa in Sakishima islands. cpSSR analysis identified two haplotypes, and Bayesian clustering analysis (nuclear SSR) revealed two genetic clusters. Analysis of molecular variance (nuclear SSR) showed significant population differentiations. Pairwise tests consistently revealed significant differentiation between most of the population pairs; however, the degrees of differentiations are generally correspondent to the relative geographical distances as suggested from pairwise FST and cpSSR genetic distances. Moreover, Mantel tests showed some signals of correlations between genetic distances (nuclear and chloroplast) and geographical distances. These results suggest that combined contribution of gene flow via pollen and propagule dispersal in R. stylosa mostly occurred between neighboring river basins. The appearances of two cpSSR haplotypes (maternal lineages) as well as two nuclear genetic clusters (putative ancestral lineages) at various river basins support the hypothesis that present-day R. stylosa populations across the Sakishima islands were established from few identical founders; however, significant differentiations among various river basins most likely resulted from the limited gene flow and high inbreeding.

Withania coagulans is an under-utilized, endangered medicinal plant that can be found scarcely as fragmented populations in South Asia. Theoretically, the fragmented population should show low diversity within population and higher diversity among population with low rate of gene flow. To test this hypothesis, we conducted diversity analysis of 7 populations of W. coagulans from the districts of Kohat and Karak in NWFP (North West Frontier Province), Pakistan using PBA (P450 based analogue) markers. Our results showed contrary findings from the hypothesis for fragmented population. The findings showed higher diversity within population and lower diversity among population like larger unfragmented populations even though the population size was less than 100 in all populations. Percentage of polymorphic bands (PPB) in these populations was 50 to 71.95% with gene diversity (H) of 0.192 to 0.298. AMOVA (Analysis of molecular variance) test showed that there was low genetic diversity among populations (17%) and high genetic diversity within population (83%). FST value showed low genetic differentiation (0.0911) and high gene flow (Nm 2.494) among populations. Isolation by Distance Model revealed no correlation between genetic and geographic distances as well as ecotypes (soil variation) vs genetic distances. Presumably, the larger fragments, formed long time ago due to geological changes, were reduced into smaller fragments recently due to the human pressure. the fruits of the plant are exploited for commercial purposes and the whole plant is used as fodder and fuelwood thus threatening the current survival of the limited fragmented populations. Conservation measures for the species existence are also discussed and recommended.

Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper. A low genetic diversity at the population level (PPB=36.99%) and a high genetic diversity at the species level (PPB=85.54%) were revealed. Analysis of molecular variance (AMOVA) also detected a significant differentiation among the populations. Unweighted pair-group method with arithmetic averaging (UPGMA) clustered the 10 population into 3 groups, and no significant correlation was found between the genetic distance and the corresponding geographic distance among the populations, which is consistent with the results of principal coordinate analysis (PCoA). The genetic variation between the artificial and wild populations revealed a decreased genetic diversity and aggravated genetic differentiation in the artificial populations. A conservation strategy of Eucommia ulmoides is discussed based on the information of the population genetic structure and variation. Key words : Eucommia ulmoides , inter-simple sequence repeat (ISSR), genetic diversity, genetic structure, conservation.

While many introduced invasive species can increase genetic diversity through multiple introductions and/or hybridization to colonize successfully in new environments, others with low genetic diversity have to persist by alternative mechanisms such as epigenetic variation. Given that Phragmites australis is a cosmopolitan reed growing in a wide range of habitats and its invasion history, especially in North America, has been relatively well studied, it provides an ideal system for studying the role and relationship of genetic and epigenetic variation in biological invasions. We used amplified fragment length polymorphism (AFLP) and methylation‐sensitive (MS) AFLP methods to evaluate genetic and epigenetic diversity and structure in groups of the common reed across its range in the world. Evidence from analysis of molecular variance (AMOVA) based on AFLP and MS‐AFLP data supported the previous conclusion that the invasive introduced populations of P. australis in North America were from European and Mediterranean regions. In the Gulf Coast region, the introduced group harbored a high level of genetic variation relative to originating group from its native location, and it showed epigenetic diversity equal to that of the native group, if not higher, while the introduced group held lower genetic diversity than the native. In the Great Lakes region, the native group displayed very low genetic and epigenetic variation, and the introduced one showed slightly lower genetic and epigenetic diversity than the original one. Unexpectedly, AMOVA and principal component analysis did not demonstrate any epigenetic convergence between native and introduced groups before genetic convergence. Our results suggested that intertwined changes in genetic and epigenetic variation were involved in the invasion success in North America. Although our study did not provide strong evidence proving the importance of epigenetic variation prior to genetic, it implied the similar role of stable epigenetic diversity to genetic diversity in the adaptation of P. australis to local environment.

BackgroundNelumbo nucifera Gaertn., a perennial aquatic macrophyte species, has been cultivated in several Asian countries for its economic importance, and medicinal uses. Two distinct ecotypes of the species are recognized based on the geographical location where the genotypes are adapted, i.e., tropical lotus and temperate lotus. The genetic diversity levels and differentiation of the tropical lotus from poorly studied geographic regions still remain unclear. Here, the population genetic diversity and structure of 15 tropical lotus populations sampled from the previous understudied natural distribution ranges, including India, Thailand, and Australia, were assessed using nine polymorphic SSR markers.ResultsThe SSR markers used to genotype the 216 individuals yielded 65 alleles. The highest and lowest genetic diversity estimates were found in Thailand and Indian populations, respectively. STRUCTURE analysis revealed three distinct genetic clusters, with relatively low admixtures, supported by PCoA cluster analysis. Low levels of gene flow (mean N⁠m = 0.346) among the three genetic clusters signified the Mantel test for isolation by distance, revealing the existence of a positive correlation between the genetic and geographic distances (r = 0.448, P = 0.004). Besides, AMOVA analysis revealed a higher variation among populations (59.98%) of the three groups. Overall, the populations used in this study exposed a high level of genetic differentiation (FST = 0.596).ConclusionsThe nine polymorphic microsatellite markers used in our study sufficiently differentiated the fifteen tropical N. nucifera populations based on geography. These populations presented different genetic variability, thereby confirming that populations found in each country are unique. The low genetic diversity (HE = 0.245) could be explained by limited gene flow and clonal propagation. Conserving the available diversity using various conservation approaches is essential to enable the continued utilization of this economically important crop species. We, therefore, propose that complementary conservation approaches ought to be introduced to conserve tropical lotus, depending on the genetic variations and threat levels in populations.

Psammochloavillosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well‐defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei's standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (GST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.

Microsatellite Libraries Enriched for Several Microsatellite Sequences in Plants

Genetic variation provides the raw material for natural selection, enabling species to maintain adaptive potential, respond to environmental changes, and resist pathogens. Reduced genetic diversity can severely compromise long‐term viability, particularly in small, isolated populations prone to inbreeding, genetic drift, and restricted gene flow—a vicious cycle known as the “extinction vortex”. Assessing genetic diversity in threatened species is therefore critical for effective conservation strategies. The black‐and‐white snub‐nosed monkey ( Rhinopithecus bieti ) is an Endangered primate that has experienced significant population decline and habitat fragmentation, raising concerns about its genetic diversity. We utilized major histocompatibility complex (MHC) class I genes, whose encoded proteins recognize antigens central to immune responses, to assess the adaptive genetic diversity of a semi‐provisioned subpopulation of this species. Species‐specific multi‐locus primers targeting exons 2 and 3 of MHC class I genes were designed using published R. bieti whole‐genome sequences. Amplicon‐based next‐generation sequencing was employed to genotype these exons in the studied subpopulation inhabiting Baima Snow Mountain National Nature Reserve, Yunnan, China. A total of 16 MHC class I sequences (7 exon 2 sequences and 9 exon 3 sequences) were identified from 47 individuals and assigned to 5 loci. Exon 2 exhibited low heterozygosity ( H e = 0.349) and moderate polymorphism (PIC = 0.281), whereas exon 3 showed extremely low heterozygosity ( H e = 0.147) and low polymorphism (PIC = 0.131). In addition, positive selection signatures were detected in both exons, and phylogenetic analyses indicated trans‐species evolutionary patterns in class I loci. These results underscore the role of balancing selection in maintaining adaptive genetic variation. However, low genetic diversity is likely to have diminished the studied subpopulation's capacity to adapt to environmental change, thereby undermining its long‐term viability. This study emphasizes the urgent need to assess adaptive genetic diversity across all R. bieti populations in order to develop targeted management strategies. The data generated in this studied subpopulation provide the baseline for comparison.

Tetracentron sinense Oliv. (T. sinense), as a tertiary living fossil, has experienced a significant decline in population numbers. Currently, genetic resources depletion and human activities have led to habitat fragmentation of relict and endangered plants, despite the abundant evidence of its medicinal, economic, and ecological value. Conservation strategies were clarified and evaluated based on the genetic structure characteristics and diversity patterns among 25 wild populations using Restriction site-associated DNA sequencing (RAD-seq) technology. Through SNP calling, filtering, genetic diversity analysis, discriminant analysis of principal components (DAPC), maximum-likelihood phylogenetic tree, and ADMIXTURE clustering, significant population structure and differentiation were identified. The results revealed a total of 2,169 single nucleotide polymorphisms (SNPs), indicating lower genetic variation but higher genetic differentiation (He: 0.10, I: 0.16, Fst: 0.33). Analysis of molecular variance (AMOVA) showed that genetic variation within populations accounted for 77% of the total variance. DAPC, maximum-likelihood phylogenetic tree, and ADMIXTURE clustering analysis grouped the 25 populations into five distinct clades influenced by isolation, restricted gene flow, and complex topography. To preserve the genetic integrity of T. sinense, it is recommended to establish conservation units corresponding to different geographic clades, with a focus on populations with low/high genetic diversity by implementing artificial reproduction and germplasm resource nurseries. Given the species' vulnerable conservation status, urgent implementation of the aforementioned conservation strategies is necessary to safeguard the remaining genetic resources.

Tetracentron sinense Oliv. (T. sinense), as a tertiary living fossil, has experienced a significant decline in population numbers. Currently, genetic resources depletion and human activities have led to habitat fragmentation of relict and endangered plants, despite the abundant evidence of its medicinal, economic, and ecological value. Conservation strategies were clarified and evaluated based on the genetic structure characteristics and diversity patterns among 25 wild populations using Restriction site-associated DNA sequencing (RAD-seq) technology. Through SNP calling, filtering, genetic diversity analysis, discriminant analysis of principal components (DAPC), maximum-likelihood phylogenetic tree, and ADMIXTURE clustering, significant population structure and differentiation were identified. The results revealed a total of 2,169 single nucleotide polymorphisms (SNPs), indicating lower genetic variation but higher genetic differentiation (He: 0.10, I: 0.16, Fst: 0.33). Analysis of molecular variance (AMOVA) showed that genetic variation within populations accounted for 77% of the total variance. DAPC, maximum-likelihood phylogenetic tree, and ADMIXTURE clustering analysis grouped the 25 populations into five distinct clades influenced by isolation, restricted gene flow, and complex topography. To preserve the genetic integrity of T. sinense, it is recommended to establish conservation units corresponding to different geographic clades, with a focus on populations with low/high genetic diversity by implementing artificial reproduction and germplasm resource nurseries. Given the species' vulnerable conservation status, urgent implementation of the aforementioned conservation strategies is necessary to safeguard the remaining genetic resources.

Influence of Host Shift on Genetic Differentiation of the Oriental Fruit Fly, Bactrocera dorsalis

Simple SummaryAn endangered giant water bug species, Diplonychus esakii, is one of the top predators in Korean freshwater ecosystems. This study investigates D. esakii populations in South Korea, a species potentially endemic to this region, and identifies 11 haplotypes with a haplotype diversity value of 0.623 out of 318 individuals across 27 sites. Through AMOVA (analysis of molecular variance) and FST analyses, we discovered significant genetic differentiation among populations and limited gene flow, indicating potential vulnerability to environmental changes. Consequently, we emphasize the need for conservation efforts to protect D. esakii. We also highlight the value of the Upo Wetland and Jeju Island populations as important conservation units to conserve the genetic diversity of Korean D. esakii. We also suggest an evaluation of the conservation status of D. esakii compared to the level of genetic diversity known from other endangered insect species. The genetic information in this study will provide valuable data for developing effective conservation strategies.Diplonychus esakii, a water bug from the family Belostomatidae, plays an important role in freshwater ecosystems as one of the top predators. In this study, we investigated the genetic diversity and population structure of D. esakii by analyzing 318 specimens across 27 sites in South Korea. We found that the populations of D. esakii possess 11 haplotypes with a haplotype diversity of 0.623. This represents a relatively low level of genetic diversity compared to other known belostomatids and endangered species. AMOVA and FST analyses revealed significant genetic differentiation among populations, with most populations harboring only 1–2 haplotypes, suggesting restricted gene flow between populations and a low level of genetic diversity. This low genetic diversity and limited gene flow suggest a potential vulnerability to environmental changes and an increased risk of extinction, indicating that D. esakii should be designated as a protected species in South Korea as part of future conservation efforts. Based on the results of this study, Upo Wetland, which maintains relatively high levels of genetic diversity and Jeju Island, which, despite its lower genetic diversity compared to the mainland, does not share haplotypes with other regions, should be considered key conservation units for this species. This study highlights the importance of incorporating genetic information into conservation status assessments under the Red List Categories and Criteria and also emphasizes the need to evaluate this species on the Korean Red List. The data provided here will serve as essential baseline information and valuable resources for the development of effective conservation strategies.

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D.cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D.cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D.cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D.cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.