Iron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.

Investigating genetic structure and diversity is crucial for rice improvement strategies, including mapping quantitative trait loci with the potential for improved productivity and adaptation to the upland ecology. The present study elucidated the population structure and genetic diversity of 176 rice germplasm adapted to the upland ecology using 7063 genome-wide single nucleotide polymorphism (SNP) markers from the Diversity Array Technology (DArT)-based sequencing platform (DArTseq). The SNPs were reasonably distributed across the rice genome, ranging from 432 SNPs on chromosome 9 to 989 SNPs on chromosome 1. The minimum minor allele frequency was 0.05, while the average polymorphism information content and heterozygosity were 0.25 and 0.03, respectively. The model-based (Bayesian) population structure analysis identified two major groups for the studied rice germplasm. Analysis of molecular variance revealed that all (100%) of the genetic variance was attributable to differences within the population, and none was attributable to the population structure. The estimates of genetic differentiation (PhiPT = 0.001; P = 0.197) further showed a negligible difference among the population structures. The results indicated a high genetic exchange or gene flow (number of migrants, Nm = 622.65) and a substantial level of diversity (number of private alleles, Pa = 1.52 number of different alleles, Na = 2.67; Shannon's information index, I = 0.084; and percentage of polymorphic loci, %PPL = 55.9%) within the population, representing a valuable resource for rice improvement. The findings in this study provide a critical analysis of the genetic diversity of upland rice germplasm that would be useful for rice yield improvement. We suggested further breeding and genetic analyses.

Understanding existing levels of genetic variability of camel populations is capital for conservation activities. This study aims to provide information on the genetic diversity of four dromedary populations, including Guerzni, Harcha, Khouari and Marmouri. Blood samples from 227 individuals belonging to the aforementioned populations were obtained and genotyped by 16 microsatellite markers. A total of 215 alleles were observed, with the mean number of alleles per locus being 13.4 ± 6.26. All loci were polymorphic in the studied populations. The average expected heterozygosity varied from a maximum of 0.748 ± 0.122 in Guerzni population to a minimum of 0.702 ± 0.128 in Harcha population; Guerzni population showed the highest value of observed heterozygosity (0.699 ± 0.088), whereas Harcha population the lowest (0.646 ± 0.130). Mean estimates of F-statistics obtained over loci were FIS = 0.0726, FIT = 0.0876 and FST = 0.0162. The lowest genetic distance was obtained between Guerzni and Khouari (0.023), and the highest genetic distance between Harcha and Marmouri (0.251). The neighbour-joining phylogenetic tree showed two groups of populations indicating a cluster of Guerzni, Khouari and Marmouri, and a clear isolation of Harcha. The genetic distances, the factorial correspondence analysis, the analysis of genetic structure and the phylogenetic tree between populations revealed significant differences between Harcha and other populations, and a high similarity between Guerzni, Khouari and Marmouri. It is concluded from this study that the camel genetic resources studied are well diversified. However, the herd management, especially the random selection of breeding animals, can increase the level of genetic mixing between different populations, mainly among Guerzni, Khouari and Marmouri, that live in the same habitat and grazing area.

During the Pleistocene in the northern part of Europe and Asia, the presence of ice sheets not only limited the range of species but also influenced landscape and thus the contemporary habitat system that determines the pattern of biodiversity. The aim of the research was to find out whether and how a lowland landscape, which formed as a result of subsequent Pleistocene glaciations (five) that in Eurasia covered various and generally successively smaller areas, affected the genetic differentiation of a species. The research was carried out in eastern Poland on the root vole Microtus oeconomus (Arvicolinae, Rodentia), a model boreal and hygrophilous species. Samples were collected from 549 vole individuals at 33 locations. Based on the analysis of 12 microsatellite loci and the 908 bp of cytochrome b sequences (mitochondrial DNA), the genetic structure of M. oeconomus in the landscape zones of the Polish Lowlands was determined. The results show that the latitudinal variability of the relief in eastern Poland (resulting from different ranges of Pleistocene ice sheets) and the related specific configuration of hydrogenic habitats are reflected in the genetic differentiation of the root vole. Therefore, it may be concluded that the history of landscape development affects the genetic structure of hydrophilic species.

Patterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.

Habitat fragmentation creates habitat edges, and ecological edge effects can cause major changes in the ecology and distribution of many taxa. However, these ecological changes may in turn influence animal movements and lead to molecular edge effects and edge-related genetic structure, matters that are largely unexplored. This study aims to infer molecular edge effects and to test three possible underlying mechanisms in the Endangered golden-brown mouse lemur Microcebus ravelobensis, a nocturnal species in the dry deciduous forest of the Ankarafantsika National Park in north-western Madagascar. Mouse lemurs were sampled in one edge and two interior habitats in close proximity to each other (500–1,400 m) in a continuous forest. A total of 41 mouse lemur samples were genotyped with seven nuclear microsatellites, and a fragment of the mitochondrial control region was sequenced for all samples. The overall genetic diversity (allelic richness, heterozygosity, haplotype richness, nucleotide diversity) was lower in the edge habitat compared to the two interior sites and all subpopulations showed signals of relatively low genetic exchange and significant genetic differentiation between them despite the short geographical distances, supporting the local preference model. These findings can be interpreted as preliminary signals of a molecular edge effect and suggest the potential for local adaptation. They are highly relevant for the conservation of fragmented populations, because a further subdivision of already small populations may increase their vulnerability to stochastic demographic changes and collapse.

Thousand Island Lake (TIL) is a typical fragmented landscape and an ideal model to study ecological effects of fragmentation. Partial fragments of the mitochondrial cytochrome oxidase subunit I gene of 23 island populations of Dendrolimus punctatus in TIL were sequenced, 141 haplotypes being identified. The number of haplotypes increased significantly with the increase in island area and shape index, whereas no significant correlation was detected between three island attributes (area, shape and isolation) and haplotype diversity. However, the correlation with number of haplotypes was no longer significant when the ‘outlier’ island JSD (the largest island) was not included. Additionally, we found no significant relationship between geographic distance and genetic distance. Geographic isolation did not obstruct the gene flow among D. punctatus populations, which might be because of the high dispersal capacity of this pine moth. Fragmentation resulted in the conversion of large and continuous habitats into isolated, small and insular patches, which was the primary effect on the genetic diversity of D. punctatus in TIL. The conclusion to emphasize from our research is that habitat fragmentation reduced the biological genetic diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection.

Prodiplosis longifila is reported as a pest of a wide range of species cultivated in America, including citrus, solanaceous species and asparagus. This species has different behavioural traits that are primarily centred on the oviposition habit and the feeding of larvae, which can change depending on the host. However, scarce information is available on population studies and the natural history of this insect, and uncertainty exists about the taxonomic identity and the geographic distribution of this species. The main objective was to perform a phylogenetic and genetic study of P. longifila populations and to define whether the North American and South American populations belong to the same species or whether a differentiation process had occurred due to geographic distance. A second objective was to determine whether this species showed genetic differentiation by host specialization in South America. The phylogenetic and population analyses based on DNA barcodes (cytochrome oxidase I gene) and a region of the ribosomal DNA (ITS2) revealed divergent clades attributable to geographic distance and host specificity. The North American and South American P. longifila insects were confirmed to be genetically distinct, and the genetic distances exceeded the values expected for intraspecific variation. In South America, the population analysis of P. longifila from tomato, sweet pepper (Solanaceae), Tahiti lime and key lime (Rutaceae) hosts evidenced high genetic differentiation between populations associated with different hosts and an absence of gene flow between these groups, suggesting the corresponding formation of cryptic species.

Bactrospora dryina is an epiphytic lichen-forming fungus specifically related to old-growth floodplain forests, which have dramatically declined in Europe over the past centuries. In order to promote conservation management of such forest remnants, we aimed to study population genetics of this rare and threatened lichen. The newly developed 16 microsatellite markers are specific for the mycobiont of B. dryina and reliably amplify either single fruiting bodies or a sterile thallus. This allows the use of these markers for the identification of sterile crusts and for quantification of recent dispersal of the species into restored habitats. We tested the markers in 264 samples collected from 10 pedunculate oak trees growing in three localities in north-eastern Switzerland. All markers were polymorphic and showed two to five alleles per locus, and unbiased gene diversity varied from 0·06 to 0·71 over three populations. The relatively low number of alleles in B. dryina is possibly the consequence of colonization of secondary habitats created by forest management. Although oaks were largely covered with a single, continuous B. dryina colony, the microsatellite markers identified single or complex multi-genotype colonizations per tree. For future population genetic studies, we recommend collection of 5–15 specimens from one tree which would enable detection of 60–80% of the multilocus genotypes present. Hierarchical AMOVA revealed high variation (70%) on host trees, and a relatively high differentiation (12%) among the three locations in NE Switzerland indicated limited gene flow between those regions. Thus, the newly developed markers showed their applicability in population genetics at different spatial scales. They will play an important role in monitoring habitat restoration for the conservation of B. dryina and associated forests and riverscapes.

The Mediterranean region has a rich history of domestication and cultivation of lentil (Lens culinaris Medik.). Landraces have been grown and repeatedly selected by local farmers under different agro-environments. Characterization of molecular variation and genetic differentiation helps to ensure enhanced valorization, conservation and use of these genetic resources. Nineteen Simple Sequence Repeat DNA markers were used for molecular variance analysis (AMOVA) and population structure assessment underlying 74 lentil landraces from four Mediterranean countries: Morocco, Italy, Greece and Turkey. Based on AMOVA, presence of population structure and genetic differentiation at different levels were evidenced. Genetic diversity among Turkish landraces was higher than that of other countries. These landraces were more homogeneous as shown by low genetic differentiation among individuals within each landrace. Whereas Moroccan landraces followed by Italian and Greek provenances showed higher diversity and differentiation among individuals within landraces. The wide genetic variability of these landraces could help to better adaptation to biotic and abiotic stresses. Moreover, they could provide useful alleles related to adaptive traits for breeding purposes. Based on structure analysis, we obtained indications of possible presence of two major gene pools: a northern gene pool composed of Turkish, Italian and Greek landraces, and a southern gene pool composed of Moroccan landraces. Our results could be of interest when designing future diversity studies, collection missions, conservation and core collection construction strategies on Mediterranean lentil landraces.

Crofton weed is a noxious invasive weed worldwide. However, the mechanisms underlying its invasiveness are still not well understood. We hypothesize that genetic differentiation and plasticity may help the plant invade heterogeneous habitats. To test this hypothesis, we compared the differences in seed morphometric and germination traits among 14 populations of the plant located at different elevations (640–2,430 m) in south Yunnan Province of southwest China. Germination capacity (GC) and index (GI) were markedly different among the 14 populations at the same temperature or water treatment. The results indicated genetic differentiations in these traits; maternal effects were not excluded. GC and GI were also different for each population across temperature or water treatments, showing phenotypic plasticity. Croton weed seed size and weight also responded genetically or plastically (or both) to different elevations. Seed width, weight, GC, and GI at each temperature increased with the increase of the elevation of origin, showing clinal variation patterns that reveal local adaptations to habitats encountered by the plant. The large seeds, high GC, and high GI could improve emergence, establishment, growth, and survival of seedlings at high elevation; the low GI could prevent seed germination before the onset of the rainy season at low elevation. On the basis of the results, genetic differentiation and plasticity in seed size and germination traits may help crofton weed acclimate to different elevations, facilitating its invasiveness.

Resistance to the thiocarbamates has been selected in early watergrass populations within the rice-growing region of California. To elucidate the processes contributing to the spread of resistance among rice fields, we characterized the genetic diversity and differentiation of thiobencarb-resistant (R) and thiobencarb-susceptible (S) populations across the Central Valley using microsatellite markers. A total of 406 individuals from 22 populations were genotyped using seven nuclear microsatellite primer pairs. Three analytical approaches (unshared allele, Shannon–Weaver, and allelic-phenotype statistics) were used to assess genetic diversity and differentiation in the allohexaploid species. Low levels of genetic variation were detected within populations, consistent with other highly selfing species, with S populations tending to be more diverse than R populations. FST values indicated that populations were genetically differentiated and that genetic differentiation was greater among S populations than R populations. Principal coordinate analysis generated two orthogonal axes that explained 88% of the genetic variance among early watergrass populations and differentiated populations by geographical region, which was associated with resistance phenotype. A Mantel test revealed that genetic distances between R populations were positively correlated with the geographical distances separating populations. Taken together, our results suggest that both short- and long-distance seed dispersal, and multiple local and independent evolutionary events, are involved in the spread of thiobencarb-resistant early watergrass across rice fields in the Sacramento Valley. In contrast, resistance was not detected in early watergrass populations in the San Joaquin Valley.

Pudong White (PW) pigs are distributed in the Taihu region of China and are characterized by their completely white coats. A heated debate concerning this genetic resource and its relationship to Taihu and western pig breeds has arisen, due to the white coat of the animals. To determine whether PW is a unique genetic resource, we performed a detailed assessment of the genetic relationships among PW, six breeds from the Taihu population and three western pig breeds, based on whole-genome single nucleotide polymorphism (SNP) data. A total of 68 102 SNPs were identified in the genomes of the tested populations by next-generation sequencing technology, of which, 64 were determined as the potentially specific to PW breed. The genetic distance between PW pigs and the Taihu population was shorter than that between PW and western breeds. The genetic distance within the PW population was small and neighbour-joining tree analysis revealed that all PW individuals clustered into a separated group, indicating a close genetic relationship among PW individuals which may result from a small effective population size (Ne) and inbreeding. The results of both principal component analysis and evaluation using fastSTRUCTURE demonstrated that PW was clearly differentiated from other breeds. Together, these results indicate that PW is a distinctive genetic resource with a unique genetic structure separate from other Taihu and western pig breeds. Furthermore, this genome-wide comprehensive survey of the relationships among PW, Taihu and western pig breeds, demonstrates the rationality of the current breed classification of PW. The results also provide evidence about the unique genetic resource of PW, based on genome-wide genetic markers. These data will improve our understanding of the genetic structure and current state of PW breed, and facilitate the development of a national project for the conservation and utilization of these pigs.

Callosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0–47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191–0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (FST) values ranged from 0.049 to 0.441 with a total FST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster.

Luffa cylindrica (L.) M. Roem. is an underutilized vegetable and a potential biodiesel crop for future. Its fruits are edible and used as vegetable. To aid in the selection of lines for breeding, genetic variation and structure of ten populations of L. cylindrica were determined with three morphological characters and 23 sequence-related amplified polymorphism (SRAP) markers. All the three morphological characters were found diverse among 45 accessions. The SRAP primers produced a total of 177 bands, out of which 129 were polymorphic. Informative markers assessed by different measures (polymorphism information content = 0.18, marker index = 1.26, resolving power = 2.87) will direct the selection of primers for cultivar identification in L. cylindrica. Low level of genetic differentiation among populations and higher level within populations (Gst= 0.4073, Nm= 0.7277, He= 0.124, I= 0.20) was detected that might be due to cross-pollinated nature of L. cylindrica. The clustering pattern obtained through dendrogram and principal coordinate analysis was loosely concordant with the geographical distribution. The Bayesian structure analysis indicated an admixture type of population distribution. The results designate that SRAP and morphological markers are informative for characterization of L. cylindrica and identification of distinctive cultivars.

The pearl oyster, Pinctada radiata, shows great variation in shell morphology throughout its distribution. This variation can be related to phenotypic plasticity, genetic variability or a combination of both. Using geometric morphometric and microsatellite DNA analyses, two morphologically distinct populations of the pearl oyster were studied in the northern Persian Gulf, i.e. from the Lavan and Hendourabi Islands. Ten landmarks were selected to define the shape of the left shell. In addition, concentration of Zn, Mg, Fe, Cu, Pb, Cd, Mn and Cr of the soft tissues were measured using atomic absorption spectrometry. Six microsatellite loci were used to assess the population genetic structure of the pearl oyster. There were morphometric differences between the populations suggesting the existence of two morphotypes. There was a significant difference between the two populations in concentrations of Fe, Mg, Zn, Cd, Mn and Cr indicating that the specimens from the Lavan Island experience a more stressful environment than those from the Hendourabi Island. Analysis of molecular variance (AMOVA) indicated that the proportion of the genetic variation attributed to differences among populations of the pearl oyster was highly significant for both FST and RST (FST = 0.066, RST = 0.265, P < 0.001). Our findings showed that stressful conditions resulting from heavy metals may have a direct influence on the separation of the populations in Lavan and Hendourabi despite the lack of a physical barrier.

The mealybug species Phenacoccus solenopsis (P. solenopsis) has caused much agricultural damage since its recent invasion in China. However, the source of this invasion remains unclear. This study uses molecular methods to clarify the relationships among different population of P. solenopsis from China, USA, Pakistan, India, and Vietnam to determine the geographic origin of the introduction of this species into China. P. solenopsis samples were collected from 25 different locations in three provinces of Southern China. Samples from the USA, Pakistan, and Vietnam were also obtained. Parts of the mitochondrial genes for cytochrome oxidase I (COI) were sequenced for each sample. Homologous DNA sequences of the samples from the USA and India were downloaded from Gen Bank. Two haplotypes were found in China. The first was from most samples from the Guangdong, Guangxi, and Hainan populations in the China and Pakistan groups, and the second from a few samples from the Guangdong, Guangxi, Hainan populations in the China, Pakistan, India, and Vietnam groups. As shown in the maximum likelihood of trees constructed using the COI sequences, these samples belonged to two clades. Phylogenetic analysis suggested that most P. solenopsis mealybugs in Southern China are probably closely related to populations in Pakistan. The variation, relationship, expansion, and probable geographic origin of P. solenopsis mealybugs in Southern China are also discussed.

Sustainable development of a breeding programme depends on having sufficient genetic variability to achieve genetic gains in each selection cycle. The aim of this study was to molecularly characterize families of the oil palm, Elaeis guineensis Jacq., of different origins using microsatellite molecular markers. The value of the observed heterozygosity was higher than that of the expected heterozygosity in all of the progenies. The coefficients (G ST= 0.207 and F ST= 0.174) and AMOVA showed genotypic differences among the evaluated families. Likewise, this was reflected in the groups obtained by the dendrogram and principal coordinate analyses. This difference could have evolved due to the enrichment of some of the families with germplasm from different origins. Therefore, genetic relationships estimated from molecular data would be convenient to select families more distant from each group and palms more distant from each family selected to reserve genetic variability. This information will guide us in the decision-making process when planning breeding programmes focused on crosses to develop new populations with an acceptable broad genetic base and adaptability. In this way, sources of resistance to biotic and abiotic factors can be identified for the development of new varieties with competitive advantages for the sector.

Fragmented populations are usually exposed to the negative effects of reduced gene flow, genetic drift and population differentiation. These effects result in the collective loss of genetic variation, thereby reducing the probability of population adaptation to new environmental conditions and increasing the risk of extinction. Forest fragments commonly exhibit suboptimal site conditions, which can result in enhanced clonal reproduction, and a potential reduction in clonal diversity due to increased selfing and inbreeding depression. The clonal diversity, genetic diversity and structure of Heliconia angusta (Heliconiaceae) were assessed using AFLP-markers. We analysed six patches in the continuous forest (Atlantic rain forest, State of Rio de Janeiro) and eight patches (155 leaf samples in total) in five nearby forest fragments (age of oldest fragment: c. 50 y; size range: < 5–100 ha). Clonal diversity (Pd) of patches was slightly, yet significantly, lower in forest fragments compared with continuous forest. Measures of genetic diversity of patches in forest fragments did not differ from those in the continuous forest. A STRUCTURE analysis did not show any clear clustering of patches in the continuous forest and forest fragments. Our results suggest that H. angusta has not yet suffered from the anticipated negative effects of fragmentation.

The USA is experiencing a prolific invasion of the wood-boring emerald ash borer, Agrilus planipennis. Native to Asia, this beetle completes its life cycle on ash trees and results in nearly complete mortality of all infested trees. In the present study, we examined the levels of genetic diversity and differentiation among eight populations of Fraxinus pennsylvanica (green ash) using five polymorphic microsatellite loci. Genetic information was used to design guidelines for the establishment of a seed collection sampling strategy to conserve the genetic diversity of ash trees. We found high levels of genetic diversity, as indicated by the allelic richness, both across the populations (16.4 ± 5.18 alleles per locus) and within them (8.03 ± 1.21 alleles per locus). The expected and observed heterozygosity was also high (0.805 ± 0.38 and 0.908 ± 0.04, respectively), and there was moderate genetic differentiation among the populations (FST= 0.083) with members of these eight populations grouped into three distinct clusters. We examined the relationship between the number of individuals sampled and the number of alleles captured in a random sample taken from a population of 10,000 individuals. Only sample sizes of 100 individuals captured most of the alleles (average = 78.74 alleles), but only seven of 50 samples effectively captured all the 82 alleles. Smaller samples did not capture all alleles. A probabilistic model was used to determine an optimal sampling strategy, and it was concluded that a collection of 200 seeds from each of five mother trees would have the highest likelihood of capturing all alleles in a population.