Genetic analysis of southern African gemsbok (Oryx gazella) reveals high variability, distinct lineages and strong divergence from the East African Oryx beisa

We carried out a population genetic analysis of five southern African gemsbok (Oryx gazella) populations based on 530 bp of the mitochondrial control region and ten microsatellites in 75 individuals. Both markers show the high variability often observed in African bovids. Three of the populations which can be traced back to very small founding or current sizes do not show any signs of reduced variability compared to the remaining populations. The mitochondrial haplotypes form three distinct lineages which most likely originated in the Pleistocene when climate fluctuations led to periodical reduction and spreading of gemsbok habitat and which, today, are found throughout the distribution range. Bayesian microsatellite analyses yielded two groups, suggesting a more recent geographical differentiation following the admixture of the mtDNA lineages. Combining our sequences with available published data of the remaining oryx species allowed for a direct molecular comparison of O. gazella and O. beisa which have sometimes been considered a single species. The average genetic divergence between haplotypes from the two taxa was very high (39.9%), supporting their classification into two different species.     

Low genetic variability in the rare,recently differentiated Aquilegia paui (Ranunculaceae)

Aquilegia paui is a narrow endemic species from the north-eastern Iberian Peninsula. It has a reduced number of populations in the limestone mountain massif of Els Ports. Genetic diversity was evaluated through allozyme electrophoresis in this rare columbine, together with its widespread congener Aquilegia vulgaris. Low levels of genetic diversity were detected in both taxa, especially for A. paui. Genetic identity between the two columbines was particularly high (I = 0.990), and the allele pool of A. paui is a subset of that of its widespread congener (with the exception of a low-frequency allele that was only detected in one population of A. paui). A. paui may have recently evolved from nearby populations of A. vulgaris. Speciation of this taxon, which may still be ongoing, seems to be driven by ecological differentiation, as generally occurred for the European columbines as well as in many Mediterranean endemic species.     

Dynamics of polyploid formation and establishment in the allotetraploid rock fern Asplenium majoricum

Background and Aims

Successful establishment of newly formed polyploid species depends on several interlinked genetic and ecological factors. These include genetic diversity within and among individuals, chromosome behaviour and fertility, novel phenotypes resulting from novel genomic make-up and expression, intercytotypic and interspecific competition, and adaptation to distinct habitats. The allotetraploid rock fern Asplenium majoricum is known from one small population in Valencia, Spain, and several larger populations on the Balearic island of Majorca. In Valencia, it occurs sympatrically with its diploid parents, A. fontanum subsp. fontanum and A. petrarchae subsp. bivalens, and their diploid hybrid A. × protomajoricum. This highly unusual situation allowed the study of polyploid genetic diversity and its relationship to the formation and establishment of nascent polyploid lineages.

Methods

Genetic variation for isozyme and chloroplast DNA markers was determined for A. majoricum and A. × protomajoricum sampled thoroughly from known sites in Majorca and Valencia. Results were compared with variation determined previously for the diploid parent taxa.

Key Results

A highly dynamic system with recurring diploid hybrid and allotetraploid formation was discovered. High diversity in the small Valencian A. majoricum population indicates multiple de novo origins from diverse parental genotypes, but most of these lineages become extinct without becoming established. The populations on Majorca most probably represent colonization(s) from Valencia rather than an in situ origin. Low genetic diversity suggests that this colonization may have occurred only once.

Conclusions

There is a striking contrast in success of establishment of the Majorcan and Valencian populations of A. majoricum. Chance founding of populations in a habitat where neither A. fontanum subsp. fontanum nor A. petrarchae subsp. bivalens occurs appears to have been a key factor enabling the establishment of A. majoricum on Majorca. Successful establishment of this polyploid is probably dependent on geographic isolation from diploid progenitor competition.     

Cranial morphometrics and mitochondrial DNA sequences distinguish cryptic species of the longface emperor (Lethrinus olivaceus), an emblematic fish of Indo-West Pacific coral reefs

Range-wide morphometric variability (cranial measurements) and genetic variability (nucleotide sequences of the cytochrome b gene) were investigated in the longface emperor, Lethrinus olivaceus (Lethrinidae), an emblematic large predatory fish of Indo-West Pacific coral reefs. Two cranial morphotypes were observed, one present from the Indian Ocean to the Coral Triangle and the other one, from the Coral Triangle to the western Central Pacific. The two morphotypes are concordant with reciprocally monophyletic mitochondrial lineages separated by 9.5% net nucleotide distance. These results suggest an old evolutionary history for L. olivaceus, which consists of two distinct species (Lethrinus sp. A in the Indian Ocean and Coral Triangle, Lethrinus sp. B in the western Pacific Ocean), whose distribution ranges meet or overlap in the eastern part of the Coral Triangle, in Taiwan and in West Papua. Lethrinus sp. A comprises two distinct mitochondrial lineages separated by 1.7% net nucleotide distance, one exclusive to the populations from the Indian Ocean, the other exclusive to Coral Triangle populations. The latter observation might be explained by vicariance, whereby the two lineages have been isolated from one another on either side of the Sunda Shelf because of low sea level in the Pleistocene. To clarify the nomenclature of this species complex, we recommend sequencing a fragment of the cytochrome b gene of the holotypes of L. olivaceus and of its first junior synonyms L. rostratus and L. waigiensis.     

Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging,but endangered,freshwater mussel

Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure throughout its range. Mitochondrial DNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in most populations; however, all populations have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them.     

Genetic diversity of the Chinese liver fluke Clonorchis sinensis from Russia and Vietnam

Clonorchiasis is a parasitic disease of high public health importance in many countries in southeastern Asia and is caused by the Chinese liver fluke Clonorchis sinensis. However, the genetic structure and demographic history of its populations has not been sufficiently studied throughout the geographic range of the species and available data are based mainly on partial gene sequencing. In this study, we explored the genetic diversity of the complete 1560 bp cytochrome c oxidase subunit 1 (cox1) gene sequence for geographically isolated C. sinensis populations in Russia and Vietnam, to our knowledge for the first time. The results demonstrated low nucleotide and high haplotype differentiation within and between the two compared regions and a clear geographical vector for the distribution of genetic diversity patterns among the studied populations. These results suggest a deep local adaptation of the parasite to its environment including intermediate hosts and the existence of gene flow across the species’ range. Additionally, we have predicted an amino acid substitution in the functional site of the COX1 protein among the Vietnamese populations, which were reported to be difficult to treat with praziquantel. The haplotype networks consisted of several region-specific phylogenetic lineages, the formation of which could have occurred during the most extensive penultimate glaciations in the Pleistocene Epoch. The patterns of genetic diversity and demographics are consistent with population growth of the liver fluke in the late Pleistocene following the Last Glacial Maximum, indicating the lack of a population bottleneck during the recent past in the species’ history. The data obtained have important implications for understanding the phylogeography of C. sinensis, its host-parasite interactions, the ability of this parasite to evolve drug resistance, and the epidemiology of clonorchiasis under global climate change.     

Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring

Theoretically, the dynamics of clonal and genetic diversities of clonal plant populations are strongly influenced by the competition among clones and rate of seedling recruitment, but little empirical assessment has been made of such dynamics through temporal genetic surveys. We aimed to quantify 3 years of evolution in the clonal and genetic composition of Zostera marina meadows, comparing parameters describing clonal architecture and genetic diversity at nine microsatellite markers. Variations in clonal structure revealed a decrease in the evenness of ramet distribution among genets. This illustrates the increasing dominance of some clonal lineages (multilocus lineages, MLLs) in populations. Despite the persistence of these MLLs over time, genetic differentiation was much stronger in time than in space, at the local scale. Contrastingly with the short-term evolution of clonal architecture, the patterns of genetic structure and genetic diversity sensu stricto (that is, heterozygosity and allelic richness) were stable in time. These results suggest the coexistence of (i) a fine grained (at the scale of a 20 × 30 m quadrat) stable core of persistent genets originating from an initial seedling recruitment and developing spatial dominance through clonal elongation; and (ii) a local (at the scale of the meadow) pool of transient genets subjected to annual turnover. This simultaneous occurrence of initial and repeated recruitment strategies highlights the different spatial scales at which distinct evolutionary drivers and mating systems (clonal competition, clonal growth, propagule dispersal and so on) operate to shape the dynamics of populations and the evolution of polymorphism in space and time.     

Phylogeographic Pattern of the Striped Snakehead,Channa striata in Sundaland: Ancient River Connectivity,Geographical and Anthropogenic Singnatures

A phylogeographic study of an economically important freshwater fish, the striped snakehead, Channa striata in Sundaland was carried out using data from mtDNA ND5 gene target to elucidate genetic patterning. Templates obtained from a total of 280 individuals representing 24 sampling sites revealed 27 putative haplotypes. Three distinct genetic lineages were apparent; 1)northwest Peninsular Malaysia, 2)southern Peninsular, east Peninsular, Sumatra and SW (western Sarawak) and 3) central west Peninsular and Malaysian Borneo (except SW). Genetic structuring between lineages showed a significant signature of natural geographical barriers that have been acting as effective dividers between these populations. However, genetic propinquity between the SW and southern Peninsular and east Peninsular Malaysia populations was taken as evidence of ancient river connectivity between these regions during the Pleistocene epoch. Alternatively, close genetic relationship between central west Peninsular Malaysia and Malaysian Borneo populations implied anthropogenic activities. Further, haplotype sharing between the east Peninsular Malaysia and Sumatra populations revealed extraordinary migration ability of C. striata (>500 km) through ancient connectivity. These results provide interesting insights into the historical and contemporary landscape arrangement in shaping genetic patterns of freshwater species in Sundaland.     

Glacial-driven vicariance in the amphipod Gammarus duebeni

We have examined the genetic diversity using mitochondrial COI and ND2 sequence data from 306 specimens of the amphi-Atlantic-distributed amphipod Gammarus duebeni. Marine populations from the Atlantic Ocean, the Baltic and North Sea, as well as freshwater populations from Ireland, Cornwall and Brittany were analysed.G. duebeni is a complex of five allopatric lineages. Freshwater populations result from multiple invasions of marine ancestors, represented by distinct lineages. We interpret the recent distribution of lineages as the outcome of a series of spatio-temporal vicariant events caused by Pleistocene glaciations and sea level changes. The freshwater lineages are therefore regarded as ‘glacial relicts’. Furthermore, inter-specific competition with, for example, Gammarus pulex (which is absent in Ireland and western Brittany) may be another important determinant in the distribution of freshwater G. duebeni. In Ireland and Brittany, three freshwater refugia are suggested. The significantly limited gene flow detected among marine populations is more likely due to inter-specific competition than to salinity. The G. duebeni-complex represents a model system for the study of allopatric speciation accompanied by major habitat shifts. The pattern of spatio-temporal origins of the freshwater entities we describe here provides an excellent system for investigating evolutionary adaptations to the freshwater environment. Our data did not confirm the presently used subspecies classification but are only preliminary in the absence of nuclear genetic analyses.     

Genetic Connectivity in Corals on the Flower Garden Banks and Surrounding Oil/Gas Platforms, Gulf of Mexico

The northern Gulf of Mexico (GOM) currently possesses ∼ 3,600 offshore oil and gas production platforms. These platforms serve as artificial reefs on the continental shelf, where, until their introduction, shallow hard substrata were rare. This newly available substrate has helped to expand scleractinian coral populations in the GOM. Here, we conduct molecular genetic analyses on adult scleractinian corals on the Flower Garden Banks (FGB) coral reefs (∼ 180 km SE of Galveston, TX) and on surrounding oil and gas platforms. We have attempted to determine the degree of genetic affinity among the natural populations and those on the surrounding platforms. The three most abundant hermatypic scleractinian species were sampled: Madracis decactis, Diploria strigosa, and Montastraea cavernosa. Tissue samples were collected from the East (E-) and West (W-) FGB, and seven platforms within a 65 km radius of the FGB, at a depth range of 5-37 m. Genetic variation was assessed using Amplified Fragment Length Polymorphisms (AFLPs). The large number of polymorphic markers generated by AFLPs allowed for the use of standard genetic analysis tools (AMOVA) as well as population allocation techniques (AFLPOP). AMOVA analyses indicated that the E- and W-FGB were genetically homogeneous for populations of Madracis decactis and Diploria strigosa; Montastraea cavernosa populations, however, were significantly different there. In all species, genetic distance (FST) increased significantly with geographic distance between populations. In the brooding species Madracis decactis, this pattern was even stronger when one considered distance between the platforms and the perimeters of the FGB, particularly the nearest FGB, suggesting that the FGB may be a source of larvae for platform populations. AFLPOP analyses showed that the degree of self-allocation to home sites also increased with inter-site distance. Cross allocations between sites dropped significantly and exponentially in all species within only one to several kms of the FGB. Madracis decactis, a brooder with extended larval release periods and near-immediate settlement competence, showed greater affinity to the FGB with distance than Diploria strigosa, a broadcaster. This brooder appears to be more effective at colonizing small, nearby target sites and expanding its geographic range at the meso-scale. The low degree of genetic affinity exhibited by all species on the platforms may be attributed to genetic drift/founder effect or relatively small samples sizes, although total populations were sampled. In general, genetic affinity decreased with inter-site distance. Young coral populations are highly differentiated at the meso-scale during early stages of community succession, implying that much time and repeated colonization of patchy habitats around larger potential larval sources will be required before genetic equilibrium or homogeneity is reached.     

Two species of swimming crabs of the genus Achelous (Crustacea,Brachyura): environmental requirements determining the niche

Some holoplanktonic species are cosmopolitan and have continuous distribution in the world’s oceans. For most of these species it is not clear whether there is unhampered gene flow between far distant populations or they represent a complex of cryptic species. In the present study we investigated genetic diversity of the cosmopolitan chaetognath Eukrohnia hamata in order to identify its spatial structure. DNA-barcode fragment of the mitochondrial COI gene was determined and analyzed for E. hamata specimens collected in the Arctic Ocean, Atlantic Ocean, and Atlantic sector of the Southern Ocean. Five lineages were determined by the phylogenetic analysis with robust statistical support. Three lineages: Antarctic (Eh-1), Subantarctic (Eh-2), and Arctic (Eh-3) had significant genetic differences and were geographically separated. Two other lineages: Eh-4 and Eh-5, that had the smallest genetic difference, were observed together in tropical waters, but they were geographically separated from the other lineages. We suppose that geographical distribution of most of the E. hamata lineages is shaped by the large-scale oceanic fronts, considered as biogeographic boundaries for numerous zooplankton species. Genetic homogeneity of Arctic, Subantarctic, and Antarctic lineages was also shown, each within its regions of inhabit.     

A cornucopia of cryptic species - a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha,Gobiiformes)

A genetic analysis of partial mitochondrial 5’ cytochrome c oxidase I gene (DNA barcode) sequences of 473 specimens assigned to 52 morphological species (including four known, but not formally named, species) of the gobiid genus Trimma revealed the presence of 94 genetic lineages. Each lineage was separated by > 2% sequence divergence. Thus there were an additional 42 haplogroups recognizable as provisional candidate species given that a value of > 2% difference is typical of different species of fishes. Such a high degree of apparently different cryptic species is, in our experience, virtually unprecedented among vertebrates. These results have precipitated further morphological research in a few cases, which has uncovered subtle differences independently corroborating the genetic results. However, such efforts are limited by the dearth of traditional systematists available to undertake the necessary time-consuming, and highly detailed, morphological research. In some cases, the genetic results we present are consistent with, and confirm, minor taxonomic distinctions based on morphology and/or colour pattern. In other instances, what had been recognized as a single species consists of several genetic lineages - up to eight in, for example, what we have identified based on morphology as Trimma okinawae. The increase from 52 to 94 potential species in our sampling raises the predicted total number of species in this genus from about 110 to nearly 200 (versus the 73 valid described species currently recognized).     

Host associations and evolutionary relationships of avian blood parasites from West Africa

The host specificity of blood parasites recovered from a survey of 527 birds in Cameroon and Gabon was examined at several levels within an evolutionary framework. Unique mitochondrial lineages of Haemoproteus were recovered from an average of 1.3 host species (maximum = 3) and 1.2 host families (maximum = 3) while lineages of Plasmodium were recovered from an average of 2.5 species (maximum = 27) and 1.6 families (maximum = 9). Averaged within genera, lineages of both Plasmodium and Haemoproteus were constrained in their host distribution relative to random expectations. However, while several individual lineages within both genera exhibited significant host constraint, host breadth varied widely among related lineages, particularly within the genus Plasmodium. Several lineages of Plasmodium exhibited extreme generalist host-parasitism strategies while other lineages appeared to have been constrained to certain host families over recent evolutionary history. Sequence data from two nuclear genes recovered from a limited sample of Plasmodium parasites indicated that, at the resolution of this study, inferences regarding host breadth were unlikely to be grossly affected by the use of parasite mitochondrial lineages as a proxy for biological species. The use of divergent host-parasitism strategies among closely related parasite lineages suggests that host range is a relatively labile character. Since host specificity may also influence parasite virulence, these results argue for considering the impact of haematozoa on avian hosts on a lineage-specific basis.     

Genetic diversity and historical biogeography of the Maltese wall lizard,Podarcis filfolensis (Squamata: Lacertidae)

Podarcis filfolensis is an endemic lizard from the Maltese archipelago. There is evidence of human-mediated decline and even extirpation of some insular populations of this species. However, information about the intraspecific genetic diversity and phylogeographic patterns of this species is limited. Here we analyze genetic markers from a multi-locus dataset (mtDNA, 2,533 bp; nuclear c-mos gene, 353 bp; 11 microsatellites) for individuals from extant populations of P. filfolensis. Despite generally low genetic variability, two main mitochondrial groupings were clearly identified. In general, individuals from the main island of Malta were genetically distinct from those from Gozo, Comino, Cominotto and Small Blue Lagoon Rock, and also from Linosa and Lampione individuals. Three genetic clusters were detected based on microsatellite data: one was found at higher frequency on Malta, while the other two included samples from the remaining islands, showing some concordance with the mtDNA pattern. A time-calibrated Bayesian tree for the principal mitochondrial lineages indicated strong statistical support for two P. filfolensis lineages that originated in the Pleistocene (105.4–869 Ka). We show that these lineages largely meet the criteria for recognition as evolutionary significant units despite some recent admixture (possibly due to recent translocations between islands). Human disturbance, low genetic variability, evidence of bottlenecks and extirpation on one island indicate that a thorough review of the current conservation status of P. filfolensis would be timely.     

Estimating genetic and environmental components of variance using sexual and clonal Artemia

Reproductive and life span traits were measured for two obligately parthenogenetic (Artemia parthenogenetica) and three sexual (two A. franciscana and one A. sinica) brine shrimp populations. For each population, clonal lineages or single mating pairs were followed through one life cycle. The relative contributions of environmental and genetic components to total phenotypic variation for 10 life-history traits in response to environmental stress (0, 10, 25 ppb Cu) were estimated. Within treatment variation (CV_W) was 39% higher for sexual populations than parthenogenetic populations, with significant (p<0.05) differences in total number of offspring and number of nauplii. CV_A (the change in variance due to rearing in different environments), when averaged for all traits and all populations, increased variability by 9.9%. CV_A was 44.2% higher for sexual than parthenogenetic populations, with significant differences in number of broods, total number of offspring, and number of nauplii. The average genetic component of variation for the 10 traits was 23.44%, ranging from 5.26% for number of cysts to 44.87% for number of nauplii. For all traits, the environmental component of variance is greater than the genetic component measured, but every trait has a genetic component, which can potentially be acted upon by selection.     

Microsatellite diversity and population genetic structure of yellowcheek, Elopichthys bambusa (Cyprinidae) in the Yangtze River

Yellowcheek carp (Elopichthys bambusa) is the only species of genus Elopichthys. It is widely distributed in Chinese freshwaters but currently its populations have declined to threatening level. We examined the genetic diversity and population structure of E. bambusa in the Yangtze River basin. A total of nine polymorphic microsatellite markers were employed to study five populations occurring in middle and lower reaches of the river. The results revealed low-to-moderate genetic diversity. The number of alleles per locus varied between 3 and 8 with an average of 4.8. Observed heterozygosity ranged from 0.15 to a maximum of 1.00. Significant deviations (P < 0.01) from Hardy–Weinberg equilibrium were observed for all the tested locus-population combinations with clear heterozygosity deficits. AMOVA indicated that majority of the variance lies within populations (93.81%) than among the populations (7.05%). Pairwise F_ST and unbiased genetic distance pointed out significant differentiation among the samples from populations with different connections to the Yangtze River. In the UPGMA dendrogram, clustering pattern of populations indicated that most of the populations are reproductively isolated due to anthropogenic interventions. Clustering of PYL and DTL populations shows ongoing gene flow through the mainstream. The recent hydrological alterations and overfishing are major factors shaping the current genetic structure. These results can be helpful for effective management and sustainable conservation of E. bambusa populations.     

Genetic diversity and population structure of the endangered and medically important Rheum tanguticum (Polygonaceae) revealed by SSR Markers

Rheum tanguticum (Polygonaceae), an endangered plant, is endemic to the Qinghai-Tibetan Plateau. A total of 114 individual of R. tanguticum from 10 geographically separate populations were analyzed using seven pairs simple sequence repeats (SSR) markers. 102 alleles were recorded, with an average of 14.6 alleles per locus (ranging from 13 to 17) and the expected heterozygosity (H_e) ranged from 0.384 to 0.515 (average 0.459). The genetic differentiation between populations was relatively high (F_st = 0.249); the gene flow (N_m = 0.754), however, was limited, which suggested that around 21.18% of the total genetic variations occurred between populations. Our results revealed high levels of genetic variations within and between populations. The endangered status of this species is probably due to harvesting of the wild populations, rather than a lack of the genetic diversity. Anthropologic effects as well as other factors may, together, have shaped the genetic structure of this species.     

Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera,Tephritidae)

We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area.     

Host-associated genetic differentiation in rice grasshopper, Oxya japonica, on wild vs. cultivated rice

Rice grasshopper, Oxya japonica, is one of the most important pests in south China, mainly inhabiting fields of wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa). In this study, we used AFLP marker to investigate the genetic diversity and population structure of rice grasshoppers collected from south China, with emphasis on testing the hypothesis that there was significant genetic differentiation among grasshopper populations associated with different hosts (i.e. wild vs. cultivated rice). Seven populations consisting of 104 individuals were sampled from Hainan Island and the mainland of south China. Eight primer combinations produced 564 reliable bands, of which 563 were polymorphic. O. japonica showed considerable genetic variation at population level, with gene diversity (H_E) ranging from 0.1103 to 0.2035. Genetic diversity were studied on seven populations, and generally three populations from wild rice had higher levels of genetic diversity (H_E = 0.1635) than the other four populations feeding on cultivated rice (H_E = 0.1327). We observed high population differentiation, with F_st ranging from 0.4172 to 0.7652 among the seven populations. However, Mantel test detected no significant correlation between genetic distance and geographical distance (r = 0.3541; p = 0.0689). By contrast, we found significant genetic differentiation between groups collected from different hosts. These data suggested that the anthropogenic activity in cultivated rice fields (i.e. pesticides, fertilization and cultivation) could have played an important role in shaping the genetic structure of O. japonica.