Low Clonal Diversity Research Articles

Molecular characterization of the 17D-204 yellow fever vaccine

IntroductionThe worldwide use of yellow fever (YF) live attenuated vaccines came recently under close scrutiny as rare but serious adverse events have been reported. The population identified at major risk for these safety issues were extreme ages and immunocompromised subjects. Study NCT01426243 conducted by the French National Agency for AIDS research is an ongoing interventional study to evaluate the safety of the vaccine and the specific immune responses in HIV-infected patients following 17D-204 vaccination. As a preliminary study, we characterized the molecular diversity from E gene of the single 17D-204 vaccine batch used in this clinical study. Materials and methodsEight vials of lyophilized 17D-204 vaccine (Stamaril®, Sanofi-Pasteur, Lyon, France) of the E5499 batch were reconstituted for viral quantification, cloning and sequencing of C/prM/E region. ResultsThe average rate of virions per vial was 8.68±0.07log10 genome equivalents with a low coefficient of variation (0.81%). 246 sequences of the C/prM/E region (29–33 per vials) were generated and analyzed for the eight vials, 25 (10%) being defective and excluded from analyses. 95% of sequences had at least one nucleotide mutation. The mutations were observed on 662 variant sites distributed through all over the 1995 nucleotides sequence and were mainly non-synonymous (66%). Genome variability between vaccine vials was highly homogeneous with a nucleotide distance ranging from 0.29% to 0.41%. Average p-distances observed for each vial were also homogeneous, ranging from 0.15% to 0.31%. ConclusionThis study showed a homogenous YF virus RNA quantity in vaccine vials within a single lot and a low clonal diversity inter and intra vaccine vials. These results are consistent with a recent study showing that the main mechanism of attenuation resulted in the loss of diversity in the YF virus quasi-species.

Clonality as a driver of spatial genetic structure in populations of clonal tree species.

Random genetic drift, natural selection and restricted gene dispersal are basic factors of the spatial genetic structure (SGS) in plant populations. Clonal reproduction has a profound effect on population dynamics and genetic structure and thus emerges as a potential factor in contributing to and modelling SGS. In order to assess the impact of clonality on SGS we studied clonal structure and SGS in the population of Populus alba. Six hundred and seventy-two individuals were mapped and genotyped with 16 nuclear microsatellite markers. To answer the more general question regarding the relationship between SGS and clonality we used Sp statistics, which allows for comparisons of the extent of SGS among different studies, and the comparison of published data on SGS in clonal and non-clonal tree species. Sp statistic was extracted for 14 clonal and 27 non-clonal species belonging to 7 and 18 botanical families, respectively. Results of genetic investigations conducted in the population of P. alba showed over-domination of clonal reproduction, which resulted in very low clonal diversity (R = 0.12). Significant SGS was found at both ramet (Sp = 0.095) and genet level (Sp = 0.05) and clonal reproduction was indicated as an important but not sole driving factor of SGS. Within-population structure, probably due to family structure also contributed to high SGS. High mean dominance index (D = 0.82) indicated low intermingling among genets. Literature survey revealed that clonal tree species significantly differ from non-clonal species with respect to SGS, having 2.8-fold higher SGS. This led us to conclude that clonality is a life-history trait that can have deep impact on processes acting in populations of clonal tree species leading to significant SGS.

Clonal and genetic structure of Iris odaesanensis and Iris rossii (Iridaceae): insights of the Baekdudaegan Mountains as a glacial refugium for boreal and temperate plants

The main Korean mountain range that stretches from north to south (the Baekdudaegan) has been suggested to harbor an important glacial refugium for boreal and temperate plant species. Under this scenario, we expect high levels of within-population genetic variation and low or moderate degree of among-population differentiation within these species. To test this hypothesis, we examined clonal diversity and levels of allozyme diversity in the boreal Iris odaesanensis and in its temperate congener Iris rossii. In addition, we compiled data on boreal and temperate species whose distribution in the Korean Peninsula is mostly centered in the Baekdudaegan to determine if there is a common pattern. We found lower clonal diversity in I. odaesanensis compared to I. rossii. Both studied species maintained high levels of genetic variation as well as a moderate genetic differentiation (%P = 52.5 and 47.5, A = 1.70 and 1.58, H e = 0.158 and 0.150, and F ST = 0.196 and 0.189 for I. odaesanensis and I. rossii, respectively), in line with what occurs for the species distributed on the Baekdudaegan (n = 14, %P = 46.7, A = 1.73, H e = 0.161, and F ST = 0.190). This study strongly suggests that the Baekdudaegan may have acted as a refugium for boreal and temperate species, in a similar way to the southern Appalachians in the eastern United States.

TESTING SEX RATIO THEORY WITH THE MALARIA PARASITEPLASMODIUM MEXICANUMIN NATURAL AND EXPERIMENTAL INFECTIONS

The malaria parasite (Plasmodium) life history accords well with the assumptions of local mate competition (LMC) of sex ratio theory. Within a single meal of the blood-feeding vector, sexually dimorphic gametocyte cells produce gametes (females produce one, males several) that mate and undergo sexual recombination. The theory posits several factors drive the Plasmodium sex ratio: male fecundity (gametes/male gametocyte), number and relative abundance of parasite clones, and gametocyte density. We measured these traits for the lizard malaria parasite, Plasmodium mexicanum, with a large sample of natural infections and infections from experiments that manipulated clonal diversity. Sex ratio in single-clone infections was slightly female-biased, but matched predictions of theory for this low-fecundity species. Sex ratio was less female-biased in clonally diverse infections as predicted by LMC for the experimental, but not natural infections. Gametocyte density was not positively related to sex ratio. These results are explained by the P. mexicanum life history of naturally low clonal diversity and high gametocyte production. This is the first study of a natural malaria system that examines all traits relevant to LMC in individual vertebrate hosts and suggests a striking example of sex ratio theory having significance for human public health.

High clonality and diversity of virulence determinants among blaPSE-positive Salmonella Typhimurim isolates recovered in three geographically distant Spanish hospitals

Molecular typing, the presence of Salmonella genomic island 1 (SGI1), and virulence factors were studied in 45 blaPSE-positive S. Typhimurium isolates from 3 hospitals. All isolates belonged to sequence type ST19, presented low clonal diversity, and harbored SGI1. The wide diversity of virulence factors was classified into 3 major virulotype groups.

Estimation of the Genetic Composition of a Near-Threatened Tidal Marsh Plant, Carex rugulosa, in Japan

As human alterations such as riverbed excavation and harbor improvements have diminished natural littoral regions and estuarine basins, the numbers of organisms living in tidal marsh have declined. The tidal marsh halophyte Carex rugulosa has been commonly observed along the Japanese coastline over the past centuries; however, this species has recently been designated as near threatened. To determine the genetic structure of C. rugulosa, we examined the genetic composition within and among populations and attempted to clarify habitat salinity. Large populations along the Pacific Ocean exhibit relatively high clonal diversity and repeated seedling recruitment, which maintain the genotypic diversity in those populations. Conversely, lower clonal diversity is observed at the distributional margins, suggesting that marginal populations have low seedling recruitment. In terms of habitat salinity, high genetic diversities were observed between 5 and 15 psu in the Hii River watershed. The extant populations in Japan comprise three genetically distinct clusters whose population divisions correspond to the geological distribution and direction of ocean currents around Japan. Our results suggest that most C. rugulosa populations have relatively high inbreeding coefficients or low clonal diversities due to low seed recruitment or fragmentation and that reduction of genetic connectivity among populations is one causality for this low genetic diversity.

Population genetics of Tuberolachnus salignus, an obligate parthenogenetic aphid

This study reports the results obtained in an investigation of the putatively parthenogenetic aphid species Tuberolachnus salignus Gmelin. Tuberolachnus salignus is one of the largest aphid species in the world but where and how it overwinters is not known. It has recently become noteworthy because it is increasingly found on commercially grown willows used in bioenergy production. Seven newly‐developed polymorphic microsatellite markers were used to investigate the genetic diversity of the species, and also to confirm its reproduction strategy. Tuberolachnus salignus shows very low clonal diversity; only 16 genotypes were found in 660 specimens from 27 populations in five countries. There was limited geographical structuring in the samples, although the two most common genotypes, which comprised more than half of the specimens collected, had a very wide distribution. Furthermore, we determined that these aphids, which live in very dense colonies, can consist of more than one genotype, suggesting aggregation of colonizing T. salignus. These results confirm the parthenogenetic nature of T. salignus and demonstrate the presence of common genotypes that are widespread in time and space.

Spatial genetic structure in wild cherry (Prunus avium L.): I. variation among natural populations of different density

Conservation of forest genetic resources requires intensive knowledge of the spatial arrangement of genetic diversity. In this study, we used four natural Prunus avium stands in Germany with contrasting for densities to understand patterns of spatial genetic structure. To this end, we genotyped adults and saplings at eight microsatellite markers, 54 AFLP loci and at the gametophytic incompatibility locus. We estimated levels of clonal propagation, spatial genetic structure and gene dispersal. High mortality occurred among young clonal individuals, as depicted by the lower clonal diversity in saplings. Contrasting levels of spatial genetic structure were observed among markers, ontogenic stages and populations. AFLP were more efficient for detecting spatial autocorrelation but did not allow us to differentiate low and high density populations, while high density populations showed substantially stronger spatial genetic structure at microsatellite loci. Furthermore, kinship decreased with tree age only in low density stands. We discuss the present results in terms of population history, pollen and seed dispersal and population density. Although conspecific density seems to be an interesting indicator of genetic diversity for conservation programmes, we still need to disentangle the relative influence of clonal propagation and density on the strength of spatial genetic structure. Simulation studies are needed to further address this question.

Long-term adaptation of Daphnia to toxic environment in Lake Orta: the effects of short-term exposure to copper and acidification

Because of its 80-year history of heavy pollution and re-colonization, Lake Orta provides a good opportunity for investigating the response of zooplankton organisms to heavy metals and acidification as well as the mechanisms involved. After the recent establishment of Daphnia galeata Sars, and the detection of an extremely low clonal diversity of Lake Orta population, we carried out a study to investigate the lethal tolerance to ionic copper, as well as to acidity, and the impact of newborn Daphnia exposure to sublethal concentrations of copper for their later development and reproduction. We conducted acute toxicity tests to estimate the EC50 for ionic copper and tolerance to low pH, as well as life table experiments. Tolerance to ionic copper was high, three times that reported in literature. An increased mortality soon after exposure to low pH confirmed a high sensitivity to acidity and explained the success of the species in Lake Orta only after pH recovery. An analysis of reproductive and demographic parameters revealed that D. galeata Sars was stressed at concentrations of ionic copper only twice higher than those presently recorded in the lake (i.e., ca 3 μg L-1). An increased cumulative number of eggs produced by each female were in fact counterbalanced by an increasing abortion rate, which resulted in an unaltered or lower intrinsic rate of population increase. Our results are likely due to the strong selective pressure, more than physiological processes (acclimation), in a polluted area in which only specific adapted clones are able to grow, confirming the results previously obtained on Lake Orta's D. obtusa Kurz population. The reproductive response and the relatively low within treatment variability suggest that clone specificity, rather than physiological acclimation, was the driving force. The low variability confirmed results previously obtained from life tables experiments on Lake Orta's D. obtusa clone. Overall, our results suggest that, despite the chemical recovery, Lake Orta may be regarded as highly vulnerable to biodiversity loss.

Clonal composition of Brachionus plicatilis s.s. and B. sp. ‘Austria’ hatchery strains based on microsatellite data

The recent application of different molecular techniques to Brachionus plicatilis hatchery strains has revealed the presence of five members of what is now known as the B. plicatilis complex of cryptic species and has offered new perspectives to the aquaculture industry via a genetically-oriented strain management. In this work, we have employed the high versatility of microsatellites to increase the resolution of previous genetic analyses and study the clonal composition of two of the rotifer species found in hatcheries, namely the B. plicatilis s.s. and B. sp. ‘Austria’. A total of 69 B. plicatilis s.s. and 78 B. sp. ‘Austria’ individual rotifers from 13 hatchery strains were genotyped at seven and three microsatellite loci, respectively. Wild population samples and laboratory clones were used as reference material. Sample relationships were inferred using genetic distance estimates from the allele frequencies of the resulted genotypes. A notably low clonal diversity was found in hatcheries. Some of the strains were actually clonal cultures. In many cases, rotifers with the same multilocus genotype were present in two or three different strains. Interestingly, most B. sp. ‘Austria’ rotifers found in hatcheries have significant genetic similarities. Overall, our results indicate that hatcheries exploit a very small fraction of the available Brachionus genetic diversity even at the intra-specific level. Rotifer circulation practices seem to be a major cause for this outcome. There is a growing evidence that the aquaculture industry could benefit from the use of new Brachionus clones and/or species.

Seagrass meadows at the extreme of environmental tolerance: the case of Posidonia oceanica in a semi‐enclosed coastal lagoon

AbstractAtoll‐like structures of the endemic Mediterranean seagrass Posidonia oceanica were encountered in the innermost area of the Stagnone di Marsala, a semi‐enclosed coastal lagoon along the western coasts of Sicily. The area is characterized by limited water exchange with the open sea and by a marked seasonal variation of water salinity and temperature, reaching beyond the theoretical tolerance limits of the species. In the present study we determined the genetic composition of the atoll‐like structures, as well as the growth performance and flowering rate of these stands. We also assessed whether and to what extent the atoll‐like structures are genetically isolated from plants growing in meadows outside the lagoon. For this purpose we utilized 13 microsatellite markers to genotype single shoots sampled inside and outside the lagoon. Lepidochronological analyses were performed on the same shoots to determine the annual rhizome growth rate, the number of leaves and the inflorescences formed as an estimate of growth‐ and reproductive performance over the years. The innermost area of the lagoon showed a lower number of alleles, a lower percentage of polymorphic loci, a lower clonal diversity, but higher heterozygosis excess with respect to the other areas analysed. Spatial autocorrelation was here significant, up to slightly below 300 m. Shoots collected in the atolls exhibited a 25% lower vertical growth rate and 16% lower leaf formation in comparison to those in open‐sea meadows. No flowering events were recorded during 24 years of investigation, whereas inflorescences were observed frequently in meadows outside the lagoon. Results from Fst and factorial correspondence analysis confirmed the expected genetic isolation of the confined atolls with respect to the meadows outside the lagoon and revealed limited gene flow within the lagoon itself. Apparently, the enclosed system of the Stagnone lagoon is genetically isolated, with a possible selection of genotypes adapted to persistent stressful conditions, consistent with reduced growth and lack of flowering events.

Structure and urovirulence characteristics of the fecal Escherichia coli population among healthy women

The fecal Escherichia coli population structure may influence the occurrence and etiology of extraintestinal infection, but is poorly understood. Accordingly, fecal E. coli from 39 healthy women (30 putative colonies per subject) were characterized for clonal identity, urinary tract infection-associated virulence traits, and phylogenetic background. The 120 unique E. coli clones (mean, three per sample) were distributed by phylogenetic group as follows: A (33%), D (31%), B1 (19%), and B2 (17%). However, 36% of women carried ≥1 clone from group B2, and 87% had clones from groups B2 and/or D. Of the B2 clones, 90% were from pauciclonal fecal samples (≤4 clones), compared with 47% and 52% of A and B1 clones ( P = .001 and P = .007, respectively). Group B2 and D clones more often were dominant within the source sample than group A and B1 clones (60% vs. 41%: P = .05). Dominant clones exhibited higher virulence scores than non-dominant clones (mean 4.4 vs. 3.1: P = .015). In multilevel regression models, pauciclonal sample, B2, and clonal prevalence significantly predicted virulence score. In conclusion, within the intestinal E. coli population, virulence-associated traits, clonal prevalence, and low fecal clonal diversity are related. Virulence-associated traits of group B2/D E. coli may enhance fitness within the gut, thereby increasing strains’ likelihood of causing extraintestinal infection.

Genetic Diversity and Geographic Differentiation in the Threatened Species Dysosma pleiantha in China as Revealed by ISSR Analysis

Dysosma pleiantha, an important threatened medicinal plant species, is restricted in distribution to southeastern China. The species is capable of reproducing both sexually and asexually. In this study, inter-simple sequence repeat marker data were obtained and analyzed with respect to genetic variation and genetic structure. The extent of clonality, together with the clonal and sexual reproductive strategies, varied among sites, and the populations under harsh ecological conditions tended to have large clones with relatively low clonal diversity caused by vegetative reproduction. The ramets sharing the same genotype show a clumped distribution. Across all populations surveyed, average within-population diversity was remarkably low (e.g., 0.111 for Nei's gene diversity), with populations from the nature reserves maintaining relatively high amounts of genetic diversity. Among all populations, high genetic differentiation (AMOVA: Phi(ST) = 0.500; Nei's genetic diversity: G (ST) = 0.465, Bayesian analysis: Phi(B) = 0.436) was detected, together with an isolation-by-distance pattern. Low seedling recruitment due to inbreeding, restricted gene flow, and genetic drift are proposed as determinant factors responsible for the low genetic diversity and high genetic differentiation observed.

Vicariance patterns in the Mediterranean Sea: east–west cleavage and low dispersal in the endemic seagrass Posidonia oceanica

AbstractAim The seagrass, Posidonia oceanica is a clonal angiosperm endemic to the Mediterranean Sea. Previous studies have suggested that clonal growth is far greater than sexual recruitment and thus leads to low clonal diversity within meadows. However, recently developed microsatellite markers indicate that there are many different genotypes, and therefore many distinct clones present. The low resolution of markers used in the past limited our ability to estimate clonality and assess the individual level. New high‐resolution dinucleotide microsatellites now allow genetically distinct individuals to be identified, enabling more reliable estimation of population genetic parameters across the Mediterranean Basin. We investigated the biogeography and dispersal of P. oceanica at various spatial scales in order to assess the influence of different evolutionary factors shaping the distribution of genetic diversity in this species.Location The Mediterranean.Methods We used seven hypervariable microsatellite markers, in addition to the five previously existing markers, to describe the spatial distribution of genetic variability in 34 meadows spread throughout the Mediterranean, on the basis of an average of 35.6 (± 6.3) ramets sampled.Results At the scale of the Mediterranean Sea as a whole, a strong east–west cleavage was detected (amova). These results are in line with those obtained using previous markers. The new results showed the presence of a putative secondary contact zone at the Siculo‐Tunisian Strait, which exhibited high allelic richness and shared alleles absent from the eastern and western basins. F statistics (pairwise θ ranges between 0.09 and 0.71) revealed high genetic structure between meadows, both at a small scale (about 2 to 200 km) and at a medium scale within the eastern and western basins, independent of geographical distance. At the intrameadow scale, significant spatial autocorrelation in six out of 15 locations revealed that dispersal can be restricted to the scale of a few metres.Main conclusions A stochastic pattern of effective migration due to low population size, turnover and seed survival is the most likely explanation for this pattern of highly restricted gene flow, despite the importance of an a priori seed dispersal potential. The east–west cleavage probably represents the outline of vicariance caused by the last Pleistocene ice age and maintained to this day by low gene flow. These results emphasize the diversity of evolutionary processes shaping the genetic structure at different spatial scales.

Local forest environment largely affects below‐ground growth, clonal diversity and fine‐scale spatial genetic structure in the temperate deciduous forest herb Paris quadrifolia

Paris quadrifolia (herb Paris) is a long-lived, clonal woodland herb that shows strong differences in local population size and shoot density along an environmental gradient of soil and light conditions. This environmentally based structuring may be mediated by differences in clonal growth and seedling recruitment through sexual reproduction. To study the interrelationship between environmental conditions and spatial patterns of clonal growth, the spatial genetic structure of four P. quadrifolia populations growing in strongly contrasting sites was determined. In the first place, plant excavations were performed in order to (i) determine differences in below-ground growth of genets, (ii) investigate connectedness of ramets and (iii) determine total genet size. Although no differences in internode length were found among sites, clones in moist sites were much smaller (genets usually consisted of 1-3 interconnected shoots, most of them flowering) than genets in dry sites, which consisted of up to 15 interconnected shoots, the majority of which were vegetative. Further, amplified fragment length polymorphism (AFLP) markers were used. Clonal diversity was higher in populations located in moist and productive ash-poplar forests compared to those found in drier and less productive mixed forest sites (G/N: 0.27 and 0.14 and Simpson's D: 0.84 and 0.75, respectively). Patterns of spatial population genetic structure under dry conditions revealed several large clones dominating the entire population, whereas in moist sites many small genets were observed. Nevertheless, strong spatial genetic structure of the genet population was observed. Our results clearly demonstrate that patterns of clonal diversity and growth form of P. quadrifolia differ among environments. Limited seedling recruitment and large clone sizes due to higher connectedness of ramets explain the low clonal diversity in dry sites. In moist sites, higher levels of clonal diversity and small clone sizes indicate repeated seedling recruitment, whereas strong spatial genetic structure suggests limited seed dispersal within populations.

Genetic structure and clonal diversity of an introduced pest in Chile, the cereal aphid Sitobion avenae

In Chile, the aphid Sitobion avenae is of recent introduction, lives on cultivated and wild Poaceae, and is thought to reproduce by permanent parthenogenesis. In order to study the genetic variability and population structure of this species, five microsatellite loci were typed from individual aphids collected from different cultivated and wild host plants, from different geographical zones, and years. Chilean populations showed a high degree of heterozygosity and a low genetic variability across regions and years, with four predominant genotypes representing nearly 90% of the sample. This pattern of low clonal diversity and high heterozygosity was interpreted as the result of recent founder events from a few asexually reproducing genotypes. Most geographical and temporal variation observed in the genetic composition resulted from fluctuations of a few predominant clones. In addition, comparisons of the genotypes found in Chile with those described in earlier surveys of S. avenae populations in Western Europe led us to identify 'superclones' with large geographical distribution and high ecological success, and to make a preliminary exploration of the putative origin(s) of S. avenae individuals introduced to Chile.

Microevolution, low clonal diversity and genetic affinities of parthenogenetic sitobion aphids in new zealand

In sharp contrast to their southeast Asian and European counterparts, Sitobion miscanthi and S. near fragariae aphids in Australia exhibit a complete absence of sexual reproduction. This demands an explanation within the context of the evolution and maintenance of sex and parthenogenesis. Accordingly, we executed a genetic analysis of the two species in neighbouring New Zealand. Microsatellites and single-stranded conformation polymorphism/sequence analysis of the nuclear gene elongation factor 1alpha were used to identify aphid clones and confirm species identification, respectively. Karyotypic variation was also investigated. The New Zealand fauna showed few (nonrecombining) genotypes and appears to have received migrants from both Australia and Asia. Other genotypes have apparently arisen in situ in New Zealand, exhibiting stepwise mutation of microsatellite alleles and also karyotypic change. Thus, these data represent rare evidence of evolution within wild-living parthenogenetic lineages. Karyotypic changes appear to occur at a rate even greater than that of microsatellite evolution. Strong geographical partitioning of genotypes/karyotypes was found, with certain ones predominating over large areas. These data suggest that clonal selection could be important in the distribution and patterning of genetic variation. We present a model to explain the genetic patterns, with particular reference to the absence of sexual reproduction in Sitobion aphids in New Zealand and Australia.

Among-populational genetic differentiation in the cyclical parthenogen Daphnia magna (Crustacea, Anomopoda) and its relation to geographic distance and clonal diversity

Using allozyme data based on four polymorphic enzymeloci, we present an analysis of geneticdifferentiation among eight Daphnia magnapopulations, separated by less than 100 m to more than500 km from each other. In spite of the large range ofgeographic distances, there was only a slight tendencyfor an increase in genetic differentiation withincreasing geographic distance between populations,and the relation was not significant. This was mainlydue to the fact that neighbouring populations werealready highly genetically differentiated. Our resultssuggest that in populations in which only a fewabundant clones are present after a period of strongclonal selection, among-populational geneticdifferentiation as revealed by allozyme markers isinflated as a result of stochasticity involving chanceassociations of alleles with specific abundantgenotypes. Indices quantifying genetic differentiationwere much higher among populations with a low clonaldiversity than among populations with a high clonaldiversity.

Genotypic diversity of asexual Ostracoda from a low arctic site

AbstractThe crustacean subclass Ostracoda shows an exceptionally high incidence of transitions from sexual to asexual reproduction, whose cause remains uncertain. In the current study, patterns of allozymic variation were examined in 12 species of asexual ostracodes at a low arctic site. Populations of 11 species had genotypic frequencies consistent with apomixis, having gross departures from Hardy‐Weinberg expectations and non‐random associations between loci. Allozyme phenotypes suggest that polyploidy is common in most asexual ostracode species in arctic ponds. Although most species had low clonal diversity, 3 had unusually high diversity, with a maximum of 18 clones detected per pond. Asexual species belonging to genera with sexual relatives had higher clonal diversities than those from genera without sexuals, suggesting that sexuals may serve as the source of this clonal diversity.