Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation

Background and Aims

Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity.

Methods

Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure.

Key Results

High within-population genetic diversity (H_E = 0·76) and a relatively low inbreeding coefficient (F_IS = 0·022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G′_ST = 0·53). A significant isolation-by-distance relationship was found (r = 0·62, P < 0·001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population.

Conclusions

The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear western–eastern differentiation in this species merits consideration in future conservation efforts.Key words: Alpine plant, Campanula thyrsoides, genetic diversity, gene flow, genetic differentiation, glacial history, G′_ST, habitat isolation, microsatellites, monocarpy, SSR     

Biased morph ratios and skewed mating success contribute to loss of genetic diversity in the distylous Pulmonaria officinalis

Background and Aims

In heterostylous plant species, skewed morph ratios are not uncommon and may arise from a range of factors. Despite the recognized importance of skewed morph ratios on overall reproductive success within populations, little is known about the impact of skewed morph ratios on population genetic diversity and differentiation in heterostylous species. This study specifically aimed to clarify the effect of population size and morph bias on population genetic diversity and differentiation in the temperate forest herb Pulmonaria officinalis. This species is characterized by a distylous breeding system and shows morph-specific differences in reproductive success.

Methods

Genetic diversity was determined for 27 P. officinalis populations in northern Belgium by using eight recently developed microsatellite markers. Multiple regressions were used to assess the relationship between genetic diversity, morph bias and population size, and F_ST-values were calculated for short- and long-styled morphs separately to study genetic differentiation as a function of morph type.

Key Results

For all genetic measures used, morph bias was more important in explaining patterns of genetic diversity than population size, and in all cases patterns of population genetic diversity followed a quadratic function, which showed a symmetrical decrease in genetic diversity with increasing morph bias. However, probably due to the reproductive advantage of L-morphs relative to S-morphs, maximum genetic diversity was found in populations showing an excess of L-morphs (60·7 % L-morph). On the other hand, no significant difference in pairwise genetic distances between populations was observed between L- (0·107) and S-morphs (0·106).

Conclusions

Our results indicate that significant deviations from equal morph ratios not only affect plant reproductive success but also population genetic diversity of heterostylous plant species. Hence, when defining conservation measures for populations of heterostylous plant species, morph ratios should be considered as an important trait affecting their long-term population viability.     

Geographical structuring of genetic diversity across the whole distribution range of Narcissus longispathus, a habitat-specialist, Mediterranean narrow endemic

Background and Aims

High mountain ranges of the Mediterranean Basin harbour a large number of narrowly endemic plants. In this study an investigation is made of the levels and partitioning of genetic diversity in Narcissus longispathus, a narrow endemic of south-eastern Spanish mountains characterized by a naturally fragmented distribution due to extreme specialization on a rare habitat type. By using dense sampling of populations across the species'' whole geographical range, genetic structuring at different geographical scales is also examined.

Methods

Using horizontal starch-gel electrophoresis, allozyme variability was screened at 19 loci for a total of 858 individuals from 27 populations. The data were analysed by means of standard statistical approaches in order to estimate gene diversity and the genetic structure of the populations.

Key Results

Narcissus longispathus displayed high levels of genetic diversity and extensive diversification among populations. At the species level, the percentage of polymorphic loci was 68 %, with average values of 2·1, 0·11 and 0·14 for the number of alleles per locus, observed heterozygosity and expected heterozygosity, respectively. Southern and more isolated populations tended to have less genetic variability than northern and less-isolated populations. A strong spatial patterning of genetic diversity was found at the various spatial scales. Gene flow/drift equilibrium occurred over distances <4 km. Beyond that distance divergence was relatively more influenced by drift. The populations studied seem to derive from three panmictic units or ‘gene pools’, with levels of admixture being greatest in the central and south-eastern portions of the species'' range.

Conclusions

In addition to documenting a case of high genetic diversity in a narrow endemic plant with naturally fragmented populations, the results emphasize the need for dense population sampling and examination of different geographical scales for understanding population genetic structure in habitat specialists restricted to ecological islands.Key words: Allozymes, genetic diversity, geographical scale, habitat isolation, Narcissus longispathus, Mediterranean endemism, mountain range, natural fragmented distribution     

Microsatellites reveal substantial among-population genetic differentiation and strong inbreeding in the relict fern Dryopteris aemula

Background and Aims

A previous study detected no allozyme diversity in Iberian populations of the buckler-fern Dryopteris aemula. The use of a more sensitive marker, such as microsatellites, was thus needed to reveal the genetic diversity, breeding system and spatial genetic structure of this species in natural populations.

Methods

Eight microsatellite loci for D. aemula were developed and their cross-amplification with other ferns was tested. Five polymorphic loci were used to characterize the amount and distribution of genetic diversity of D. aemula in three populations from the Iberian Peninsula and one population from the Azores.

Key Results

Most microsatellite markers developed were transferable to taxa close to D. aemula. Overall genetic variation was low (H_T = 0·447), but was higher in the Azorean population than in the Iberian populations of this species. Among-population genetic differentiation was high (F_ST = 0·520). All loci strongly departed from Hardy–Weinberg equilibrium. In the population where genetic structure was studied, no spatial autocorrelation was found in any distance class.

Conclusions

The higher genetic diversity observed in the Azorean population studied suggested a possible refugium in this region from which mainland Europe has been recolonized after the Pleistocene glaciations. High among-population genetic differentiation indicated restricted gene flow (i.e. lack of spore exchange) across the highly fragmented area occupied by D. aemula. The deviations from Hardy–Weinberg equilibrium reflected strong inbreeding in D. aemula, a trait rarely observed in homosporous ferns. The absence of spatial genetic structure indicated effective spore dispersal over short distances. Additionally, the cross-amplification of some D. aemula microsatellites makes them suitable for use in other Dryopteris taxa.     

Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

Background and Aims

The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest.

Methods

Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers.

Key Results

For nuclear microsatellites, allelic richness (R) and heterozygosity (H_e,nuc) differed between types of forest: R = 7·36 and R = 9·55, H_e,nuc = 0·64 and H_e,nuc = 0·80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (N_a,nuc) and the fixation index F_IS differed significantly: N_a,nuc = 9·41 and N_a,nuc = 13·18, F_IS = 0·06 and F_IS = 0·15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (F_ST,nuc = 0·08) and moderate for chloroplast microsatellites (F_ST,cp = 0·49). A clear relationship was observed between genetic and geographic distance (r = 0·42 P < 0·01 and r = 0·42 P = 0·03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations.

Conclusions

Residual diversity and genetic structure of populations of D. monticola in Madagascar suggest a limited impact of fragmentation on molecular genetic parameters.     

Rapid loss of genetic variation in a founding population of Primula elatior (Primulaceae) after colonization

Background and Aims

Land-use changes and associated extinction/colonization dynamics can have a large impact on population genetic diversity of plant species. The aim of this study was to investigate genetic diversity in a founding population of the self-incompatible forest herb Primula elatior and to elucidate the processes that affect genetic diversity shortly after colonization.

Methods

AFLP markers were used to analyse genetic diversity across three age classes and spatial genetic structure within a founding population of P. elatior in a recently established stand in central Belgium. Parentage analyses were used to assess the amount of gene flow from outside the population and to investigate the contribution of mother plants to future generations.

Results

The genetic diversity of second and third generation plants was significantly reduced compared with that of first generation plants. Significant spatial genetic structure was observed. Parentage analyses showed that <20 % of the youngest individuals originated from parents outside the study population and that >50 % of first and second generation plants did not contribute to seedling recruitment.

Conclusions

These results suggest that a small effective population size and genetic drift can lead to rapid decline of genetic diversity of offspring in founding populations shortly after colonization. This multigenerational study also highlights that considerable amounts of gene flow seem to be required to counterbalance genetic drift and to sustain high levels of genetic diversity after colonization in recently established stands.Key words: AFLP, colonization, forest regeneration, genetic diversity, genetic drift, parentage analysis, spatial genetic structure     

Population genetic structure of two Medicago species shaped by distinct life form, mating system and seed dispersal

Background and Aims

Life form, mating system and seed dispersal are important adaptive traits of plants. In the first effort to characterize in detail the population genetic structure and dynamics of wild Medicago species in China, a population genetic study of two closely related Medicago species, M. lupulina and M. ruthenica, that are distinct in these traits, are reported. These species are valuable germplasm resources for the improvement of Medicago forage crops but are under threat of habitat destruction.

Methods

Three hundred and twenty-eight individuals from 16 populations of the annual species, M. lupulina, and 447 individuals from 15 populations of the perennial species, M. ruthenica, were studied using 15 and 17 microsatellite loci, respectively. Conventional and Bayesian-clustering analyses were utilized to estimate population genetic structure, mating system and gene flow.

Key Results

Genetic diversity of M. lupulina (mean H_E = 0·246) was lower than that of M. ruthenica (mean H_E = 0·677). Populations of M. lupulina were more highly differentiated (F_ST = 0·535) than those of M. ruthenica (F_ST = 0·130). For M. lupulina, 55·5 % of the genetic variation was partitioned among populations, whereas 76·6 % of the variation existed within populations of M. ruthenica. Based on the genetic data, the selfing rates of M. lupulina and M. ruthenica were estimated at 95·8 % and 29·5 %, respectively. The genetic differentiation among populations of both species was positively correlated with geographical distance.

Conclusions

The mating system differentiation estimated from the genetic data is consistent with floral morphology and observed pollinator visitation. There was a much higher historical gene flow in M. ruthenica than in M. lupulina, despite more effective seed dispersal mechanisms in M. lupulina. The population genetic structure and geographical distribution of the two Medicago species have been shaped by life form, mating systems and seed dispersal mechanisms.Key words: Medicago lupulina, Medicago ruthenica, microsatellite, genetic diversity, gene flow, forage legume     

Range expansion of a selfing polyploid plant despite widespread genetic uniformity

Background and Aims

Ongoing and previous range expansions have a strong influence on population genetic structure of plants. In turn, genetic variation in the new range may affect the population dynamics and the expansion process. The annual Ceratocapnos claviculata (Papaveraceae) has expanded its Atlantic European range in recent decades towards the north and east. Patterns of genetic diversity were investigated across the native range to assess current population structure and phylogeographical patterns. A test was then made as to whether genetic diversity is reduced in the neophytic range and an attempt was made to identify source regions of the expansion.

Methods

Samples were taken from 55 populations in the native and 34 populations in the neophytic range (Sweden, north-east Germany). Using amplified fragment length polymorphism markers an analysis was made of genetic variation and population structure (Bayesian statistical modelling) and population differentiation was quantified. Pollen/ovule ratio was analysed as a proxy for the breeding system.

Key Results

Genetic diversity at population level was very low (mean H_e = 0·004) and two multilocus genotypes dominated large parts of the new range. Population differentiation was strong (F_ST = 0·812). These results and a low pollen/ovule ratio are consistent with an autogamous breeding system. Genetic variation decreased from the native to the neophytic range. Within the native range, H_e decreased towards the north-east, whereas population size increased. According to the Bayesian cluster analysis, the putative source regions of the neophytic range are situated in north-west Germany and adjacent regions.

Conclusions

Ceratocapnos claviculata shows a cline of genetic variation due to postglacial recolonization from putative Pleistocene refugia in south-west Europe. Nevertheless, the species has expanded successfully during the past 40 years to southern Sweden and north-east Germany where it occurs as an opportunistic neophyte. Recent expansion was mainly human-mediated by single long-distance diaspore transport and was facilitated by habitat modification.     

Evolution under domestication: ongoing artificial selection and divergence of wild and managed Stenocereus pruinosus (Cactaceae) populations in the Tehuac��n Valley, Mexico

Background and Aims

The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations.

Methods

Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations.

Key Results

Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours others than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (H_E = 0·743) was higher than in wild (H_E = 0·726) and cultivated (H_E = 0·700) populations. Most of the genetic variation (90·58 %) occurred within populations. High gene flow (Nm_FST > 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations.

Conclusions

Traditional management of S. pruinosus involves artificial selection, which, despite the high levels of gene flow, has promoted morphological divergence and moderate genetic structure between wild and managed populations, while conserving genetic diversity.     

Somatic mutations contribute to genotypic diversity in sterile and fertile populations of the threatened shrub, Grevillea rhizomatosa (Proteaceae)

Background and Aims

Grevillea rhizomatosa is a spreading shrub which exhibits multiple breeding strategies within a narrow area in the fire-prone heathlands of eastern Australia. Reproductive strategies include self-compatibility, self-incompatibility and clonality (with and without sterility). The close proximity of contrasting breeding systems provides an opportunity to explore the evolution of sterility and to compare and contrast the origins of genotypic diversity (recombinant or somatic) against degrees of sexual expression.

Methods

ISSR markers for 120 band positions (putative loci) were used to compare genetic diversity among five populations at a macro-scale of 5 m between samples (n = 244 shrubs), and at a micro-scale of nearest neighbours for all plants in five 25-m² quadrats with contrasting fertilities (n = 162 shrubs). Nearest-neighbour sampling included several clusters of connected ramets. Matrix incompatibility (MIC) analyses were used to evaluate the relative contribution of recombination and somatic mutation to genotype diversity.

Key Results

High levels of genotypic diversity were found in all populations regardless of fertilities (fertile populations, G/N ≥ 0·94; sterile populations, G/N ≥ 0·97) and most sterile populations had a unique genetic profile. Somatic mutations were detected along connected ramets in ten out of 42 ramet clusters. MIC analyses showed that somatic mutations have contributed to diversity in all populations and particularly so in sterile populations.

Conclusions

Somatic mutations contribute significantly to gene diversity in sterile populations of Grevillea rhizomatosa, the accumulation of which is the likely cause of male and female sterility. High levels of genetic diversity therefore may not always be synonymous with sexual fitness and genetic health. We hypothesize that frequent fires drive selection for clonal reproduction, at the cost of flowering such that sexual functions are not maintained through selection, and the build-up of somatic mutations in meristems results in high genotype diversity at the cost of pollen and ovule fertilities.     

Genetic connectivity and inter-population seed dispersal of Banksia hookeriana at the landscape scale

Background and Aims

Landscape genetics combines approaches from population genetics and landscape ecology, increasing the scope for conceptual advances in biology. Banksia hookeriana comprises clusters of individuals located on dune crests (geographical populations) physically separated by uninhabitable swales, with local extinctions common through frequent fire and/or severe drought.

Methods

A landscape genetics approach was used to explore landscape-scale genetic connectivity and structure among geographical populations of B. hookeriana on 18 physically separated dunes located within a heterogeneous landscape of 3 × 5 km. These geographical populations were separated by approx. 0·1 to >1 km of unsuitable intervening swale habitat. Using 11 highly variable microsatellite loci, we utilized a Bayesian approach to identify genetic discontinuities within and between these geographical populations. Population allocation tests were then used to detect inter-dune seed dispersal inferred from assignment of individuals to a source population other than that from which they were collected.

Key Results

For the modal number of genetically distinct clusters (n = 17 genetic populations), two coincided with the geographical (dune) populations, eight spanned two to four geographical populations, and the remaining seven were spread among various parts of the sampled dunes, so that most geographical populations were spatially defined mosaics of individuals (subpopulations) belonging to two or more genetic populations. We inferred 25 inter-dune immigrants among the 582 individuals assessed, with an average distance between sink and source dunes of 1·1 km, and a maximum of 3·3 km.

Conclusions

The results show that genetic structure in an apparently strongly spatially structured landscape is not solely dependent on landscape structure, and that many physically defined geographical populations were genetic mosaics. More strikingly, there were physically separated individuals and groups of individuals that were part of the same genetically defined populations. We attribute this mismatch between spatially and genetically defined population structure to the varying closeness of the dunes and the ability of seeds to disperse long distances.     

Population genetics of two asexually and sexually reproducing psocids species inferred by the analysis of mitochondrial and nuclear DNA sequences

Background

The psocids Liposcelis bostrychophila and L. entomophila (Psocoptera: Liposcelididae) are found throughout the world and are often associated with humans, food stores and habitations. These insects have developed high levels of resistance to various insecticides in grain storage systems. However, the population genetic structure and gene flow of psocids has not been well categorized, which is helpful to plan appropriate strategies for the control of these pests.

Methodology/Principal Findings

The two species were sampled from 15 localities in China and analyzed for polymorphisms at the mitochondrial DNA (Cytb) and ITS (ITS1-5.8S-ITS2) regions. In total, 177 individual L. bostrychophila and 272 individual L. entomophila were analysed. Both Cytb and ITS sequences showed high genetic diversity for the two species with haplotype diversities ranged from 0.154±0.126 to 1.000±0.045, and significant population differentiation (mean F _ST = 0.358 for L. bostrychophila; mean F _ST = 0.336 for L. entomophila) was also detected among populations investigated. A Mantel test indicated that for both species there was no evidence for isolation-by-distance (IBD). The neutrality test and mismatch distribution statistics revealed that the two species might have undergone population expansions in the past.

Conclusion

Both L. bostrychophila and L. entomophila displayed high genetic diversity and widespread population genetic differentiation within and between populations. The significant population differentiation detected for both psocids may be mainly due to other factors, such as genetic drift, inbreeding or control practices, and less by geographic distance since an IBD effect was not found.     

Investigating the effects of topography and clonality on genetic structuring within a large Norwegian population of Arabidopsis lyrata

Background and Aims

The gene flow through pollen or seeds governs the extent of spatial genetic structure in plant populations. Another factor that can contribute to this pattern is clonal growth. The perennial species Arabidopsis lyrata ssp. petraea (Brassicaceae) is a self-incompatible, clonal species found in disjunctive populations in central and northern Europe.

Methods

Fourteen microsatellite markers were employed to study the level of kinship and clonality in a high-altitude mountain valley at Spiterstulen, Norway. The population has a continuous distribution along the banks of the River Visa for about 1·5 km. A total of 17 (10 m × 10 m) squares were laid out in a north–south transect following the river on both sides.

Key Results

It is shown that clonal growth is far more common than previously shown in this species, although the overall size of the genets is small (mean diameter = 6·4 cm). Across the whole population there is no indication of isolation by distance, and spatial genetic structure is only visible on fine spatial scales. In addition, no effect of the river on the spatial distribution of genotypes was found.

Conclusions

Unexpectedly, the data show that populations of small perennials like A. lyrata can behave like panmictic units across relatively large areas at local sites, as opposed to earlier findings in central Europe.     

High clonal diversity in threatened peripheral populations of the yellow bird's nest (Hypopitys monotropa; syn. Monotropa hypopitys)

Background and Aims

Peripheral populations of plant species are often characterized by low levels of genetic diversity as a result of genetic drift, restricted gene flow, inbreeding and asexual reproduction. These effects can be exacerbated where range-edge populations are fragmented. The main aim of the present study was to assess the levels of genetic diversity in remnant populations of Hypopitys monotropa (syn. Monotropa hypopitys; yellow bird''s nest) at the edge of the species'' European range in Northern Ireland, since these remnant populations are small and highly fragmented.

Methods

Every plant found through surveys of 21 extant populations was genotyped for eight microsatellite loci to estimate levels and patterns of genetic diversity and clonality.

Key Results

Levels of genetic diversity were relatively high in the populations studied, and the incidence of clonal reproduction was generally low, with a mean of only 14·45 % of clonal individuals. Clones were small and highly spatially structured. Levels of inbreeding, however, were high.

Conclusions

The observed low levels of clonality suggest that the majority of genets in the populations of H. monotropa studied are fertile and that reproduction is predominantly sexual. As the species is highly self-compatible, it is likely that the high levels of inbreeding observed in the populations in the present study are the result of self-pollination, particularly given the small numbers of individuals in most of the patches. Given this extent of inbreeding, further genetic monitoring would be advisable to ensure that genetic diversity is maintained.     

Mixed mating in androdioecious Mercurialis annua inferred using progeny arrays and diploid-acting microsatellite loci in a hexaploid background

Background and Aims

The frequency at which males can be maintained with hermaphrodites in androdioecious populations is predicted to depend on the selfing rate, because self-fertilization by hermaphrodites reduces prospective siring opportunities for males. In particular, high selfing rates by hermaphrodites are expected to exclude males from a population. Here, the first estimates are provided of the mating system from two wild hexaploid populations of the androdioecious European wind-pollinated plant M. annua with contrasting male frequencies.

Methods

Four diploid microsatellite loci were used to genotype 19–20 progeny arrays from two populations of M. annua, one with males and one without. Mating-system parameters were estimated using the program MLTR.

Key Results

Both populations had similar, intermediate outcrossing rates (t_m = 0·64 and 0·52 for the population with and without males, respectively). The population without males showed a lower level of correlated paternity and biparental inbreeding and higher allelic richness and gene diversity than the population with males.

Conclusions

The results demonstrate the utility of new diploid microsatellite loci for mating system analysis in a hexaploid plant. It would appear that androdioecious M. annua has a mixed-mating system in the wild, an uncommon finding for wind-pollinated species. This study sets a foundation for future research to assess the relative importance of the sexual system, plant-density variation and stochastic processes for the regulation of male frequencies in M. annua over space and time.     

Conspecific crop-weed introgression influences evolution of weedy rice (Oryza sativa f. spontanea) across a geographical range

Background

Introgression plays an important role in evolution of plant species via its influences on genetic diversity and differentiation. Outcrossing determines the level of introgression but little is known about the relationships of outcrossing rates, genetic diversity, and differentiation particularly in a weedy taxon that coexists with its conspecific crop.

Methodology/Principal Findings

Eleven weedy rice (Oryza sativa f. spontanea) populations from China were analyzed using microsatellite (SSR) fingerprints to study outcrossing rate and its relationship with genetic variability and differentiation. To estimate outcrossing, six highly polymorphic SSR loci were used to analyze >5500 progeny from 216 weedy rice families, applying a mixed mating model; to estimate genetic diversity and differentiation, 22 SSR loci were analyzed based on 301 weedy individuals. Additionally, four weed-crop shared SSR loci were used to estimate the influence of introgression from rice cultivars on weedy rice differentiation. Outcrossing rates varied significantly (0.4∼11.7%) among weedy rice populations showing relatively high overall Nei''s genetic diversity (0.635). The observed heterozygosity was significantly correlated with outcrossing rates among populations (r² = 0.783; P<0.001) although no obvious correlation between outcrossing rates and genetic diversity parameters was observed. Allelic introgression from rice cultivars to their coexisting weedy rice was detected. Weedy rice populations demonstrated considerable genetic differentiation that was correlated with their spatial distribution (r² = 0.734; P<0.001), and possibly also influenced by the introgression from rice cultivars.

Conclusions/Significance

Outcrossing rates can significantly affect heterozygosity of populations, which may shape the evolutionary potential of weedy rice. Introgression from the conspecific crop rice can influence the genetic differentiation and possibly evolution of its coexisting weedy rice populations.     

The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

Background and Aims

Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants.

Methods

The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed and the G × E interactions were examined with respect to genotype-specific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus.

Key Results

WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets. These effects of virus infection differ greatly among host genotypes, representing a strong G × E interaction. Moreover, the relative fitness and associated ranking of genotypes changed significantly between control and virus treatments. This shift in relative fitness among genotypes suggests the potential for WClMV to provoke differential selection on T. repens genotypes, which may lead to negative frequency-dependent selection in host populations.

Conclusions

The apparent G × E interaction and evident repercussions for relative fitness reported in this study stress the importance of viruses for ecological and evolutionary processes and suggest an important role for viruses in shaping population dynamics and micro-evolutionary processes.     

Genetic structure of the tree peony (Paeonia rockii) and the Qinling Mountains as a geographic barrier driving the fragmentation of a large population

Background

Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers.

Methodology/Principal Findings

Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (F_ST value of 0.302). Moderate genetic diversity at the population level (H_S of 0.516) and high population diversity at the species level (H_T of 0.749) were detected. Significant excess homozygosity (F_IS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier''s maximum-difference algorithm.

Conclusions/Significance

Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of this species and for improving the genetic basis for breeding its cultivars.     

Genetic Diversity and Population Structure of Indian Golden Silkmoth (Antheraea assama)

Background

The Indian golden saturniid silkmoth (Antheraea assama), popularly known as muga silkmoth, is a semi-domesticated silk producing insect confined to a narrow habitat range of the northeastern region of India. Owing to the prevailing socio-political problems, the muga silkworm habitats in the northeastern region have not been accessible hampering the phylogeography studies of this rare silkmoth. Recently, we have been successful in our attempt to collect muga cocoon samples, although to a limited extent, from their natural habitats. Out of 87 microsatellite markers developed previously for A. assama, 13 informative markers were employed to genotype 97 individuals from six populations and analyzed their population structure and genetic variation.

Methodology/Principal Findings

We observed highly significant genetic diversity in one of the populations (WWS-1, a population derived from West Garo Hills region of Meghalaya state). Further analysis with and without WWS-1 population revealed that dramatic genetic differentiation (global F_ST = 0.301) was due to high genetic diversity contributed by WWS-1 population. Analysis of the remaining five populations (excluding WWS-1) showed a marked reduction in the number of alleles at all the employed loci. Structure analysis showed the presence of only two clusters: one formed by WWS-1 population and the other included the remaining five populations, inferring that there is no significant genetic diversity within and between these five populations, and suggesting that these five populations are probably derived from a single population. Patterns of recent population bottlenecks were not evident in any of the six populations studied.

Conclusions/Significance

A. assama inhabiting the WWS-1 region revealed very high genetic diversity, and was genetically divergent from the five populations studied. The efforts should be continued to identify and study such populations from this region as well as other muga silkworm habitats. The information generated will be very useful in conservation of dwindling muga culture in Northeast India.     

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.