Clonal diversity in a Rhododendron ferrugineum L. (Ericaceae) population inferred from AFLP markers

In the European Alps, Rhododendron ferrugineum can constitute dense populations with almost 100% of cover. The developmental pattern by layering and the resulting complexity of population structure make it difficult to identify distinct clones even by excavation. Therefore genotypic structure of a R. ferrugineum population, in the French Alps, was inferred from AFLP markers. In a first step, we analysed 400 samples using AFLP profiles generated by one selective primer pair. Seventeen bands out of 25 were polymorphic (68%). We identified a total of 32 multilocus genotypes. In a second step, the 32 genotypes were verified by applying two additional primer pairs to the two most distant samples from each genotype. The mean similarity (proportion of band sharing) between pairs of clones was 0.85 (range from 0.52 to 0.94). The spatial distribution of clones showed that vegetative spreading mainly occurred down a slope. Based on an annual shoot mean growth of 2.6 cm/year and the size of the widest clone, we estimated the age of the oldest individual to be at least 300 years. A single genotype can occupy a large surface and sometimes form a dense patch, suggesting that this species adopts a phalanx growth form with limited intermingling of some genets.     

Floral distribution,clonal structure,and their effects on pollination success in a self-incompatible <Emphasis Type="Italic">Convallaria keiskei</Emphasis> population in northern Japan

In plant species, when clonal growth produces a patchy structure and flowering ramets are clustered, the amount of pollen contributing to reproductive success is often regulated by pollinator efficiency and geitonogamy. The spatial population structure may influence reproductive success. We examined the clonal structure, the spatial ramet distribution, and their combined effects on fruit set in a natural population of the insect-pollinated, self-incompatible clonal herb, Convallaria keiskei, in northern Japan. The number of shoots, flowers, and fruits in 1-m² quadrats were counted at every 5 m grid point in an established 100 × 90-m study plot. From all the quadrats where shoots existed, leaf samples were collected for allozyme analysis. Using the two spatial parameters of flowering ramet densities and genotypes, we then constructed individual-based fruit-set models. A total of 236 quadrats contained shoots, and 135 contained flowering ramets, which indicated expanded distribution of this plant throughout the study plot, while shoots, flowers and fruits all showed clustering distributions. Allozyme analysis of 282 samples revealed 94 multilocus genotypes. The largest clone extended to more than 40 m, whereas 56 genotypes were detected in only one sample. Several large clones and many small clones were distributed close to each other. Fine-scale spatial modelling revealed that the neighbouring flower numbers of different genotypes, compared with local genet or flower diversity, more influenced fruit set, in which the range of the neighbour was 14.5 m. These findings indicate that the compatible pollen dispersed by insect pollinators has a significant effect on sexual reproduction, in this C. keiskei population. Consequently, the spatial structure, which includes both genet distribution and clonal expansion by ramets, had a significant effect on pollination success.     

Genetic diversity among Brazilian isolates of Beauveria bassiana: comparisons with non-Brazilian isolates and other Beauveria species

Aims:  The genetic diversity of Beauveria bassiana was investigated by comparing isolates of this species to each other (49 from different geographical regions of Brazil and 4 from USA) and to other Beauveria spp.
Methods and Results:  The isolates were examined by multilocus enzyme electrophoresis (MLEE), amplified fragment length polymorphism (AFLP), and rDNA sequencing. MLEE and AFLP revealed considerable genetic variability among B. bassiana isolates. Several isolates from South and Southeast Brazil had high similarity coefficients, providing evidence of at least one population with clonal structure. There were clear genomic differences between most Brazilian and USA B. bassiana isolates. A Mantel test using data generated by AFLP provided evidence that greater geographical distances were associated with higher genetic distances. AFLP and rDNA sequencing demonstrated notable genotypic variation between B. bassiana and other Beauveria spp.
Conclusion:  Geographical distance between populations apparently is an important factor influencing genotypic variability among B. bassiana populations in Brazil.
Significance and Impact of the Study:  This study characterized many B. bassiana isolates. The results indicate that certain Brazilian isolates are considerably different from others and possibly should be regarded as separate species from B. bassiana sensu latu . The information on genetic variation among the Brazilian isolates, therefore, will be important to comprehending the population structure of B. bassiana in Brazil.     

毛乌素沙地中国沙棘无性系生长调节

根据无性系跟踪挖掘资料。分析了毛乌素沙地中国沙棘无性系生长调节规律,结果表明,无性系分株群（同一无性系所有分株的集合）结构由增长型发展到稳定型,最后演变成衰退型,在衰退过程中或其后的一段时间内,无性系能够通过分株出生调节使分株群结构（年龄和高度级）恢复到稳定型,在分株群结构变化的同时,种群通过分株的死亡调节不断改变着分株的克隆生长型,提高了无性系 种群的持久性以及对空间和资源的利用率。     

Dynamics of genotypic structure in clonal Rhododendron ferrugineum (Ericaceae) populations

Two populations of Rhododendron ferrugineum growing at subalpine level in the Pyrenees (France) were studied in two sites (Bethmale and Mourtis). Identification and delimitation of genets were inferred from amplified fragment length polymorphism (AFLP) markers, along a closure gradient (from meadow to more closed heath) in each site. Surface and age of genets, genotypic diversity (Simpson's index D), 'proportion distinguishable' genotypes and genetic relationships between genets were then estimated. Amplification of the 312 DNA samples with three selective primer pairs gave a mean of 98 detectable peaks (i.e. bands) per sample, with size ranging from 60 to 300 bp. In total 60% (Bethmale) and 70% (Mourtis) of the peaks were polymorphic, and a total of 31 and 23 multilocus genotypes were identified, in Bethmale and Mourtis, respectively. We inferred that pioneer genotypes began arriving 110 years ago mainly over a 40-year period in the Mourtis meadow, and began about 130 years ago over a 100-year period in the Bethmale meadow. After this pioneer stage, populations extended vegetatively. Two different patterns of genotypic dynamics can be identified. At Bethmale, population closure could have led to a dramatic loss of genets and to the selection of highly genetically related genotypes. In contrast, at Mourtis, genotypic diversity and genet density did not change fundamentally along the closure gradient. However the range of genetic diversity diminished from the open to the closed situation, suggesting that thinning could have occurred in the past.     

Point pattern analysis of Phyllostachys bissetti ramet population in West China Rainy Area

In this paper, point pattern analysis was conducted to study the spatial distribution of Phyllostachys bissetii ramet population and the spatial association between different age-class P. bissetii ramet populations in West China Rainy Area. The ramet population had a clumped distribution at the scale 0-0.32 m, a regular distribution at the scale 0.64-4.48 m, and a random distribution at the scale > 4.48 m. Different age-class ramet populations mainly had a random distribution at the scale 0-8.00 m, though a slight difference was observed among different age-classes. The spatial association between age-class I and age-classes II and III at the scale 1.76 - 4.16 m and 0.32-4.16 m approached to or reached to negative, respectively, while the spatial association between age-classes I and IV at the scale 0.32-3.04 m was significantly negative, indicating that the spatial negative association between younger and elder ramet populations increased with enlarged age-class difference. The spatial pattern of P. bissetii ramet population and the spatial association between different age-class ramet populations were depended on spatial scale, ramet age, and environmental factors.     

华西雨屏区白夹竹分株种群的点格局分析

采用点格局分析方法对华西雨屏区白夹竹分株种群的分布格局以及不同龄级分株之间的相互关系进行分析.结果表明：白夹竹分株种群在0～0.32 m空间尺度上呈集群分布,0.64～4.48 m空间尺度上呈均匀分布,>4.48 m空间尺度上呈随机分布.各龄级分株种群在0～8.00 m空间尺度上主要呈随机分布,龄级间略有差别.其中,Ⅰ龄级与Ⅱ、Ⅲ龄级分别在1.76～4.16 m、0.32～4.16 m尺度上接近或达到空间负关联,与Ⅳ龄级在0.32～3.04 m尺度上呈显著空间负关联,表现为随着龄级差距的加大,幼龄分株与高龄级分株的空间负关联增加.白夹竹分株种群的空间格局及不同龄级分株之间的相互关系由尺度、分株龄级及环境因素共同决定.     

Regulation of clonal growth and dynamics of Panicum virgatum (Poaceae) in tallgrass prairie: effects of neighbor removal and nutrient addition

Clones of the perennial grass Panicum virgatum were studied on the Konza Prairie in northeast Kansas to determine the effects of neighbors, nutrient availability, and physiological integration on ramet population dynamics and clonal growth and architecture. Opposite halves of established clones in the field were subjected differentially to treatments including neighbor removal and nitrogen addition, with intact or severed rhizome connections between halves. Neighborhood competition strongly influenced clone architecture and expansion rates. Removal of neighbors resulted in a >;95% increase in radial clone expansion, intraclonal ramet densities, ramet population growth rates, ramet biomass, and percent of stems flowering, averaged over a 4-year period relative to halves or clones with intact competitors. Plant responses suggest that effects of interclonal neighbors are mediated through alteration of the light environment in the clone canopy and water availability. Addition of nitrogen did not affect lateral spread or clone structure, but resulted in significant increases in ramet size, flowering, and seed production. ANOVA revealed no significant effect of rhizome severing or treatment × severing interactions, suggesting that the size of the integrated physiological unit is much smaller than clone size and/or that physiological integration had no effect on clone responses to environmental heterogeneity at the scale of the diameter of established clones.     

A new individual-based spatial approach for identifying genetic discontinuities in natural populations

The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of populations made by adopting an individual-centred approach. Our method is based on assignment tests applied in a moving window over an extensively sampled study area. For each individual, a spatially explicit probability surface is constructed, showing the estimated probability of finding its multilocus genotype across the landscape, and identifying putative migrants. Population boundaries are localized by estimating the mean slope of these probability surfaces over all individuals to identify areas with genetic discontinuities. The significance of the genetic discontinuities is assessed by permutation tests. This new approach has the potential to reveal cryptic population structure and to improve our ability to understand gene flow dynamics across landscapes. We illustrate our approach by simulations and by analysing two empirical datasets: microsatellite data of Ursus arctos in Scandinavia, and amplified fragment length polymorphism (AFLP) data of Rhododendron ferrugineum in the Alps.     

EcoGenetics: An R package for the management and exploratory analysis of spatial data in landscape genetics

The integration of ecology and genetics has become established in recent decades, in hand with the development of new technologies, whose implementation is allowing an improvement of the tools used for data analysis. In a landscape genetics context, integrative management of population information from different sources can make spatial studies involving phenotypic, genotypic and environmental data simpler, more accessible and faster. Tools for exploratory analysis of autocorrelation can help to uncover the spatial genetic structure of populations and generate appropriate hypotheses in searching for possible causes and consequences of their spatial processes. This study presents EcoGenetics, an R package with tools for multisource management and exploratory analysis in landscape genetics.     

Investigation of Germplasm Resources of the Genus Rhododendron in Baili Nature Reserve in Guizhou

In this study, we investigated Rhododendrons in Baili Rhododendron nature reserve and recorded species and detailed information of their distributions. A total of 33 species belonging to 6 subgenus, 4 sections and 11 subsecions were observed and the altitudes were ranging from 1300m to 1800m. In general, most Rhododendron species grew together in their typical habitats whereas a few species occurred fragmentally. In addition, we evaluated the conservation status of these 33 Rhododendron species. On the basis of available information, we addressed some problems taking into account the population structure and development of tourism, and suggestions regarding conservation and utilization of Rhododendrons were finally proposed.     

Genetic structure of Rhododendron ferrugineum at a wide range of spatial scales

Rhododendron ferrugineum L. (Ericaceae) is a subalpine shrub found throughout the Pyrenees and Alps at elevations of 1600-2200 m. We examined relationships between genetic and geographic distance, using 115 dominant amplified fragment length polymorphism (AFLP) markers to assess genetic structure over a wide range of spatial scales. We sampled 17 sites with distances of 4 km to more than 1000 km between them. At these scales we detected no association between geographic distance and genetic distance between populations. This suggests that genetic drift and gene flow are not in equilibrium for these populations. This pattern could have resulted from recent and rapid postglacial colonization, from more recent human disturbance, or as a function of frequent and random "natural" long-distance colonization. At two of our sites we used transects (two horizontal and two vertical with respect to slope at each site) to sample at distances ranging from 10 m to more than 5000 m. At this scale we observed a positive relationship between genetic and spatial distance along two vertical transects, one at each site. We hypothesize that isolation-by-distance at this smaller scale is a function of restricted gene flow via seed dispersal.     

Clonal genetic structure and diversity in populations of an aquatic plant with combined vs. separate sexes

Clonality is often implicated in models of the evolution of dioecy, but few studies have explicitly compared clonal structure between plant sexual systems, or between the sexes in dioecious populations. Here, we exploit the occurrence of monoecy and dioecy in clonal Sagittaria latifola (Alismataceae) to evaluate two main hypotheses: (i) clone sizes are smaller in monoecious than dioecious populations, because of constraints imposed on clone size by costs associated with geitonogamy; (ii) in dioecious populations, male clones are larger and flower more often than female clones because of sex‐differential reproductive costs. Differences in clone size and flowering could result in discordance between ramet‐ and genet‐based sex ratios. We used spatially explicit sampling to address these hypotheses in 10 monoecious and 11 dioecious populations of S. latifolia at the northern range limit in Eastern North America. In contrast to our predictions, monoecious clones were significantly larger than dioecious clones, probably due to their higher rates of vegetative growth and corm production, and in dioecious populations, there was no difference in clone size between females and males; ramet‐ and genet‐based sex ratios were therefore highly correlated. Genotypic diversity declined with latitude for both sexual systems, but monoecious populations exhibited lower genotypic richness. Differences in life history between the sexual systems of S. latifolia appear to be the most important determinants of clonal structure and diversity.     

CLONE STRUCTURE IN FOUR SOLIDAGO ALTISSIMA (ASTERACEAE) POPULATIONS: RHIZOME CONNECTIONS WITHIN GENOTYPES

We studied clone structure and degree of genotypic mixing of Solidago altissima L. (Asteraceae) clones in four old fields near Ithaca, New York. The fields differed in time from agricultural abandonment and were approximately 1, 5, 20, and 35 years old. In the three older fields, three 0.75 m² plots were excavated intact and rhizome connections among ramets were mapped. In the youngest field 30 ramets were dug up singly. The genotype of all ramets was determined using electrophoresis of four polymorphic enzyme systems. Fields differed in the number and dispersion of genotypes within plots, and the degree of connection among ramets in the same clone. The one-year-old field was composed of single ramet genotypes which had probably established from seed the previous year. The five-year-old field contained many small contiguous clones of S. altissima with highly interconnected ramets. In the oldest two fields clones were highly intermixed and ramets of the same genotype were not extensively interconnected. These results demonstrate that clones of S. altissima display considerable phenotypic variability between fields and patterns of clone development may differ. The causes of this variability remain to be identified. We suggest that either selection for different genotypes or changing habitat conditions during succession may lead to changes in clone form.     

Clonal Diversity and Fine‐scale Genetic Structure in a High Andean Treeline Population

Clonal propagation becomes more abundant with increasing altitudes as environmental conditions worsen. To date, little attention has been paid to the way in which clonal propagation affects genetic diversity and the fine‐scale spatial genetic structure (FSGS) of clonal alpine trees. An AFLP study was undertaken to quantify the clonal and genetic diversity and FSGS of the vulnerable treeline species Polylepis reticulata in Ecuador. We successfully genotyped 32 and 75 ramets within 4 m × 100 m (coarse scale) and 4 m × 4 m (fine scale) transects of one population, respectively. Higher genotypic diversity was detected at the coarse scale than at the fine scale, while lower genetic diversity was detected for P. reticulata than other Polylepis spp. at both scales. Significantly stronger FSGS was detected at the ramet level than the genet level for P. reticulata within a spatial distance of 3 m. The studied P. reticulata population showed pronounced FSGS (Sp = 0.012 at the genet level, a statistic reflecting declining pairwise kinship with distance) revealed restricted gene dispersal, which implies restricted seed dispersal for this population, assuming pollen flow is as extensive as that described for other wind‐pollinated tree species. Our results revealed that clonal diversity is a function of both sample size and the spatial scale of the sampling area. The findings highlights that clonal propagation has affected FSGS within a spatial distance of 3 m for this species.     

Genetic Diversity and Ecological Success of Staphylococcus aureus Strains Colonizing Humans

The genetic determinants and phenotypic traits which make a Staphylococcus aureus strain a successful colonizer are largely unknown. The genetic diversity and population structure of 133 S. aureus isolates from healthy, generally risk-free adult carriers were investigated using four different typing methods: multilocus sequence typing (MLST), amplified fragment length polymorphism analysis (AFLP), double-locus sequence typing (DLST), and spa typing were compared. Carriage isolates displayed great genetic diversity which could only be revealed fully by DLST. Results of AFLP and MLST were highly concordant in the delineation of genotypic clusters of closely related isolates, roughly equivalent to clonal complexes. spa typing and DLST provided considerably less phylogenetic information. The resolution of spa typing was similar to that of AFLP and inferior to that of DLST. AFLP proved to be the most universal method, combining a phylogeny-building capacity similar to that of MLST with a much higher resolution. However, it had a lower reproducibility than sequencing-based MLST, DLST, and spa typing. We found two cases of methicillin-resistant S. aureus colonization, both of which were most likely associated with employment at a health service. Of 21 genotypic clusters detected, 2 were most prevalent: cluster 45 and cluster 30 each colonized 24% of the carrier population. The number of bacteria found in nasal samples varied significantly among the clusters, but the most prevalent clusters were not particularly numerous in the nasal samples. We did not find much evidence that genotypic clusters were associated with different carrier characteristics, such as age, sex, medical conditions, or antibiotic use. This may provide empirical support for the idea that genetic clusters in bacteria are maintained in the absence of adaptation to different niches. Alternatively, carrier characteristics other than those evaluated here or factors other than human hosts may exert selective pressure maintaining genotypic clusters.     

Microspatial population genetic structure of the Mediterranean shrub Fumana thymifolia

Fumana thymifolia (Cistaceae) is an insect-pollinated, gravity-dispersed evergreen shrub, which is a common component of fire-prone Mediterranean shrubland ecosystems. Despite the availability of basic knowledge on its ecology, little is known of its breeding system and no information is available on its population genetic structure. We explored the within-population genetic structure of this species using amplified fragment length polymorphism (AFLP) molecular markers and related this to predictions based on its breeding system, pollen and seed dispersal. Existing information on the reproductive ecology of F. thymifolia was supplemented by artificial pollination experiments. We determined that self-fertilisation can occur in F. thymifolia but results in reduced fruit set. Significant genetic structuring was detected within the population, a likely consequence of localised seed dispersal in combination with a mixed mating system. In a study site covering approximately 0.5 ha, amova revealed that approximately 9% of genetic variability was distributed among population subsamples. Significant spatial genetic structure was detected, with kinship coefficients being significantly elevated above the null expectation in the first six distance classes (maximum 5 m), and a value of Sp of up to 0.0342, comparable with species having similar ecological characteristics. Weak isolation by distance at the plot scale was detected, suggesting that insect-mediated pollen flow is non-random, despite being more extensive than seed dispersal. Fumana thymifolia provides a promising model for the investigation of both short- and long-term population dynamics in relation to fire frequency within this plant community.     

松嫩平原栽培条件下羊草无性系构件的结构

羊草是长根茎型禾草,是典型的无性系植物,在松嫩平原的生长季末期,栽培条件下羊草无性系分株由分蘖株和分蘖苗组成,在具有充分生长空间而又没有种间竞争的风沙土上,羊草分株的分蘖节在一个生长季内可以繁殖4个世代,按分蘖节的繁殖世代划分龄级,现实与潜在无性系构件的年龄谱均以1龄级比重最大,随着龄级的增加明显减少,呈增长型的年龄结构,羊草无性系分株的生产力主要与分株形成及生长的时间长短有关,形成时间越早、生长时间越长的分蘖株对无性系的物质生产和营养繁殖的贡献越大,羊草无性系在空间扩展与物质贮存上具有一定的可调节性。     

伊犁特克斯河河岸带镰叶锦鸡儿灌丛分株结荚特征

以伊犁特克斯河河岸带阶地和河漫滩两种生境镰叶锦鸡儿(Caragana aurantiaca)灌丛为对象,研究了结荚数量、重量、荚果大小与灌丛分株高度、分枝数量、丛径等指标的关系,探讨了荚果生产过程在种群更新中的作用。结果表明,阶地中的镰叶锦鸡儿荚果数量、荚果长度和荚果生物量显著高于河漫滩,而有性繁殖分配和单个荚果重显著低于河漫滩。荚果数量和荚果生物量大小分布特征较一致,均呈现L型分布格局,符合gamma分布,集中于0~20枚和0~0.5 g。单荚重在两个生境符合对数-正态分布,集中于10~30 mg。两种生境荚果大小变异性主要由大个体引起。标准主轴回归分析表明,除河漫滩生境的荚果生物量与分株高的回归方程未达到显著水平之外,荚果数量、荚果重与分株高、分枝数、丛径的回归方程均达到显著水平。不论荚果数量还是荚果重,在两种生境中的斜率大小顺序均遵循分株高>丛径>分枝数的变化规律,其中分株高和丛径的斜率差异不明显,但均显著大于分枝数。两种生境镰叶锦鸡儿均可产生大量的荚果,在阶地中倾向于产生大量、小的荚果,河漫滩倾向于产生少、大的荚果,种群更新不存在种源限制,生产管理中应注意增加灌丛高度和丛径,提高结荚量,促进种群的自我更新和维持。     

Modelling the morphological response to nutrient availability in the clonal plant Trientalis europaea L.

The morphological responses to changes in environmental quality shown by many clonal plants have been interpreted as an expression of foraging behaviour, as they allow the ramets to become concentrated in more favourable microhabitats. The morphological response to increased nutrient availability in the pseudoannual plant Trientalis europaea was studied in a field experiment. The response was largely size-dependent and consistent with enhanced clonal growth. Fertilized ramets produced more tubers and a larger main tuber. In contrast, stolon length was not affected by the treatment. A spatially explicit simulation model calibrated with data from the field experiment examined the population dynamics of T. europaea ramets in a spatially hetereogeneous, temporally constant, environment. The model showed that T. europaea was effective at concentrating its ramets in favourable patches, but this process was strongly influenced by patch size. The analysis of this response at the clone level showed that ramet aggregation was mainly due to the enhanced performance of clones located initially in the favourable patches, or clones that located a favourable patch by chance. In these clones, the simultaneous increase of ramet size and survival accelerated the production of ramets. The temporal and spatial scale at which the aggregation of ramets in favourable patches was manifested suggests that the effectiveness of the morphological response in T. europaea is favoured by a high spatio-temporal predictability in the environment. Overall, the model emphasized the important role of population dynamics in understanding the nature of the foraging response.