Genetic relatedness and genetic diversity of ornamental mei (Prunus mume Sieb. et Zucc.) as analysed by AFLP markers

The genetic diversity and genetic relatedness of mei (Prunus mume; 2n = 16) were studied using amplified fragment length polymorphism (AFLP) markers. Eight EcoRI–PstI AFLP primer combinations were applied to 121 distinct genotypes of mei cultivars and related species. A total of 508 AFLP product bands were produced, of which 382 were polymorphic. The unweighted pair group method with arithmetic averages analysis was carried out based on these AFLP markers. From this analysis, “Qugeng Mei,” “Yan Mei,” “Chaodou Mei,” and mei cultivars were seen to share the same P. mume genetic stem. The AFLP data were able to clearly discriminate P. mume from other species in the genus Prunus, with P. armeniaca aligning as its closest related species. Two major groups and nine subgroups of mei flower were identified, and there was a strong coincidence of these AFLP-based groupings with the respective morphological characters of the accessions. The genetic diversity of mei accessions was greatest in the Yunnan Province and decreased toward Eastern China and Japan, so supporting the hypothesis that the southwest of China represents the genetic diversity center of the species.     

Coexistence of congeneric spiny lobsters on coral reefs: differences in conspecific aggregation patterns and their potential antipredator benefits

Den sharing by conspecific spiny lobsters (aggregation) is modulated by chemical attraction but may confer several, not necessarily mutually exclusive, antipredator byproduct benefits: a “guide effect”, which only benefits the individual attracted to a sheltered conspecific; a “dilution effect”, which reduces per-capita risk of predation simply through aggregation; or active “group defense”. Each potential benefit has a different set of predictors (relationships between aggregation and conspecific or predator densities), but conflicting results could suggest the simultaneous operation of more than one benefit. These predictions were tested for coexisting Panulirus guttatus (a reef-obligate) and Panulirus argus (a temporary reef-dweller) using data collected during 11 surveys on fixed sites over a coral reef in Mexico. P. guttatus greatly outnumbered P. argus, but P. argus showed a greater tendency to aggregate. All three benefits of den sharing operated for the more social P. argus, with “group defense” being of the most benefit for larger individuals, and the “guide” and “dilution” effects for smaller individuals recently immigrating into the reef habitat and sharing dens with larger conspecifics. P. guttatus did not display “group defense” and its aggregations appeared to be modulated by the interplay between attraction and aggressive behaviors. This species relied more on solitary crypticity, especially at larger sizes, but appeared to benefit from a “guide effect” at high conspecific densities. In experimental tanks, each species tended to aggregate when tested separately, but when tested jointly, aggregation among P. guttatus was significantly reduced. The experimental results reflect the differential patterns of aggregation between the fore-reef, where P. guttatus dominated, and the back-reef, where coexistence of both species was greater.     

人为干扰对栲树次生林群落物种多样性和土壤理化性质的影响

为探究人为干扰对栲树群落的影响,采用典型样地法研究不同程度人为干扰对碧峰峡栲树(Castanopsis fargesii)次生林群落的物种多样性和土壤理化性质的影响。结果表明,碧峰峡栲树群落共有维管植物148种,隶属60科106属。乔木层和草本层物种多样性指数随干扰强度的加强先增加后减小,灌木层物种多样性水平最高。乔木层优势种以栲树、杉木(Cunninghamia lanceolata)等为主,灌木层物种丰富,优势种较多,草本层优势种数量为中度干扰轻度干扰重度干扰。土壤有机碳、钾含量和含水量与群落物种多样性水平显著相关(P0.05)。中度干扰在一定程度上能够促进碧峰峡栲树群落物种多样性并改善土壤性质,土壤有机碳、钾含量和含水量对物种多样性有显著影响。     

Footnote on Breeding of Paradise Flycatcher

Bird community diversity was assessed in semi-arid savanna in the Northern Cape province of South Africa and related to vegetation diversity and foliage height diversity. As this is an area in which shrub encroachment is common, the effects of shrub or bush encroachment on bird species diversity were specifically addressed. An experiment in which the dominant encroaching species, Acacia mellifera, was removed from ten 1 ha plots was used and compared with ten controls. A strong positive association with foliage height diversity was shown. No effect of experimental removal of the dominant encroacher, A. mellifera, on bird species diversity or species richness was found. However, four species increased in relative abundance in cut plots and two species decreased in relative abundance in these plots.     

Plant population and community responses to removal of dominant species in the shortgrass steppe

Question: What are the plant population‐ and community‐level effects of removal of dominant plant species in the shortgrass steppe? Location: The Shortgrass Steppe Long‐Term Ecological Research site in northern Colorado, USA. Methods: We annually measured plant cover and density by species for 10 years after a one‐time aboveground removal of the dominant perennial grass, Bouteloua gracilis. Removal and control plots (3 m × 3 m) were within grazed and ungrazed locations to assess the influence of grazing on recovery dynamics. Our analyses examined plant species, functional type, and community responses to removal, paying special attention to the dynamics of subdominant and rare species. Results: Basal cover of B. gracilis increased by an average of 1% per year, but there was significantly less plant cover in treatment compared to control plots for 5 years following removal. In contrast to the lower cover in treatment plots, the plant density (number of plants m^?2) of certain subdominant perennial grasses, herbaceous perennial and annual forbs, a dwarf shrub, and cactus increased after removal of the dominant species, with no major change in species richness (number of species per 1 m × 1 m) or diversity. Subdominant species were more similar between years than rare species, but dominant removal resulted in significantly lower similarity of the subdominant species in the short term and increased the similarity of rare species in the long term. Conclusions: Removal of B. gracilis, the dominant perennial grass in the shortgrass steppe, increased the absolute density of subdominant plants, but caused little compensation of plant cover by other plants in the community and changes in species diversity.     

Edge effects created by clear-cutting on habitat use by sika deer on Mt. Goyo,northern Honshu,Japan

Clear-cutting increased the species diversity and amount of undergrowth plants in a habitat of Sika deer (Cervus nippon) on Mt. Goyo, northern Japan. The number of species increased from 15 to 48 as a result of clear-cutting. Among the plants,Sasa nipponica (a dwarf bamboo), an important forage plant for Sika deer, was predominant. Fecal pellets of deer were abundant in the forest and at the “adjacent zone” (from the edge to 150 m out of the forest) and thereafter decreased suddenly. The intensity of utilization ofSasa nipponica was also heavy in the forest, moderate at the adjacent zone and light 200 m from the forest edge. Since the amount of the bamboo in the forest was small, the removal of bamboo was greatest at the adjacent zone. Clear-cutting creates a favorable feeding area for Sika deer in this zone by increasing the available plant production and securing forest cover.     

牛洛河自然保护区东京龙脑香林群落特征研究

东京龙脑香(Dipterocarpus retusus)是国家I级重点保护野生植物,是东南亚热带雨林的标志性树种,目前有关该群落学的研究尚处于空白。该研究通过实地踏查,采用典型选样法布设4个30 m×30 m的群落样地、20个10 m×10 m的种群样方,记录样地内的物种及其株高、胸径、数量,群落特征等,并通过分布区类型划分、群落物种多样性分析及种群年龄结构划分等方法,分析了东京龙脑香林群落学与种群学特征。结果表明:(1)样地中共记录种子植物181种,隶属76科143属,其中热带性质科有58科、热带性质属有126属、热带性质种有162种,科、属、种热带成分比例分别为76.32%、88.11%、89.50%,表明该群落具有强烈的热带性质。(2)该群落物种多样性指数整体较高,多样性指数(d_(Ma)、H')在群落不同层次中均表现为灌木层乔木层草本层的特征;均匀度指数(J_(sw))在不同层次中比较接近;优势度指数(D)表现为草本层乔木层灌木层。(3)从乔木层重要值来看,东京龙脑香的最大,为26.85,显示出绝对的优势,是该群落的优势种、建群种。(4)该种群年龄结构为正金字塔型,表明该种群处于增长时期,为增长型种群。     

Native and invasive plant interactions in wetlands and the minimal role of invasiveness

The effects of invasive plants on plants native to areas that are being invaded can be quite variable, depending on the species of the invasive plant involved as well as the physical characteristics of the location being invaded. My study focuses on the effects of Phragmites australis Linnaeus (common reed) and Lythrum salicaria L. (purple loosestrife) on the same native plant community. Uninvaded plots dominated by native plants Typha angustifolia L. (narrowleaf cattail) and Typha latifolia L. (broadleaf cattail) served as the control. I surveyed percent cover of species during early summer and midsummer for 3 years in six Hudson River freshwater tidal wetlands (sites). Differences in species richness, composition and abundance were small, but significant among invaded and uninvaded plots and among sites. However, these differences remained significant when data for dominant species (invasive and native) were removed. Differences in native plant species abundance were attributed to invasive plant species-specific characteristics and differences in species richness and composition were attributed to physical location (zonation) in these freshwater tidal marshes. “Invasive” status of a dominant plant species was less important in invasive plant–native plant interactions than species-specific characteristics and zonation. Further research into the effects of site and land-use on invasive plant impacts is recommended.     

The relative importance of sexual reproduction versus clonal spread in an aridland bunchgrass

Festuca idahoensis (Idaho fescue) is a perennial caespitose grass, common in semi-arid rangelands of the Intermountain West. To determine how individuals are recruited into a population, we studied two long-term monitoring plots that were established in 1937 at the Northern Great Basin Experimental Range in southeastern Oregon. The plots measured 3.05×3.05 m, and were located approximately 30 m apart. One plot was ungrazed, the other was subject to moderate levels of cattle grazing. The number of F. idahoensis plants in both plots increased ten-fold between 1937 and 1996, but whether this was due primarily to reproduction by seed or clonal fragmentation was unknown. In 1996, we mapped and sampled 160 plants of F. idahoensis. We used dominant inter-simple sequence repeat (ISSR) markers and codominant allozyme markers in order to identify genetic individuals and measure genetic diversity. Both plots were characterized by high levels of genetic and clonal diversity. When information from ISSRs, allozymes and sample location were combined, 126 genets were recognized, each consisting of one to four samples (ramets). By measuring the diameter of clones surrounding plants that were present in 1937, we estimated that clonal spread occurred at a rate of approximately 3.7 cm per decade, and thus was of secondary importance in the maintenance and increase of F. idahoensis stands. Sexual reproduction, rather than clonal fragmentation, accounted for most of the recruitment of new plants into these plots. The grazed plot had fewer ramets, genotypes, and clones than the ungrazed plot, but the ramets were significantly larger. Levels of genetic diversity did not differ in the grazed and ungrazed plots, but there was some evidence for a small, but significant level of genetic differentiation between the two. The results also indicate that F. idahoensis has the potential to be a long-lived species with some individuals persisting in excess of 60 years. This study demonstrates how long-term monitoring can be supplemented by genetic analysis to obtain detailed information on the population dynamics of plants. In the case of this community dominant species, this provides essential information for understanding succession and developing management and restoration strategies.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00442-003-1332-2     

Indicators for plant species richness in pine (<Emphasis Type="Italic">Pinus sylvestris</Emphasis> L.) forests of Germany

Forestry is obliged to record as well as maintain and/or enhance biological diversity in forests due to national and international agreements. Accordingly, it is necessary to work out methodological approaches for the assessment of biodiversity in forests. In the study presented here, we focus on the total plant species pool (563 vascular plant and bryophyte species) of pine (Pinus sylvestris L.) forests in NE Germany to identify indicators for plant species richness. We distinguished several groups like “herb”, “grass-like”, “woody”, “endangered”, and “exotic species”, for which we detected indicators for low (class #1), intermediate (class #2), and high (class #3) species numbers. From a total of 84 species, which were identified by a three-step procedure, most indicators were found for class #3. Only few indicators have been revealed for intermediate species numbers, i.e. class #2. With help of Ellenberg’s ecological indicator values and information on the main occurrence in Central European vegetation types and plant communities, respectively, we characterized the indicator species ecologically. The ecological site preferences of the indicator species in general reflect the fact that species richness is highest in base-rich, light, and anthropogenically disturbed pine forests. On the contrary, species-poor forests were revealed by indicators, which mainly occur on acidic sites. It is concluded that a considerable set of indicators for species richness can help facilitate biodiversity assessments in forestry and ecosystem restoration practice. Electronic Supplementary Material  The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Response of reed community to the environment gradient-water depth in the Yellow River Delta, China

We investigated and monitored a reed community in the fields. Data on the bio-ecological characteristics and β-diversity of reed communities in different environmental gradients (mainly based on water depth) of the Yellow River Delta were collected through multianalysis, extremum analysis and β-diversity index analysis. In accordance with the square sum of deviations (Ward) cluster analysis, 10 sampling plots were divided into six types with the dominant plants in different plots varying according to the change in environmental gradients. The dominant plants in these plots varied from aquatic plants to xerophytes and salt tolerant plants as water depth decreased. The average height and diameter of the reeds at breast level were significantly correlated with the average water depth. The fitness curves of average density and coverage with average water depth were nonlinear. When the average water depth was 0.3 m, the average density and coverage of reeds reached the apex value, while the height and diameter of the reeds at breast level increased with the water depth. There were obvious changes to the environmental gradient in the Yellow River Delta. The transitional communities were also found to exist in the Yellow River Delta by β-diversity analysis. Vicarious species appeared with the change in water depth. The occurrence of substitute species is determined by the function of common species between adjacent belts. The different functions of common species led to differences in community structure and function and differences in dominant plants. The result reflects the variations of species present in different habitats and directly reflects environmental heterogeneity. The values of β-diversity indices of adjacent plots were higher than those of nonadjacent plots. There are transition zones between the xerophytes and aquatic plants in the Yellow River Delta. In an aquatic environment, the similarity of reed community is higher than that of xeromorphic plants. The β-diversity index can reflect plant succession trends caused by the change in environmental gradients in the Yellow River Delta. The β-diversity index reveals plant responses to changes in environmental gradient and is helpful in observing changes in patterns of species diversity in relation to environmental gradient change and evolving trends in the future, which in turn plays a prominent role when environmental water requirements of wetland are discussed. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1533–1541 [译自: 生态学报]     

Culturable Fungi of Stored ‘Golden Delicious’ Apple Fruits: A One-Season Comparison Study of Organic and Integrated Production Systems in Switzerland

The effects of organic and integrated production systems on the culturable fungal microflora of stored apple fruits from five matched pairs of certified organic and integrated ‘Golden Delicious’ farms were studied at five representative production sites in Switzerland. Isolated fungi were identified morphologically. Colonization frequency (percentage of apples colonized), abundance (colony numbers), and diversity (taxon richness) were assessed for each orchard. The standard quality of the stored fruits was comparable for both organic and integrated apples and complied with national food hygiene standards. Yeasts (six taxa) and the yeast-like fungus Aureobasidium pullulans were the dominant epiphytes, filamentous fungi (21 taxa) the dominant endophytes. The most common fungi occurred at all sites and belonged to the “white” and “pink” yeasts, yeast-like A. pullulans, filamentous fungi Cladosporium spp., Alternaria spp., and sterile filamentous fungi. Canonical correspondence analysis of the total fungal community revealed a clear differentiation among production systems and sites. Compared to integrated apples, organic apples had significantly higher frequencies of filamentous fungi, abundance of total fungi, and taxon diversity. The effects of the production system on the fungal microflora are most likely due to the different plant protection strategies. The incidence of potential mycotoxin producers such as Penicillium and Alternaria species was not different between production systems. We suggest that higher fungal diversity may generally be associated with organic production and may increase the level of beneficial and antagonistically acting species known for their potential to suppress apple pathogens, which may be an advantage to organic apples, e.g., in respect to natural disease control.     

金佛山方竹经营对扁刺栲群落物种多样性和优势种种群结构的影响

为探讨金佛山方竹经营对扁刺栲群落物种多样性和优势种种群结构的影响,该研究以金佛山的扁刺栲自然群落和金佛山方竹经营群落为对象,分析了两类群落的物种组成特征、物种多样性及优势种种群结构。结果表明:(1)两种群落内共记录维管束植物84种,隶属于40科63属,以樟科、蔷薇科、壳斗科、山茶科物种为主; 扁刺栲为群落优势种,中华木荷和灰柯为次优势种,金佛山方竹为灌木层优势种,扁刺栲群落组成与亚热带其他地区的扁刺栲群落组成相似。(2)金佛山方竹经营群落的灌木层物种丰富度显著低于自然群落,草本层Shannon-Wiener指数和Pielou指数均显著低于自然群落。(3)扁刺栲和灰柯在自然群落中为稳定型种群,而在金佛山方竹经营群落中为衰退型种群,中华木荷在两类群落中均为衰退型种群。(4)自然群落中扁刺栲、中华木荷、灰柯种群的萌枝率、有萌个体率和幼苗相对优势度均高于金佛山方竹经营群落。综上认为,金佛山方竹经营对金佛山扁刺栲群落灌木层和草本层物种多样性产生了负面影响,并显著影响扁刺栲群落优势种种群更新和维持。     

Restudy and reassignment ofDentalium antiquum Goldfuss, 1841 (Middle Devonian)

Dentalium antiquum is one of two moderately well-known Devonian “scaphopods” in the German literature. Examination of the type material and a few specimens in other institutions indicates more individual variability than is to be expected in species of the molluscan class Scaphopoda. The species is transferred with question toColeolus Hall, a fossil presumed to be a calcareous “worm” tube.      

Haplotype Diversity in “Source-Sink” Dynamics of <Emphasis Type="Italic">Escherichia coli</Emphasis> Urovirulence

FimH, the mannose-specific, type 1 fimbrial adhesin of Escherichia coli, acquires amino acid replacements adaptive in extraintestinal niches (the genitourinary tract) but detrimental in the main habitat (the large intestine). This microevolutionary dynamics is reminiscent of an ecological “source-sink” model of continuous species spread from a stable primary habitat (source) into transient secondary niches (sink), with eventual extinction of the sink-evolved populations. Here, we have adapted two ecological analytical tools—diversity indexes D _S and α—to compare size and frequency distributions of fimH haplotypes between evolutionarily conserved FimH variants (“source” haplotypes) and FimH variants with adaptive mutations (putative “sink” haplotypes). Both indexes show two- to threefold increased diversity of the sink fimH haplotypes relative to the source haplotypes, a pattern that ran opposite to those seen with nonstructural fimbrial genes (fimC and fimI) and housekeeping loci (adk and fumC) but similar to that seen with another fimbrial adhesin of E. coli, papG-II, also implicated in extraintestinal infections. The increased diversity of the sink pool of adhesin genes is due to the increased richness of the haplotypes (the number of unique haplotypes), rather than their evenness (the extent of similarity in relative abundances). Taken together, this pattern supports a continuous emergence and extinction of the gene alleles adaptive to virulence sink habitats of E. coli, rather than a one-time change in the habitat conditions. Thus, ecological methods of species diversity analysis can be successfully adapted to characterize the emergence of microbial virulence in bacterial pathogens subject to source-sink dynamics. [Reviewing Editor: Dr. Margaret Riley]     

Assessment of the Neva Estuary ecosystem state on the basis of structural characteristics of benthic animal communities in 1994–2005

In the years 1994–2005, the values of the integrated index IP’ at some stations of the Neva Bay changed from 38.1 to 81.9%, water quality changed from class 3 to class 5, and the states of some areas of the ecosystem that were evaluated as “tense” went to “catastrophic.” The integrated mean assessment of water quality according to the IP’ index over the entire Neva Bay throughout 12 years (1994–2005) remained relatively stable, waters were assessed as “polluted” (fourth class), and the state of the ecosystem was considered “critical.” The state of the eastern part of the Gulf of Finland in 1994–2005 was less favorable. The species diversity of zoobenthos in the resort zone of the eastern part of the Gulf of Finland is considerably lower than in the Neva Bay. Waters of the resort zone of the eastern part of the Gulf of Finland in 1994–2005 were assessed as one class lower than in the Neva Bay, i.e., as “polluted-dirty” (fourth-fifth class), and the state of the ecosystem was assessed as being in a “crisis.” In the resort zone, there was a decline in species diversity and abundance and biomass of benthic animals; i.e., all characteristics of the degradation of benthic animal communities were observed.     

Genome-wide investigation on the genetic variations of rice disease resistance genes

Exploitation of plant disease resistance (R) gene in breeding programs has been proven to be the most efficient strategy for coping with the threat of pathogens. An understanding of R-gene variation is the basis for this strategy. Here we report a genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes, Oryza sativa L. var. Nipponbare and 93–11. We show that the allelic nucleotide diversity in 65.0% of 397 least-divergent pairs is not high (0.344% on average), while the remaining 35% display a greater diversity (5.4% on average). The majority of conserved R genes is single-copy and/or located as a singleton. The clustered, particularly the complex-clustered, R-genes contribute greatly to the rich genetic variation. Surprisingly only 11.2% of R-genes have remarkably high ratios of non-synonymous to synonymous rates, which is much less than the 17.4% observed between Arabidopsis genomes. Noticeable “artificially selective sweeping” could be detected in a large proportion of the conserved R-genes, a scenario described in the “arms race” co-evolutionary model. Based on our study, a variation pattern of R-genes is proposed and confirmed by the analysis of R-genes from other rice lines, indicating that the observed variation pattern may be common in all rice lines.Electronic Supplementary Material Supplementary material is available for this article at     

浙江省红楠生境地群落数量分类和环境解析

为探讨群落结构与环境因子对红楠Machilus thunbergii在浙江省分布及发展的影响,采用双向指示种分类(TWINSPAN)、典范对应分析(CCA)并结合种间联结分析,对浙江省172个红楠生境地群落进行数量分类排序与环境解析。结果表明:(1)TWINSPAN将172个样地群落分成8个群落类型,红楠在群落中为优势种或主要伴生种。群落类型的不同是影响红楠生长及更新的重要原因。(2)海拔高度及坡度是决定红楠分布及发展的主导环境因子。红楠作为优势种的生境地主要特征为海拔900m以下、坡度35°以下。(3)甜槠(Castanopsis eyrei)、青冈(Cyclobalanopsis glauca)、木荷(Schima superba)为群落中的稳定优势种,种间联结结果显示与红楠均为显著正关联。