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Similarity Index (similarity + index)

Distribution by Scientific Domains

Life Sciences	60%
Medical Sciences	7%
Humanities and Social Sciences	7%

Distribution within Life Sciences

Plant Science	23%
Conservation Science	16%
Ecology & Organismal Biology	11%

Selected Abstracts

Comparative QSAR Studies on Toxicity of Phenol Derivatives Using Quantum Topological Molecular Similarity Indices

CHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2010
Bahram Hemmateenejad
Quantitative structure activity relationship (QSAR) analyses using a novel type of electronic descriptors called quantum topological molecular similarity (QTMS) indices were operated to describe and compare the mechanisms of toxicity of phenols toward five different strains (i.e., Tetrahymena pyriformis, L1210 Leukemia, Pseudomonas putida, Raja japonica and Cucumis sativus). The appropriate QSAR models for the toxicity data were obtained separately employing partial least squares (PLS) regression combined with genetic algorithms (GA), as a variable selection method. The resulting QSAR models were used to identify molecular fragments of phenol derivatives whose electronic properties contribute significantly to the observed toxicities. Using this information, it was feasible to discriminate between the mechanisms of action of phenol toxicity to the studied strains. It was found that toxicities of phenols to all strains, except with L1210 Leukemia, are significantly affected by electronic features of the phenolic hydroxyl group (C-O-H). Meanwhile, the resulting models can describe the inductive and resonance effects of substituents on various toxicities. [source]

Evaluating wastewater-induced plant genotoxicity using randomly amplified polymorphic DNA

ENVIRONMENTAL TOXICOLOGY, Issue 1 2008
K. M. Swaileh
Abstract Wastewater often contains genotoxic substances that can resist different stages of the treatment process. In the present study, randomly amplified polymorphic DNA technology was applied to evaluate the genotoxic effects of wastewater (treated and raw) irrigation on oat plants (Avena sativa). RAPD profiles obtained showed that both treated and raw wastewater (RWW) were having genotoxic effects on oat plants. This was apparent by the appearance/disappearance of bands in the treatments compared with the control plants. From the 15 primers used, 186 bands were obtained with an average of 12.4 bands per primer. Irrigating plants with RWW caused 51 new bands to appear and 19 to disappear. Treated wastewater (TWW) caused only 16 new bands and the loss of 17 bands. This makes TWW less genotoxic than RWW. The Euclidean distances shown on the dendrogram, revealed the presence of two clusters according to dissimilarity values. One cluster contained the control plants and those irrigated with TWW, whereas the second contained the plants irrigated with RWW. Similarity indices calculated between the treatments and the control plants showed that the control and the plants irrigated with TWW had a similarity index of 0.87, the control and plants irrigated with RWW 0.73 and between the treatments 0.75. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008. [source]

Are urban bird communities influenced by the bird diversity of adjacent landscapes?

JOURNAL OF APPLIED ECOLOGY, Issue 5 2001
Philippe Clergeau
Summary 1The species diversity of adjacent landscapes influences the conservation or restoration of several animal groups in urban areas, but the effect on birds is unclear. To address this question, we compared bird species richness (BSR) and community composition between periurban (area surrounding the town) and urban (suburban and centre areas) landscapes across three spatial scales. 2At a large biogeographical scale (temperate and boreal climatic zone), relationships between the BSR of urban areas and their surrounding landscapes were examined in a meta-analysis of 18 published studies. In general, BSR was negatively correlated with latitude and urbanization. The BSR of suburban and centre landscapes correlated positively with the BSR of periurban landscapes. However, latitudinal effects were also involved, as BSR in urban and periurban landscapes declined as town latitude increased. Similarity indices were low (50%) between periurban and centre bird communities. 3At a regional scale, we assessed winter bird data from several towns within three regions of temperate and boreal countries (western France, northern Finland and eastern Canada). The type of periurban landscape, number of inhabitants and town diameter did not affect BSR. BSR was similar between the cities of a given biogeographical area. Bird communities were more similar between similar habitat types of different cities than between different habitats of the same city. 4At a local scale, we tested the influence of proximity to the periurban landscape on BSR in parks of western French towns of different size. Neither BSR nor community similarity changed in relation to the distance of the park from the periurban landscape. 5Guild composition according to diet and feeding habitat did not vary between urban and periurban locations at regional or local scales. 6We conclude that, at regional and local scales, urban bird communities are independent of the bird diversity of adjacent landscapes, and that local features are more important than surrounding landscapes in determining BSR. Whatever the biodiversity quality of the periurban landscape, site-specific actions such as shrub and tree planting, water restoration and increasing vegetation diversity can change bird diversity in towns and improve the quality of human,wildlife contacts. [source]

A simulation approach to determine statistical significance of species turnover peaks in a species-rich tropical cloud forest

DIVERSITY AND DISTRIBUTIONS, Issue 6 2007
K. Bach
ABSTRACT Use of ,-diversity indices in the study of spatial distribution of species diversity is hampered by the difficulty of applying significance tests. To overcome this problem we used a simulation approach in a study of species turnover of ferns, aroids, bromeliads, and melastomes along an elevational gradient from 1700 m to 3400 m in a species-rich tropical cloud forest of Bolivia. Three parameters of species turnover (number of upper/lower elevational species limits per elevational step, Wilson,Shmida similarity index between adjacent steps) were analysed. Significant species turnover limits were detected at 2000 (± 50) m and 3050 m, which roughly coincided with the elevational limits of the main vegetation types recognized in the study area. The taxon specificity of elevational distributions implies that no single plant group can be used as a reliable surrogate for overall plant diversity and that the response to future climate change will be taxon-specific, potentially leading to the formation of plant communities lacking modern analogues. Mean elevational range size of plant species was 490 m (± 369). Elevational range sizes of terrestrial species were shorter than those of epiphytes. We conclude that our simulation approach provides an alternative approach for assessing the statistical significance of levels of species turnover along ecological gradient without the limitations imposed by traditional statistical approaches. [source]

Genet age in marginal populations of two clonal Carex species in the Siberian Arctic

ECOGRAPHY, Issue 4 2000
Ingibjörg S. Jónsdóttir
During a Swedish-Russian expedition to northern Siberia 1994, we sampled two marginal populations of two Carex species at two high arctic sites (C, stans Drej. on Faddeyevsky Island and C. ensifolia V. Krecz ssp. arctisibirica Jurtz. at north-eastern Taymyr Peninsula), both north of previously documented localities in that areas for the two species. These populations were composed of a few distinct patches of ramet colonies, some of them shaped like fairy rings with dead centres. We measured the size of all colonies and collected samples for detailed morphometric analyses of rhizome growth. By using RAPD (random amplified polymorphic DNA) analysis we established that the largest colony at each site consisted of a single genet, based on 41 polymorphic bands amplified with three primers. Pooled samples from each of two additional colonies of C. stans on Faddeyevsky Island were analysed and showed that clones of the same species at the same site were relatively dissimilar (Dice's similarity index 0.26 0,43), We then assumed that each ramet colony represented a single genet. Based on the morphometric data, we developed a deterministic growth model that simulates the clonal growth of these species and enabled estimates of the time since establishment of the genets. The estimated age of the five C. Stans clones varied from 17 to 154 yr and the age of the two C. ensifolia ssp, arctisibirica clones was well over 3000 yr. [source]

Comparative Ant Faunas between Seonyudo and Seven Other Islands of West Sea in Korea

ENTOMOLOGICAL RESEARCH, Issue 2 2002
So-Jin HA
ABSTRACT This paper is intended as an investigation of the biogeographic characteristics of ant faunas of the eight islands in West Sea of South Korea, using quantitative genetic analyses. The faunal similarity is examined using the Nomura-Simpson's Coefficient (NSC). The obtained NSC value matrix was examined by a cluster analysis using UPGMA method. The MSC-values between the seven areas investigated range from 0.500 (Deokjeokdo Hongdo) to 0.909 (Wonsando-Hongdo). In these islands including Seonyudo, the NSC -values range from 0.571 (Deokjeokdo) to 0.778 (Bigeumdo). The cluster analysis using the similarity index (NSC) showed that eight islands were divided into two groups at the level of 41%. It was shown that Wonsando and Bigeumdo were closer (Similarity = 83%) than those between others. Deokjeokdo and Bigeumdo were remote (Similarity = 41%) from each conspecific population. That is, the species composition of Bigeumdo (Similarity = 70%) was similar to that of the Seonyudo, while that of Deokjeokdo (Similarity = 41%) was different from that. [source]

Faunal Comparison of Ants among Cheongsando and Other Islands of South Sea in Korea

ENTOMOLOGICAL RESEARCH, Issue 1 2002
Seong-Joon PARK
ABSTRACT This paper attempts to reveal the biogeographic characteristics of ant fauna of the islands among Korean South Sea, using quantitative analyses. The data treated in this paper are those from Cheongsando Is. and 10 other islands in South Sea which have been well investigated. The faunal similarity is examined using the Nomura-Simpson's Coefficient (NSC). Futhermore, the obtained NSC value matrix is examined by a cluster analysis using UPGMA method. The number of species which has been recorded in the 11 islands are 91 species belonging to 34 genera under 4 subfamilies. Among the above 11 islands, Jejudo Is., which is the largest, has the highest number of species, 67 spp., while Geogeumdo Is. has the lowest, 21 spp. Cheongsando Is. which has directly been investigated by authors has 30 species. The NSC- values between the 11 localities investigated range from 0.522 (Wando Is. to Saryangdo Is.) to 1.000 (Namhaedo Is. to Geojedo Is.). The comparative NSC value of Cheongsando Is. and 10 islands range from 0.522 (to Saryangdo Is.) to 0.833 (to Jejudo Is). The cluster analysis using a similarity index (NSC) showed that the islands of these areas could be grouped into 3, a level of 32%. The similarity of Soando Is. and Geomundo Is. were the closest, 63%, while Soando Is. and Namhaedo Is. were the remotest, 32%. The similarity of Jindo Is. and Cheongsando Is, was 63%, while that of Namhaedo Is. and Cheongsando Is. was 32%. [source]

Evaluating wastewater-induced plant genotoxicity using randomly amplified polymorphic DNA

Development and application of a fatty acid based microbial community structure similarity index

ENVIRONMETRICS, Issue 4 2002
Alan Werker
Abstract This article presents an index of similarity that has application in monitoring relative changes of complex microbial communities for the purpose of understanding the impact of community instability in biological wastewater treatment systems. Gas chromatographic data quantifying microbial fatty acid esters extracted from biosolids samples can be used to infer the occurrence of changes in mixed culture community structure. One approach to rapidly assess the relative dissimilarity between samples is to calculate a similarity index scaled between 0 and 1. The many arbitrary scales that are associated with the available calculation methods for similarity indices limits the extent of application. Therefore, a specialized index of similarity was derived from consideration of the measurement errors associated with the chromatographic data. The resultant calculation method provides a clear mechanism for calibrating the sensitivity of the similarity index, such that inherent measurement variability is accommodated and standardization of scaling is achieved. The similarity index sensitivity was calibrated with respect to an effective gas chromatographic peak coefficient of variation, and this calibration was particularly important for facilitating comparisons made between different systems or experiments. The proposed index of similarity was tested with data acquired from a recently completed study of contaminant removal from pulp mill wastewater. The results suggest that this index can be used as a screening tool to rapidly process microbial fatty acid (MFA) compositional data, with the objective of making preliminary identification of underlying trends in (MFA) community structure, over time or between experimental conditions. Copyright © 2002 John Wiley & Sons, Ltd. [source]

Detection of electrocardiogram beats using a fuzzy similarity index

EXPERT SYSTEMS, Issue 2 2007
Elif Derya Übeyli
Abstract: A new approach based on the computation of a fuzzy similarity index (FSI) is presented for the detection of electrocardiogram (ECG) beats. Four types of ECG beats (normal beat, congestive heart failure beat, ventricular tachyarrhythmia beat, atrial fibrillation beat) obtained from the Physiobank database were analysed. The ECG signals were decomposed into time,frequency representations using the discrete wavelet transform and wavelet coefficients were calculated to represent the signals. The aim of the study is detection of ECG beats by the combination of wavelet coefficients and the FSI. Toward achieving this aim, fuzzy sets were obtained from the feature sets (wavelet coefficients) of the signals under study. The results demonstrated that the similarity between the fuzzy sets of the studied signals indicated the variabilities in the ECG signals. Thus, the FSI could discriminate the normal beat and the other three types of beats (congestive heart failure beat, ventricular tachyarrhythmia beat, atrial fibrillation beat). [source]

Measuring Similarity Among Various Shapes Based on Geometric Matching

GEOGRAPHICAL ANALYSIS, Issue 4 2005
Zuoquan Zhao
The purpose of this article is to examine how to measure the degree of similarity among various shapes, including for the first time those that are fragmented and perforated, by the overlap-based elongation index. It is argued that complete removal of the effects of position, size, and orientation on shape, which is essential for the calibration of shape similarity, can be achieved by a shape similarity index that varies continuously with changes in shape. After examining the characteristics of shape change, it is demonstrated that the elongation index is sensitive to changes in the shape of two spatial objects only when the centroids of the two objects are coincident. Two related rules of shape similarity are then presented. The applicability of the elongation index is evaluated by comparing several simple and complex shapes. The principal contribution of this article is that for the first time similarity among various shapes, fragmented or perforated, can be identified using the elongation index. [source]

Elevated air temperature alters an old-field insect community in a multifactor climate change experiment

GLOBAL CHANGE BIOLOGY, Issue 4 2009
SHAWN N. VILLALPANDO
Abstract To address how multiple, interacting climate drivers may affect plant,insect community associations, we sampled insects that naturally colonized a constructed old-field plant community grown for over 2 years under simultaneous CO2, temperature, and water manipulation. Insects were sampled using a combination of sticky traps and vacuum sampling, identified to morphospecies and the insect community with respect to abundance, richness, and evenness quantified. Individuals were assigned to four broad feeding guilds in order to examine potential trophic level effects. Although there were occasional effects of CO2 and water treatment, the effects of warming on the insect community were large and consistent. Warming significantly increased Order Thysanoptera abundance and reduced overall morphospecies richness and evenness. Nonmetric multidimensional scaling found that only temperature affected insect community composition, while a Sørensen similarity index showed less correspondence in the insect community between temperature treatments compared with CO2 or soil water treatments. Within the herbivore guild, elevated temperature significantly reduced richness and evenness. Corresponding reductions of diversity measures at higher trophic levels (i.e. parasitoids), along with the finding that herbivore richness was a significant predictor of parasitoid richness, suggest trophic-level effects within the insect community. When the most abundant species were considered in temperature treatments, a small number of species increased in abundance at elevated temperature, while others declined compared with ambient temperature. Effects of temperature in the dominant insects demonstrated that treatment effects were limited to a relatively small number of morphospecies. Observed effects of elevated CO2 concentration on whole-community foliar N concentration did not result in any effect on herbivores, which are probably the most susceptible guild to changes in plant nutritional quality. These results demonstrate that climatic warming may alter certain insect communities via effects on insect species most responsive to a higher temperature, contributing to a change in community structure. [source]

Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: A study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis,

INFLAMMATORY BOWEL DISEASES, Issue 6 2007
Nadia Vasquez MS
Abstract Background: The mucosa-associated bacteria (MAB) are suspected of being involved in the pathogenesis of Crohn's disease. We analyzed and compared the MAB in noninflamed and inflamed ileal mucosa of Crohn's disease patients (n = 22). Methods: Tissue samples from the inflamed ileal mucosa and from the adjacent noninflamed ileal mucosa were taken from surgical resection specimens. The MAB were investigated using fluorescence in situ hybridization with 7 group-specific probes and temporal temperature gradient gel electrophoresis (TTGE). Results: Samples from both noninflamed and inflamed mucosa were obtained from 15 patients. The distribution of the bacterial populations was not different between noninflamed and inflamed mucosa. The Bacteroidetes phylum was dominant and accounted for 29% of MAB (0%,74%) in noninflamed tissues and 32% (0%,70%) in inflamed areas. The , Proteobacteria represented 12% (0%,70%) of MAB both in noninflamed and inflamed areas. The Clostridium coccoides group (Firmicutes phylum) represented 15% of MAB in noninflamed tissues versus 7% in inflamed areas. For most of the patients the similarity index between TTGE paired profiles was very high. Conclusion: The dominant MAB do not differ between noninflamed and inflamed ileal mucosa in Crohn's disease. This argues against a localized dysbiosis to explain the patchy distribution of mucosal lesions. (Inflamm Bowel Dis 2007) [source]

The tripartite biogeographical index: a new tool for quantifying spatio-temporal differences in distribution patterns

JOURNAL OF BIOGEOGRAPHY, Issue 4 2006
Tom Schils
Abstract Aims, First, to develop an index that quantifies biogeographical patterns based on the basic descriptors of presence/absence distribution patterns (F, frequency; C, connectivity; G, grouping). Second, to test the proposed biogeographical index on a data set of macrophyte communities in the Arabian Sea using distribution data of macro-algae and seagrasses throughout the Indian Ocean. Location, Arabian Sea (regional macrophyte community data) and the larger Indian Ocean (oceanic distribution data). Methods, The proposed index is derived from the Tulloss tripartite similarity index. The tripartite biogeographical index (TBI = ,F × C × G) is calculated for a specific taxon and incorporates several fundamental parameters of presence/absence data in grid cell (block) patterns. TBI accounts for the relative abundance of a taxon, the average grouping of its occurrences, the average of minimal absence intervals between taxon presences and the largest coherent cluster of taxon occurrences, and also incorporates dispersal aspects. The macrophytes from the case study are among the best documented marine organisms in the Indian Ocean. The regional distribution data from the Arabian Sea result from exhaustive species lists from Masirah Island (Oman) and the Socotra Archipelago (Yemen). Results, TBI values fit a linear scale corresponding to the proportional presence and the distributional spread of taxa within a given geographical area. The three functions that constitute TBI can be evaluated separately or in association with TBI, to give detailed information on the important factors that characterize the biogeographical distribution of a taxon (or larger entities consisting of multiple taxa such as communities). The case study on Arabian macrophytes clarifies the use and explanatory power of the index. Main conclusions, The biogeographical descriptors can be combined into an index which accurately quantifies taxon occurrences and distribution types on a single linear scale from rare/scattered to abundant/grouped. Together with its three functions, the index allows for a non-arbitrary selection of taxa and taxon groupings based on their distribution pattern. The analysis of TBI values for the Arabian macrophyte communities confirms previous biogeographical findings and enables more detailed statistical analyses of the distribution data. [source]

Deterioration of Organization in the First Minutes of Atrial Fibrillation: A Beat-to-Beat Analysis of Cycle Length and Wave Similarity

JOURNAL OF CARDIOVASCULAR ELECTROPHYSIOLOGY, Issue 1 2007
FLAVIA RAVELLI Ph.D.
Introduction: It has been recently suggested that many episodes of atrial fibrillation (AF) may be partially organized at the onset and thus more suitable for antitachycardia pacing therapy. Nevertheless, the time course of organization in the first minutes of AF has not been quantified yet. Methods and Results: Twenty episodes of paroxysmal AF were studied. Electrograms were recorded from the right atrium (RA), distal (CSd), and proximal coronary sinus (CSp). The time course of AF cycle length (AFCL) and the regularity of wave morphology (similarity index S) were beat-to-beat measured at each recording site during the first 7 minutes of AF. AFCL and S showed a decreasing trend after the onset of AF. AFCL decreased from 208 ± 31 to 171 ± 21 msec (P < 0.001), from 206 ± 40 to 169 ± 23 msec (P < 0.001) and from 190 ± 42 to 152 ± 18 msec (P < 0.05), respectively, in RA, CSd, and CSp. Similarly, the similarity index decreased in CSd from 0.37 ± 0.27 to 0.12 ± 0.09 (P < 0.01) and in RA from 0.40 ± 0.18 to 0.17 ± 0.16 (P < 0.001). The 80% of the decrease occurred during the first 3 minutes of the arrhythmia, while after this time both cycle length and similarity index did not change significantly anymore. Conversely, the electrical activity in CSp was highly disorganized (S = 0.05 ± 0.03) even in the first minute of AF, and no decreasing temporal trend was observed. Conclusion: Higher levels of organization and longer fibrillation intervals exist at the onset of AF. The degree of organization of the electrical activity decays within less than 3 minutes. Since antitachycardia pacing success rate increases with high levels of organization, these results suggest an early delivery of pacing treatment. [source]

Site productivity and plant size explain the response of annual species to grazing exclusion in a Mediterranean semi-arid rangeland

JOURNAL OF ECOLOGY, Issue 2 2004
Yagil Osem
Summary 1The response of an annual plant community to protection from grazing as a function of variation in site productivity was studied in a semi-arid Mediterranean rangeland in Israel over 4 years (1996,99). The abundance of species was compared in grazed vs. ungrazed plots (exclosures) in four neighbouring topographic sites (south- and north-facing slopes, hilltop and Wadi shoulders), representing a gradient of resource availability and productivity. 2Above-ground potential productivity at peak standing crop in spring (i.e. inside exclosures) varied considerably between years and topographic sites. Productivity was similar among the hilltop, south- and north-facing slopes, and was typical of semi-arid ecosystems (10,200 g,2). Productivity in the Wadi was consistently greater (up to 700 g,2) and reached the range of subhumid grassland ecosystems. 3The effect of grazing exclusion on the composition of the annual vegetation was productivity-dependent. Lower similarity (Sorenson's quantitative similarity index) between grazed and ungrazed subplots was observed in the productive Wadi compared with the less productive sites. The small-scale variation in grazing impact on species composition, due to differences in productivity, is consistent with models predicting similar trends in perennial grasslands across larger scale gradients. 4The relationship between plant size (above-ground dry-weight), site productivity and response to fencing was analysed for the 36 most abundant annual species. Large species were more abundant in more productive sites, and small species at lower productivity, although few species were restricted to particular productivity levels. The response of individual species to protection from grazing was productivity dependent, with plant size playing a central role. Larger species tended to increase and small ones to decrease in abundance after fencing, with a mixed response in species with intermediate size. 5A conceptual model is presented relating the response to protection from grazing along gradients of productivity to species plant size. [source]

A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level

MOLECULAR ECOLOGY, Issue 7 2004
ICA BRUVO
Abstract Microsatellites are powerful molecular markers, used commonly to estimate intraspecific genetic distances. With the exception of band sharing similarity index, available distance measures were developed specifically for diploid organisms and are unsuited for comparisons of polyploids. Here, we present a simple method for calculation of microsatellite genotype distances, which takes into account mutation processes and permits comparison of individuals with different ploidy levels. This method should provide a valuable tool for intraspecific analyses of polyploid organisms, which are widespread among plants and some animal taxa. An illustration is given using data from the planarian flatworm Schmidtea polychroa (Platyhelminthes). [source]

The 29°N latitudinal line: an important division in the Hengduan Mountains, a biodiversity hotspot in southwest China

NORDIC JOURNAL OF BOTANY, Issue 5 2009
Da-Cai Zhang
This paper aimed to explore the division of the southern and northern Hengduan Mountains based on gradients in species similarity and richness, and to analyze species richness in each sub-region. The Hengduan Mountain region was divided into nine latitudinal belts using one degree of latitude to define the belt after which distribution of seed plants within each latitudinal belt was recorded. Latitudinal patterns of species similarity were measured using the Jaccard similarity index for each pair of adjacent latitudinal belts. Non-metric multidimentional scaling (NMDS) was also used to analyze the similarity in species composition among the nine latitudinal belts. The latitudinal pattern of species similarity and the NMDS ordination both showed a great change in species composition across the 29°N latitudinal line, essentially dividing the Hengduan Mountain region into southern and northern sub-regions. Species richness, shown by the c-value of the species,area power function, and species,area ratio along a latitudinal gradient both showed a sharp decrease across the latitudinal belt from 29°0, to 29°59,N. The southern sub-region occupied 40% of the total area of the Hengduan Mountain region, but contained more than 80% of all the seed plants in the region. The higher species richness and endemism in the southern sub-region showed it to be the core of the Hengduan biodiversity hotspot, a result not unexpected because of the greater extremes of topography and wider diversity of habitats in the southern portion. [source]

Temporal and spatial variability in soil food web structure

OIKOS, Issue 11 2007
Matty P. Berg
Heterogeneity is a prominent feature of most ecosystems. As a result of environmental heterogeneity the distribution of many soil organisms shows a temporal as well as horizontal and vertical spatial patterning. In spite of this, food webs are usually portrayed as static networks with highly aggregated trophic groups over broader scales of time and space. The variability in food web structure and its consequences have seldom been examined. Using data from a Scots pine forest soil in the Netherlands, we explored (1) the temporal and spatial variability of a detrital food web and its components, (2) the effect of taxonomic resolution on the perception of variability over time and across space, and (3) the importance of organic matter quality as an explanatory factor for variability in food web composition. Compositional variability, expressed using the Bray-Curtis similarity index, was measured over 2.5 years using a stratified litterbag design with three organic horizons per litterbag set. Variability in community composition and organic matter degradation increased over time in the litter horizon only. Seasonal variation in community composition was larger than variation between samples from the same season in different years. Horizontal spatial variability in community composition and organic matter degradation was relatively low, with no increase in variability with increasing distance between samples. Vertically, communities and organic matter degradation was more different between the non-adjacent litter and humus horizons than between adjacent layers. These findings imply that soil food webs, at least in temperate forest plantations, are more variable than is currently appreciated in experiments and model studies, and that organic matter turnover might be an important factor explaining variability in community composition. Species composition was more variable than functional group composition, which implies that aggregated food webs will seem less sensitive to local temporal and spatial changes than they in fact are. [source]

BIODIVERSITY RESEARCH: Native-exotic species richness relationships across spatial scales and biotic homogenization in wetland plant communities of Illinois, USA

DIVERSITY AND DISTRIBUTIONS, Issue 5 2010
Hua Chen
Abstract Aim, To examine native-exotic species richness relationships across spatial scales and corresponding biotic homogenization in wetland plant communities. Location, Illinois, USA. Methods, We analysed the native-exotic species richness relationship for vascular plants at three spatial scales (small, 0.25 m2 of sample area; medium, 1 m2 of sample area; large, 5 m2 of sample area) in 103 wetlands across Illinois. At each scale, Spearman's correlation coefficient between native and exotic richness was calculated. We also investigated the potential for biotic homogenization by comparing all species surveyed in a wetland community (from the large sample area) with the species composition in all other wetlands using paired comparisons of their Jaccard's and Simpson's similarity indices. Results, At large and medium scales, native richness was positively correlated with exotic richness, with the strength of the correlation decreasing from the large to the medium scale; at the smallest scale, the native-exotic richness correlation was negative. The average value for homogenization indices was 0.096 and 0.168, using Jaccard's and Simpson's indices, respectively, indicating that these wetland plant communities have been homogenized because of invasion by exotic species. Main Conclusions, Our study demonstrated a clear shift from a positive to a negative native-exotic species richness relationship from larger to smaller spatial scales. The negative native-exotic richness relationship that we found is suggested to result from direct biotic interactions (competitive exclusion) between native and exotic species, whereas positive correlations likely reflect the more prominent influence of habitat heterogeneity on richness at larger scales. Our finding of homogenization at the community level extends conclusions from previous studies having found this pattern at much larger spatial scales. Furthermore, these results suggest that even while exhibiting a positive native-exotic richness relationship, community level biotas can/are still being homogenized because of exotic species invasion. [source]

Development and application of a fatty acid based microbial community structure similarity index

Spatial and temporal variability of the bacterial community in different chemotypes of the New Zealand marine sponge Mycale hentscheli

FEMS MICROBIOLOGY ECOLOGY, Issue 3 2010
Sally A. Anderson
Abstract Molecular fingerprinting of 16S rRNA genes using terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) was used to characterize the temporal and spatial variability among sponge-associated bacteria from Mycale hentscheli having distinct bioactive chemotypes. Cluster analysis of T-RFLP and DGGE profiles from M. hentscheli chemotypes largely grouped sponge microbial diversity to their distinct chemotype pattern. Repeat sampling of individual M. hentscheli at one location over a 21-month period showed that the T-RFLP profiles from individual sponges had similarity indices ranging from 60% to 82% and calculated DGGE similarities between 23% and 95%. However, a portion (>35% from DGGE and >19% from T-RFLP) of the microbial community from M. hentscheli appeared to be spatially conserved through all M. hentscheli populations. Sequence analysis of DGGE band fragments showed a similarity among the bands originating from different individuals, different times, and different locations. The sponge-associated relationship of these bands was confirmed, with sequences having similarity to sponge-associated bacteria reported from global locations. This study highlights the spatial and temporal complexity in the distribution of bacterial communities associated with different chemotypes of the marine sponge M. hentscheli. [source]

Assessment of Genetic Variation Within Indian Mustard (Brassica juncea) Germplasm Using Random Amplified Polymorphic DNA Markers

JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 4 2008
Muhammad Ayub Khan
Abstract Genetic diversity among 45 Indian mustard (Brassica juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession ,Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77,0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop. [source]

Effect of Seasonality on Distribution of Macroalgae in a Stream System (Xin'an Spring) in Shanxi Province, North China

JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 8 2006
Bian-Fang Hu
Abstract A survey of the seasonal distribution of macroalgae in a stream system in Shanxi Province, north China, was undertaken from July 2004 to April 2005. The relative abundance and percentage cover of macroalgae, and several environmental factors were monitored along a 20-m stretch at each of four sites, at intervals of approximately three months (one sampling per season). Several stream conditions were relatively constant over the sampling period (pH, maximum width and maximum depth), whereas others exhibited a distinct seasonal pattern (water temperature and specific conductance), and some fluctuated with no discernable seasonal pattern (current velocity and dissolved oxygen). Forty-two species of macroalgae were found, with a predominance of Chlorophyta (26 species, 61.9%). Rhodophyta and Charophyta represented the smallest proportion (1 species each, 2.38%). Six macroalgae species were the most widespread, occurring in all four sampling sites. Twelve species were found at only one site each. In terms of seasonality, eight species occurred throughout the year, whereas 16 species were found in only one season each. The macroalgal community at Xin'an Spring was species rich relative to other streams. Species richness per sampling site was negatively correlated with pH. Principal component analysis revealed that no single variable had much influence on the macroalgal seasonal dynamics. We calculated Sorensen similarity indices to compare our study with other continent-wide surveys of stream macroalgae, but the similarity indices were all very low. This study also shows that macroalgae in different locations have significant reproductive isolation. (Managing editor: Ya-Qin Han) [source]

Radiomutants of chrysanthemum (Dendranthema grandiflora Tzvelev) of the Lady group: RAPD analysis of the genetic diversity

PLANT BREEDING, Issue 3 2004
J. Lema-Rumiñska
Abstract Random amplified polymorphic DNA (RAPD) markers were used to study the molecular characterization of 10 new radiomutants of chrysanthemum. The original cultivar ,Richmond' differed in genetic distance from its Lady group mutants. The analysis of genetic similarity indices revealed low diversity within the radiomutants. The dendrogram obtained after cluster analysis separated the new cultivars as a group that differed from the original cultivar ,Richmond'. The Lady group cultivars, derived from one original cultivar by radiomutation, could be distinguished from each other by using RAPD markers of only a single primer or sets of two or three primers. Polymerase chain reaction analysis proved the efficiency of the RAPD method for DNA fingerprinting of the original cultivar ,Richmond' and its new radiomutants. [source]