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Diversity Assessment (diversity + assessment)
Selected AbstractsRapid plant diversity assessment using a pixel nested plot design: A case study in Beaver Meadows, Rocky Mountain National Park, Colorado, USADIVERSITY AND DISTRIBUTIONS, Issue 4 2007Mohammed A. Kalkhan ABSTRACT Geospatial statistical modelling and thematic maps have recently emerged as effective tools for the management of natural areas at the landscape scale. Traditional methods for the collection of field data pertaining to questions of landscape were developed without consideration for the parameters of these applications. We introduce an alternative field sampling design based on smaller unbiased random plot and subplot locations called the pixel nested plot (PNP). We demonstrate the applicability of the PNP design of 15 m × 15 m to assess patterns of plant diversity and species richness across the landscape at Rocky Mountain National Park (RMNP), Colorado, USA in a time (cost)-efficient manner for field data collection. Our results produced comparable results to a previous study in the Beaver Meadow study (BMS) area within RMNP, where there was a demonstrated focus of plant diversity. Our study used the smaller PNP sampling design for field data collection which could be linked to geospatial information data and could be used for landscape-scale analyses and assessment applications. In 2003, we established 61 PNP in the eastern region of RMNP. We present a comparison between this approach using a sub-sample of 19 PNP from this data set and 20 of Modified Whittaker nested plots (MWNP) of 20 m × 50 m that were collected in the BMS area. The PNP captured 266 unique plant species while the MWNP captured 275 unique species. Based on a comparison of PNP and MWNP in the Beaver Meadows area, RMNP, the PNP required less time and area sampled to achieve a similar number of species sampled. Using the PNP approach for data collection can facilitate the ecological monitoring of these vulnerable areas at the landscape scale in a time- and therefore cost-effective manner. [source] DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 2 2006Gian Marco Luna Summary In order to evaluate whether different DNA extraction procedures can affect estimates of benthic bacterial diversity, based on 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique, we compared two in situ lysis procedures (a SDS-based protocol and a commercial kit for DNA recovery) and one cell-extraction protocol on a variety of marine sediments. Despite the two in situ lysis procedures resulted in significantly different DNA yields (highest with the SDS in situ lysis), estimates of bacterial diversity provided a not significantly different ribotype richness, as well as similar values of the Shannon-Wiener (H,) and Margalef (d) indices of biodiversity and of evenness (Pielou index, J). Conversely, the cell-extraction procedure for DNA extraction resulted always in a significantly lower ribotype richness and diversity. The analysis of similarities (anosim) among the T-RFLP electropherograms allowed concluding that ribotypes composition did not change significantly using different protocols. However, the analysis of ,-diversity (turnover diversity) revealed that a large number of ribotypes was observed exclusively with one of the three protocols utilized. When unshared ribotypes from in situ lysis and cell extraction were pooled together, total ribotype richness resulted much higher (up to 80%). Our results indicate that estimates of ribotype diversity based on a single protocol of DNA extraction can significantly underestimate the total number of bacterial ribotypes present in the benthic domain. We recommend that future studies will not only integrate different DNA extraction procedures, but also will explore the possibility of integrating two or more different genetic markers in order to increase our ability to detect the actual bacterial diversity in environmental samples. [source] Floristic inventory and diversity assessment of a lowland African Montane Rainforest at Korup, Cameroon and implications for conservationAFRICAN JOURNAL OF ECOLOGY, Issue 3 2010Innocent Ndoh Mbue Abstract Twenty modified-Whittaker plots were stratified at different sampling locations from February to May of 2008 in the central zone of Korup National Park, Cameroon. Our interest was to assess floristic diversity and investigate their relationship with environmental variables. Diversity profiles and rank abundance,curves were used for diversity analysis while canonical correspondence analysis and species,response curves were used to investigate the relationships between the response and explanatory variables. Of the 66 families identified, the Rubiaceae (999 species) were the most abundant. The Sterculiaceae (basal area = 10.482 m2 ha,1) were the dominant family, while the co-dominant families included the Ebenaceae (basal area = 9.092 m2 ha,1) and the Euphorbiaceae (basal area = 8.168 m2 ha,1). Soil variables explained 54.3% of total variation in family distribution. Canonical axes were related to different environmental gradients: axis1 was related to increasing canopy cover (r = 0.6951); axis 2, increasing Magnesium (r = 0.8465) and effective cation exchange capacity (r = 0.5899); axis 3, increasing effective cation exchange capacity (r = 0.5536); while axis 4, increasing Phosphorus concentration (r = 0.5232). Our results demonstrate the advantage which diversity profiles have over single or combination of indices, and the importance of using a combination of methodologies in diversity analysis. Résumé De février à mai 2008, vingt parcelles de Whittaker modifié ont été stratifiées à différents sites d'échantillonnage dans la zone centrale du Parc National de Korup, au Cameroun. Nous voulions évaluer la diversité floristique et étudier son lien avec diverses variables environnementales. Nous avons employé des profils de diversité et des courbes de rangs d'abondance pour l'analyse de la diversité, tandis que nous utilisions une analyse canonique des correspondances et des courbes de réponse des espèces pour étudier les relations entre les réponses et les variables explicatives. Sur les 66 familles identifiées, les Rubiacées (999 espèces) étaient les plus abondantes. Les Sterculiacées (surface basale = 10,482 m2 ha,1) étaient la famille dominante et, parmi les familles co-dominantes, il y avait les Ebénacées (surface basale = 9,092 m2 ha,1) et les Euphorbiacées (surface basale = 8,168 m2 ha,1). Des variables du sol expliquaient 54,3% de la variation totale de la distribution des familles. Les axes canoniques ont été liés aux différents gradients environnementaux; l'axe 1 était liéà une couverture croissante de la canopée (r = 0,6951); l'axe 2 à une augmentation du magnésium (r = 0,8465) et à la capacité réelle d'échange de cations (r = 0,5899); l'axe 3 à une capacité réelle croissante d'échanges de cations (r = 0,5536); et l'axe 4 à une concentration croissante en phosphore (r = 0,5532). Nos résultats montrent l'avantage que les profils de diversité ont sur des indices uniques ou combinés et l'importance d'utiliser une combinaison de méthodologies dans une analyse de diversité. [source] Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequencesLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2007Y.H. Zeng Abstract Aim:, To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments. Methods and Results:, All nucleotide sequences of the APB marker gene pufM from cultures and environmental clones were retrieved from the GenBank database. A set of cutoff values (sequence distances 0·06, 0·15 and 0·48 for species, genus, and (sub)phylum levels, respectively) was established using a distance-based grouping program. Analysis of the environmental clones revealed that current efforts on APB isolation and sampling in natural environments are largely inadequate. Analysis of the average distance between each identified genus and an uncultured environmental pufM sequence indicated that the majority of cultured APB genera lack environmental representatives. Conclusions:, The distance-based grouping method is fast and efficient for bulk functional gene sequences analysis. The results clearly show that we are at a relatively early stage in sampling the global richness of APB species. Periodical assessment will undoubtedly facilitate in-depth analysis of potential biogeographical distribution pattern of APB. Significance and Impact of the Study:, This is the first attempt to assess the present understanding of APB diversity in natural environments. The method used is also useful for assessing the diversity of other functional genes. [source] Characterization of new microsatellite markers in mung bean, Vigna radiata (L.)MOLECULAR ECOLOGY RESOURCES, Issue 4 2006JAE-GYUN GWAG Abstract The present work reports the isolation and characterization of new polymorphic microsatellites in mung bean (Vigna radiata L.). Of 93 designed primer pairs, seven were found to amplify polymorphic microsatellite loci, which were then characterized using 34 mung bean accessions. The number of alleles ranged from two to five alleles per locus with an average of three alleles. Observed and expected heterozygosity values ranged from 0 to 0.088 and from 0.275 to 0.683, respectively. All seven loci showed significant deviations from Hardy,Weinberg equilibrium, whereas only one pairwise combination (GBssr-MB77 and GBssr-MB91) exhibited significant departure from linkage disequilibrium. These newly developed markers are currently being utilized for diversity assessment within the mung bean germplasm collection of the Korean Gene Bank. [source] Inter-annual variability in amphibian assemblages: implications for diversity assessment and conservationAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 6 2010Carola Gómez-Rodríguez Abstract 1.Diversity assessments and conservation management should take into account the dynamic nature of populations and communities, particularly when they are subject to highly variable and unpredictable environmental conditions. 2.This study evaluates the inter-annual variability in the assemblage composition (temporal turnover) of an amphibian community breeding in a highly dynamic habitat, a Mediterranean temporary pond system, during a 4-year period. 3.A comprehensive framework is provided to evaluate temporal turnover from data of a differing nature (species richness, presence/absence and relative abundance) and, especially, to discern variation in richness (species loss) from changes in the identity or abundance of species (species replacement). 4.Results show that the pond amphibian assemblages in Doñana National Park exhibited high inter-annual variability during the study period, both in the number of species, species identity and their relative abundance. This result provides evidence for the inadequacy of surveys conducted only in one breeding season to characterize the species assemblage associated with a given pond. Besides, it suggests that a given pond offers different breeding opportunities over time, being suitable for different species depending on the year. This alternation will contribute to the medium-term preservation of all species in the assemblage. 5.It is highly relevant to preserve the natural dynamism and spatial variability of temporary pond systems, which will favour the conservation of populations through their intrinsic variability. Copyright © 2010 John Wiley & Sons, Ltd. [source] Diel variation in the seagrass ichthyofaunas of three intermittently open estuaries in south-eastern Australia: implications for improving fish diversity assessmentsFISHERIES MANAGEMENT & ECOLOGY, Issue 2 2001S. P. Griffiths Diel variation in the ichthyofaunas associated with Zostera capricorni Ascherson was investigated in three intermittently open estuaries in the Illawarra region, New South Wales. Each estuary showed differing diel shifts in fish assemblages, which appeared to be related to estuary size. In the largest estuary (Lake Illawarra) significantly more species were caught during the night than the day for all months. In contrast, there was little diel variation in the fish assemblages at Werri Lagoon and Shellharbour Lagoon, although many species were only caught during the night at both estuaries. The distinct diel changes at Lake Illawarra was thought to be attributable to the relatively deep channels adjacent to the seagrass beds which are better habitats for larger fishes compared with the shallow sand bars without deep channels throughout the two smaller estuaries. The composition of fish species within the three estuaries were significantly different, although each assemblage was characterised by large numbers of small-sized fish (<100 mm FL) indicating the importance of intermittently open estuaries as fish habitats. It was concluded that night sampling provided a more complete picture of the ichthyofaunas associated with Z. capricorni. As a result, inclusion of night sampling in fish diversity assessments would increase the chance of catching diurnally rare species and therefore attain a better representation of the true community structure. [source] Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGELETTERS IN APPLIED MICROBIOLOGY, Issue 4 2002R.S. Peixoto Aim: To evaluate the rpoB gene as a biomarker for PCR-DGGE microbial analyses using soil DNA from the Cerrado, Brazil. Methods: DNA extraction from soil was followed by Polymerase Chain Reaction (PCR) amplification of rpoB and 16S rRNA genes. PCR products were compared by Denaturing Gradient Gel Electrophoresis (DGGE) to compare gene/community profiles. Results: The rpoB DGGE profiles comprised fewer bands than the 16S rDNA profiles and were easier to delineate and therefore to analyse. Comparison of the community profiles revealed that the methods were complementary. Conclusions, Significance and Impact of the Study: The gene for the beta subunit of the RNA polymerase, rpoB, is a single copy gene unlike 16S rDNA. Multiple copies of 16S rRNA genes in bacterial genomes complicate diversity assessments made from DGGE profiles. Using the rpoB gene offers a better alternative to the commonly used 16S rRNA gene for microbial community analyses based on DGGE. [source] | ||||||||||