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Rarefaction Analysis (rarefaction + analysis)
Selected AbstractsHigh bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone libraryENVIRONMENTAL MICROBIOLOGY, Issue 11 2002Udo Friedrich Summary The bacterial diversity of an industrial biofilter used for waste gas abatement in an animal-rendering plant was investigated. A 16S rDNA clone library was generated and 444 clones were screened using computer-aided amplified ribosomal DNA restriction analysis (ARDRA). Of the screened clones, 60.8% showed unique ARDRA patterns and the remaining 174 clones were clustered into 65 groups. Almost full-length 16S rDNA sequences of 106 clones were determined and 90.5% of the clones were affiliated with the two phyla Proteobacteria and Bacteroidetes. Alpha -, Beta -, and Gammaproteobacteria accounted for 22.1, 17.6 and 18.6% respectively. Minor portions were affiliated with the Actinobacteria (2.0%), Firmicutes and Verrucomicrobia (both 1.0%), and the Deltaproteobacteria and Thermomicrobia (each 0.5%). Only six out of the 106 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species indicating that a substantial fraction of the clone sequences were derived from unknown taxa. It was also evaluated whether a database containing 281 computer-simulated bacterial rDNA fragment patterns generated from published reference sequences can be used for identification purposes. The data analysis demonstrated that this was possible only for a small number of clones, which were closely related to described bacterial strains. Rarefaction analysis of ARDRA clusters demonstrated that the 444 clones screened are insufficient to describe the entire diversity of the clone library. [source] High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: identification of two new bacterial candidate divisionsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2001Vanessa M. Madrid Abstract Bacterial and archaeal community compositions in highly mobile nearshore muds typical of the Guiana coastline of South America were examined by sequence analysis of a 16S rDNA clone library. DNA was extracted from a subsurface sediment layer (10,30 cm) collected at a subtidal (,1 m deep) mud wave site between Kourou and Sinnamary, French Guiana. Analysis of 96 non-chimeric sequences showed the majority to be bacteria (98%), that diversity was high with 64 unique sequences, and that proteobacteria were dominant (46%). Two crenarchaeota sequences were found (2%). Bacterial sequences belonged to the Cytophaga-Flexibacter-Bacteroides (18%), Actinobacteria (11.5%), Planctomycetes (6.3%), Cyanobacteria (3.2%), low-GC Gram-positive (1%), ,, , and , subdivisions of Proteobacteria (27%, 16%, and 9%, respectively). Additional bacterial sequences belonged to the candidate division TM6 (1%) and to two newly proposed candidate divisions: KS-A (2%) and KS-B (3%). A sizeable fraction (22%) of sequences from the Kourou,Sinnamary library are normally found in water column populations, reflecting frequent entrainment of suspended debris into physically reworked underlying sediments. Dominant sequences (56%) were related to Gelidibacter algens (Cytophaga-Flexibacter-Bacteroides group), Actinobacteria, Sulfitobacter and Ruegeria spp. (,-proteobacteria), all of which are chemoorganotrophs, consistent with abundant labile organic carbon. The presence of sequences from potential sulfate reducers and sulfide oxidizers suggests the likelihood of sulfur cycling in these sediments, despite the dominance of suboxic (iron-reducing), non-sulfidic diagenetic properties. Rarefaction analysis indicated that bacterial diversity in the French Guiana library is not only unusually high in comparison with other marine sedimentary environments, but among the most diverse of all environments reported to date. [source] Estimating population parameters in a threatened arctic fox population using molecular tracking and traditional field methodsANIMAL CONSERVATION, Issue 4 2008T. Meijer Abstract Comprehensive population parameter data are useful for assessing effective conservation actions. The Fennoscandian arctic fox Alopex lagopus is critically endangered and the population size is estimated at 120 individuals that are fragmented into four isolated populations. Here, we use molecular tracking and visual observations to estimate population size and survival in one of the populations on the Swedish mountain tundra during a year of low food availability. We collected 98 arctic fox faecal samples during the winter of 2006 and recorded visual observations of ear-tagged individuals during the summer of 2005 and 2006. The faecal samples were analysed for variation in nine microsatellite loci and matched to the genetic profiles of previously ear-tagged individuals from 2001 to 2005. During winter 2006, the minimum number alive was 12 individuals using visual observations, 30 using molecular tracking and 36 by combining the datasets. Population size was estimated through mark,recapture for the molecular tracking and visual observation datasets and through rarefaction analyses for molecular tracking data. The mark,recapture estimate for visual observations was uninformative due to the large confidence interval (CI) (i.e. 6,212 individuals). Based on the molecular tracking dataset combined with the minimum number alive for visual observations and molecular tracking, we concluded a consensus population size of 36,55 individuals. We also estimated the age-specific finite survival rate during 1 year (July 2005 to July 2006) by combining molecular tracking with visual observations. Juvenile survival on a yearly basis was 0.08 (95% CI 0.02,0.18) while adults had a survival of 0.59 (95% CI 0.39,0.82). Juveniles displayed a lower survival than the adults during autumn (P<0.01) whereas no age-specific survival difference during spring was found. The risk of negative effects due to the small population size and low juvenile survival is accordingly considerable. [source] Functional rarefaction: estimating functional diversity from field dataOIKOS, Issue 2 2008Steven C. Walker Studies in biodiversity-ecosystem function and conservation biology have led to the development of diversity indices that take species' functional differences into account. We identify two broad classes of indices: those that monotonically increase with species richness (MSR indices) and those that weight the contribution of each species by abundance or occurrence (weighted indices). We argue that weighted indices are easier to estimate without bias but tend to ignore information provided by rare species. Conversely, MSR indices fully incorporate information provided by rare species but are nearly always underestimated when communities are not exhaustively surveyed. This is because of the well-studied fact that additional sampling of a community may reveal previously undiscovered species. We use the rarefaction technique from species richness studies to address sample-size-induced bias when estimating functional diversity indices. Rarefaction transforms any given MSR index into a family of unbiased weighted indices, each with a different level of sensitivity to rare species. Thus rarefaction simultaneously solves the problem of bias and the problem of sensitivity to rare species. We present formulae and algorithms for conducting a functional rarefaction analysis of the two most widely cited MSR indices: functional attribute diversity (FAD) and Petchey and Gaston's functional diversity (FD). These formulae also demonstrate a relationship between three seemingly unrelated functional diversity indices: FAD, FD and Rao's quadratic entropy. Statistical theory is also provided in order to prove that all desirable statistical properties of species richness rarefaction are preserved for functional rarefaction. [source] Distance Decay of Tree Species Similarity in Protected Areas on Terra Firme Forests in Colombian AmazoniaBIOTROPICA, Issue 5 2009Álvaro Duque ABSTRACT In this study, we investigated the pattern of floristic similarity as a function of geographical distances and environmental variability in well-drained uplands (terra firme) in Colombian Amazonia. The study site comprised three National Natural Parks, Tinigua, Chiribiquete, and Amacayacu, located in different geological units that represent a soil fertility gradient linked to parental materials. Differences in species richness between sites were compared using rarefaction analysis. A clear floristic transition appeared in the east,west direction following a soil fertility gradient along the first PCoA axis. In multiple regression analyses based on distance matrices, both geographical distances and geology explained 64 percent of the total floristic variation. Geographical distances alone accounted for 12 percent of variation in floristic similarities among plots, while geology alone accounted for 1 percent, and the joint effect of both explained 51 percent of the floristic variation. The species richness trend supports the existence of a latitudinal corridor southward of the geographical Equator in the Amazon basin, where tree diversity reaches the maximum expected values. A coupled effect of stochastic dispersal limitation and habitat specialization would certainly appear to be an appropriate explanation for tree species turnover in terra firme forests in Colombian Amazonia, strongly emphasizing that competition and neutrality must be supplementary rather than mutually exclusive processes. This result pinpoints the effect of dispersal on floral mixing as an ongoing active process for structuring tree communities in NW Amazonia, and the size of the reserves as a relevant issue to protect rare species from extinction by chance. 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