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Scaling Ordination (scaling + ordination)
Kinds of Scaling Ordination Selected AbstractsStream Macroinvertebrate Community Affected by Point-Source Metal PollutionINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 3 2007Hideyuki Doi Abstract The impacts of mining activities on aquatic biota have been documented in many stream ecosystems. In mining streams, point-source heavy metal pollution often appears in the stream. We hypothesize that this pollution is toxic to macroinvertebrates owing to high concentrations of metals and therefore affects macroinvertebrate community structure. We investigated macroinvertebrate community structure in mountain streams, including heavy metal-polluted sites and neutral-pH streams, to determine the relationship between community structure and environmental factors such as low pH and heavy metal concentrations. Based on multidimensional scaling ordination, the macroinvertebrate community at heavy metal pollution sites was remarkably different from that at the other sites. Inductively coupled plasma mass spectrometry revealed high concentrations of aluminum and iron in surface water at the polluted sites. Macroinvertebrate community structure at the metal pollution sites was significantly different from that at other sites in the same stream and in neutral-pH streams. Thus, point-source metal pollution may reduce the density and diversity of in situ macroinvertebrates. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The ED strategy: how species-level surrogates indicate general biodiversity patterns through an ,environmental diversity' perspectiveJOURNAL OF BIOGEOGRAPHY, Issue 8 2004D. P. Faith Abstract Biodiversity assessment requires that we use surrogate information in practice to indicate more general biodiversity patterns. ,ED' refers to a surrogates framework that can link species data and environmental information based on a robust relationship of compositional dissimilarities to ordinations that indicate underlying environmental variation. In an example analysis of species and environmental data from Panama, the environmental and spatial variables that correlate with an hybrid multi-dimensional scaling ordination were able to explain 83% of the variation in the corresponding Bray Curtis dissimilarities. The assumptions of ED also provide the rationale for its use of p-median optimization criteria to measure biodiversity patterns among sites in a region. M.B. Araújo, P.J. Densham & P.H. Williams (2004, Journal of Biogeography31, 1) have re-named ED as ,AD' in their evaluation of the surrogacy value of ED based on European species data. Because lessons from previous work on ED options consequently may have been neglected, we use a corroboration framework to investigate the evidence and ,background knowledge' presented in their evaluations of ED. Investigations focus on the possibility that their weak corroboration of ED surrogacy (non-significance of target species recovery relative to a null model) may be a consequence of Araújo et al.'s use of particular evidence and randomizations. We illustrate how their use of discrete ED, and not the recommended continuous ED, may have produced unnecessarily poor species recovery values. Further, possible poor optimization of their MDS ordinations, due to small numbers of simulations and/or low resolution of stress values appears to have provided a possible poor basis for ED application and, consequently, may have unnecessarily favoured non-corroboration results. Consideration of Araújo et al.'s randomizations suggests that acknowledged sampling biases in the European data have not only artefactually promoted the non-significance of ED recovery values, but also artefactually elevated the significance of competing species surrogates recovery values. We conclude that little credence should be given to the comparisons of ED and species-based complementarity sets presented in M.B. Araújo, P.J. Densham & P.H. Williams (2004, Journal of Biogeography31, 1), unless the factors outlined here can be analysed for their effects on results. We discuss the lessons concerning surrogates evaluation emerging from our investigations, calling for better provision in such studies of the background information that can allow (i) critical examination of evidence (both at the initial corroboration and re-evaluation stages), and (ii) greater synthesis of lessons about the pitfalls of different forms of evidence in different contexts. [source] The weed community affects yield and quality of soybean (Glycine max (L.) Merr.)JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 3 2008David J Gibson Abstract BACKGROUND: The relationship between the weed community and soybean (Glycine max (L.) Merr.) seed yield and quality was assessed in two experiments in Illinois, USA. In one field different proportions of target weeds (Ambrosia trifida L., Amaranthus rudis J. Sauer, and Setaria faberi F. Herrm) were sown into experimental plots, and the other field was naturally infested with these and other weeds. The composition of the weed communities in both fields was compared to soybean yield, biomass, canopy cover and quality (% protein, oil, relative water content, and seed weight) using non-metric dimensional scaling ordination. RESULTS: In the experimentally sown plots, low yield and low quality soybeans were harvested from plots dominated by the target weeds, particularly A. trifida, and a suite of subordinate volunteers. In the naturally infested field, highest soybean protein was associated with S. faberi early in the season and Ambrosia artemisiifolia and Ipomea hederacea later in the season, and low amounts of A. rudis throughout the growing season. CONCLUSION: Similar results from the two experiments indicate that soybean seed yield and quality are affected by the composition of the weed community. Producers need to manage the weed community to optimize seed quality. Copyright © 2007 Society of Chemical Industry [source] Association of ecotones with relative elevation and fire in an upland Florida landscapeJOURNAL OF VEGETATION SCIENCE, Issue 3 2006E.A. Boughton Abstract: Question: What are the importance of elevation and fire in maintaining ecotones of Florida scrub assemblages along a gradual topographic gradient? Location: Archbold Biological Station (ABS), 12 km south of Lake Placid, Florida, USA. Methods: Vegetation cover of upland Florida shrublands was quantified using the line-intercept method along 20 transects traversing similar elevation gradients, stratified by time since fire (TSF). We objectively identified shrubland ecotones using a split moving windows boundary analysis (SMW) with three different window widths. Non-metric multidimensional scaling ordination was used to determine relationships among plant assemblages defined by SMW. Results: We located up to four ecotones per transect, the majority of which were wide, highly heterogeneous zones. Relative elevation controlled the distribution of plant assemblages in upland Florida shrublands. Ecotones in shrublands > 30 years TSF had relatively low dissimilarity values in SMW, indicating that previously discrete plant assemblages with longer TSF were becoming more similar with time. Conclusions Split Moving Windows (SMW) analysis identified ecotones relatively well although patches generated by oak clonal growth were sometimes identified as ecotones. Fire suppression caused ecotones to become more diffuse, suggesting that without fire at least every 30 years, discrete plant assemblages within upland Florida shrublands will be more continuous. [source] Testing candidate plant barcode regions in the MyristicaceaeMOLECULAR ECOLOGY RESOURCES, Issue 3 2008S. G. NEWMASTER Abstract The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon , UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis. [source] Effects of different secondary vegetation types on bat community composition in Central Amazonia, BrazilANIMAL CONSERVATION, Issue 2 2010P. E. D. Bobrowiec Abstract The process of secondary succession on degraded lands in the Amazon depends on their land-use histories. In this scenario, little is known about how animal communities respond to different types of secondary vegetation in the region. We examined the effects of abandoned cattle pasture, Vismia - and Cecropia -dominated regrowth on the abundance of bat species and community composition in the Central Amazon, Brazil, based on 11 netting sites and on landscape characteristics. We captured 1444 bats, representing 26 species and two families (Phyllostomidae and Mormoopidae). Among the six most-captured Phyllostomidae bats, Sturnira lilium and Sturnira tildae had significantly higher capture rates in abandoned pasture, while Rhinophylla pumilio predominated in both Vismia - and Cecropia -dominated regrowth. An hybrid multidimensional scaling ordination revealed significant differences in the bat community among the three types of secondary vegetation. Phyllostominae bats were more common and richer in the less-disturbed areas of Cecropia -dominated regrowth, while Stenodermatinae species were more captured in abandoned pastures. Our results suggest that the type of secondary vegetation, together with its land-use history, affects bat community composition in the Central Amazon. The Phyllostominae subfamily (gleaning animalivores) was habitat selective and disappeared from areas experiencing constant disturbances. On the other hand, Stenodermatinae frugivorous bats often used and foraged in altered areas. We suggest that secondary vegetations in more-advanced successional stages can be used to augment the total area protected by forest conservation units. [source] Land-use legacies in a central Appalachian forest: differential response of trees and herbs to historic agricultural practicesAPPLIED VEGETATION SCIENCE, Issue 2 2010James M. Dyer Abstract Question: Are contemporary herb and tree patterns explained by historic land use practices? If so, are observed vegetation patterns associated with life-history characteristics, soil properties, or other environmental variables? Location: Southeastern Ohio, USA. Methods: Using archival records, currently forested sites were identified with distinct land use histories: cultivated, pasture (but not plowed), and reference sites which appear to have never been cleared. Trees were recorded by size and species on twenty 20 m × 20 m plots; percent cover was estimated for each herb species in nested 10 m × 10 m plots. Environmental characteristics were noted, and soil samples analysed for nutrient availability and organic matter. Nonmetric multidimensional scaling ordination was performed separately on both tree and herb datasets to graphically characterize community composition among plots. Life-history traits were investigated to explain observed compositional differences. Results: Vegetation patterns were explained by current environmental gradients, especially by land-use history. Cultivated and pasture sites had similar tree composition, distinct from reference sites. Herb composition of pasture and reference sites was similar and distinct from cultivated sites, suggesting the ,tenacity' of some forest herbs on formerly cleared sites. Tilling removes rhizomatous species, and disfavors species with unassisted dispersal. These life-history traits were underrepresented on cultivated sites, although ant-dispersed species were not. Conclusions: Historic land-use practices accounted for as much variation in species composition as environmental gradients. Furthermore, trees and herbs responded differently to past land-use practices. Life-history traits of individual species interact with the nature of disturbance to influence community composition. [source] Patterns in marine hydrozoan richness and biogeography around southern Africa: implications of life cycle strategyJOURNAL OF BIOGEOGRAPHY, Issue 4 2010Mark J. Gibbons Abstract Aim, To examine patterns of marine hydrozoan richness around southern Africa and to test the hypothesis that patterns of biogeography become weaker with increasing dispersal ability. Location, The coastline of southern Africa from 21° S, 14° E to 28° S, 33° E, extending from the intertidal zone seawards a distance of 200 nautical miles. Methods, Published and unpublished information on the distribution of marine Hydrozoa was entered as presence/absence data onto a gridded coastline of the region. A similarity matrix between the species composition of grid squares was constructed using the Bray,Curtis index and visualized using non-metric multidimensional scaling ordinations. Separate analyses were conducted, and compared, on the three major life cycle groupings: holoplanktic, meroplanktic and benthic. Results, Over 450 species of marine Hydrozoa have been reported from the region, and species richness increases eastwards, in a manner at odds with the distribution of sampling effort. There was a significant correlation between the geographic structures of the resemblance matrices generated for the three life cycle groupings. In other words, all three groups showed similar patterns of biogeography around the region, and these were broadly similar to those reported by others. However, there were differences between them that reflect the resolution at which the data were examined. At a level of 40% similarity, there was no biogeographic structure to the holoplanktic fauna, the meroplanktic taxa were simply sub-divided into cool- and warm-temperate/subtropical elements, and in the case of benthic taxa, the cool-water fauna was further split into a southern Namaqua and a depauperate northern Namib component. Even at a resolution of 70% similarity, the holopelagic taxa could be separated only into cool-temperate and warm-temperate/subtropical faunas. Main conclusions, Holoplanktic taxa show comparatively less biogeographic structure than meroplanktic taxa, which in turn show less clearly defined biogeographic structure than benthic taxa. It is suggested that this is related to the interaction between oceanography and dispersive-stage duration. The role that the Agulhas Current plays in influencing the Benguela Current fauna is highlighted. This study has implications for conservation planning exercises based on protecting representative biotopes in different biogeographic regions. [source] | |||||||||||||