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Canonical Correspondence Analysis (canonical + correspondence_analysis)
Selected AbstractsThe spatial pattern of soil-dwelling termites in primary and logged forest in Sabah, MalaysiaECOLOGICAL ENTOMOLOGY, Issue 1 2007SARAH E. DONOVAN Abstract 1.,Primary and logged lowland dipterocarp forest sites were sampled for subterranean termites using soil pits located on a grid system in order to detect any patchiness in their distribution. 2.,A spatial pattern in termite distributions was observed in the primary and logged sites, but the response differed between soil-feeding and non-soil-feeding termites. 3.,Spatial analysis showed that soil-feeding termites were homogeneously distributed in the primary forest but significantly aggregated in the logged forest. This pattern was reversed for non-soil-feeding termites and may result from differences in resource provisioning between the two sites. 4.,Gaps in termite distribution comprised a greater area than patches for both feeding groups and sites, but gaps dominated the logged site. 5.,A significant association between soil-feeding and non-soil-feeding termite distributions occurred at both sites. This arose from an association between patches in the primary forest and between gaps in the logged forest. 6.,Termite spatial pattern was optimally observed at a minimum extent of 64 m and lag of 2 m. 7.,The spatially explicit SADIE (Spatial Analysis by Distances IndicEs) analyses were more successful than (non-spatially explicit) multivariate analysis (Canonical Correspondence Analysis) at detecting associations between termite spatial distributions and that of other biotic and abiotic variables. [source] An application of canonical correspondence analysis for developing ecological quality assessment metrics for river macrophytesFRESHWATER BIOLOGY, Issue 5 2005IAN DODKINS Summary 1. Aquatic macrophyte composition and abundance is required by the European Union's Water Framework Directive for determining ecological status. Five metrics were produced that can be combined to determine the deviation of aquatic macrophytes from reference conditions in Northern Ireland's rivers. 2. Species optima and niche breadths along silt, nitrate, pH, conductivity and dissolved oxygen gradients were generated from aquatic macrophyte and water quality surveys conducted at 273 sites throughout Northern Ireland using Canonical Correspondence Analysis (CCA). Five metric scores based on these environmental gradients were determined at new monitoring sites using the mean optima of the species occurring at the site, weighted by percentage cover and niche breadth of each species. 3. A preliminary reference network of 32 sites of high physico-chemical and hydromorphological quality, and representative of the range of river types in Northern Ireland, enabled reference metric scores to be produced for each river type. Five unimpacted and twenty impacted sites were used for testing the performance of the metrics. By subtracting reference metric scores from metric scores at a monitoring site measures of ecological impact could be determined along five different impact gradients. Metrics were also combined to give a measure of total ecological change. 4. The metrics system distinguished unimpacted from impacted sites and correctly identified 77% of the known impacts. The metrics distinguished different types of impact, e.g. silt and nitrate. 5. Aquatic macrophyte occurrence and abundance has high natural variability at a site, both temporally and spatially. This method was designed to be sensitive to ecological change whilst reducing noise caused by natural variation. [source] Structure of Macroinvertebrate Communities in Relation to Environmental Variables in a Subtropical Asian River SystemINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 1 2010Xiao-Ming Jiang Abstract Subtropical Asian rivers support a highly diverse array of benthic macroinvertebrates. Yet, their biodiversity and functionality has been poorly investigated. We choose the Chishui River system, one of the largest un-dammed, first level branches upstream of the Yangtze River, China, to: 1) determine the spatial pattern of macroinvertebrate diversity and community structure, and 2) examine the influence of variables at local habitat and basin scales on the distribution of macroinvertebrate communities. Samples were collected from 43 sites in spring of 2007. After Canonical Correspondence Analysis, two basin and five habitat variables were found to be significant predictors of the macroinvertebrate community structure. Variance partitioning analysis showed that habitat physical variables had a greater influence than other environmental variables in macroinvertebrate community, which suggested that preserving habitat, especially upstream, should be strongly considered in biological conservation. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Assessment of the Ecological Status of Streams in Two Carpathian SubregionsINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 4-5 2007Il'ja Krno Abstract A multimetric assessment system was developed to determine the ecological status of two types of stream in the Carpathian ecoregion following the requirements of the WFD. The organic pollution gradient was defined using Canonical Correspondence Analysis. Classification based on physical, chemical and biological data divided the tested sites into two stream types with subsequent grouping into several ecological quality classes. From all the metrics tested, 17 for the East Carpathian streams and 15 for the West Carpathian streams, from seven metric categories, were included in the resulting multimetric index. Different kinds of response to degradation (linear, unimodal, exponential) were observed. The Saprobic index (Zelinka and Marvan), Rheoindex (Banning, with abundance classes) and Index of Biocenotic region, showed the best discriminatory ability for both stream types. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Pluralism and diversity: trends in the use and application of ordination methods 1990-2007JOURNAL OF VEGETATION SCIENCE, Issue 4 2009Henrik Von Wehrden Abstract Question: What are the trends and patterns in the application of ordination techniques in vegetation science since 1990? Location: Worldwide literature analysis. Methods: Evaluation of five major journals of vegetation science; search of all ISI-listed ecological journals. Data were analysed with ANCOVAs, Spearman rank correlations, GLMs, biodiversity indices and simple graphs. Results: The ISI search retrieved fewer papers that used ordinations than the manual evaluation of five selected journals. Both retrieval methods revealed a clear trend in increasing frequency of ordination applications from 1990 to the present. Canonical Correspondence Analysis was far more frequently detected by the ISI search than any other method. Applications such as Correspondence Analysis/Reciprocal Averaging and Detrended Correspondence Analysis have increasingly been used in studies published in "applied" journals, while Canonical Correspondence Analysis, Redundancy Analysis and Non-Metric Multidimensional Scaling were more frequently used in journals focusing on more "basic" research. Overall, Detrended Correspondence Analysis was the most commonly applied method within the five major journals, although the number of publications slightly decreased over time. Use of Non-Metric Multidimensional Scaling has increased over the last 10 years. Conclusion: The availability of suitable software packages has facilitated the application of certain techniques such as Non-Metric Multidimensional Scaling. However, choices of ordination techniques are currently less driven by the constraints imposed by the software; there is also limited evidence that the choice of methods follows social considerations such as the need to use fashionable methods. Methodological diversity has been maintained or has even increased over time and reflects the researcher's need for diverse analytical tools suitable to address a wide range of questions. [source] Role of host identity in effects of phytogenic mounds on plant assemblages and species richness on coastal arid dunesJOURNAL OF VEGETATION SCIENCE, Issue 5 2007Magdy I. El-Bana Abstract Question: Phytogenic mounds (nebkhas) - the natural accumulation of wind-blown sediments within or around the canopies of plants - have been proposed as important structures for locally maintaining high species richness in coastal and arid ecosystems. Nebkhas are assumed to increase habitat heterogeneity, but what is the importance of the nebkha host species relative to other nebkha characteristics in determining the associated plant assemblages? Are some host species more effective in creating diversity hotspots, or does a single species-area relationship apply to all nebkhas, regardless of host species? Can the influence of the host be ascribed to its indirect effects on abiotic attributes of the nebkha complex? Methods and location: We investigated plant species richness and composition on nebkhas around six psammophytic species on Mediterranean coastal dunes of the Sinai Peninsula. Results: Plant species richness was significantly related to nebkha size by the single power function according to the general prediction of island biogeography theory, but this relationship was modified - though to a limited degree - by nebkha host species identity. Canonical Correspondence Analysis revealed that nebkha host species identity and nebkha environmental and non-environmental factors significantly explained species composition on the nebkhas, but host species identity did so to a greater extent. The latter might reflect differences in seed trapping ability or free space for colonization between host species. Conclusion: Differences in community composition and richness among nebkhas formed by different host species represent a key factor in the maintenance of plant diversity on arid coastal dunes. [source] Groundwater input affecting plant distribution by controlling ammonium and iron availabilityJOURNAL OF VEGETATION SCIENCE, Issue 4 2006Esther C.H.E.T. Lucassen Abstract Question: How does groundwater input affect plant distribution in Alnus glutinosa (black alder) carrs? Location: Alder carrs along the river Meuse, SE Netherlands. Methods: Three types of site, characterized by groundwater flow, were sampled in 17 A. glutinosa carrs. Vegetation and abiotic data (soil and water chemistry) were collected and analysed using a Canonical Correspondence Analysis. Based on the results, a laboratory experiment tested the effect of groundwater input (Ca2+) on pore water chemistry (NH4+ availability). Results: Environmental factors indicating groundwater input (Ca2+ and Fe2+), correlating with the NH+4 concentration in the pore water, best explained the variation in plant distribution. NH4+ availability was determined by Ca2+ input via the groundwater and subsequent competition for exchange sites in the sediment. As a result, nutrient-poor seepage locations fully fed by groundwater were dominated by small iron resistant plants such as Caltha palustris and Equisetum fluviatile. More nutrient-rich locations, fed by a combination of groundwater and surface water, allowed the growth of taller iron resistant plant species such as Carex paniculata. Nutrient-rich locations with stagnating surface water were hardly fed by groundwater, allowing the occurrence of fast growing and less iron tolerant wetland grasses such as Glyceria fluitans and G. maxima. Conclusion: Groundwater input affects plant composition in A. glutinosa carrs along the river Meuse by determining nutrient availability (ammonium) and concentrations of toxic iron. [source] Differences in forest composition in two boreal forest ecoregions of QuebecJOURNAL OF VEGETATION SCIENCE, Issue 6 2000Sylvie Gauthier Abstract. In order to describe and compare the post-fire succession patterns of the two ecological regions (mixed-wood and coniferous ecoregions) of northwestern Quebec, 260 forest stands were sampled with the point-centred plot method. The mixed-wood ecological region belongs to the Abies balsamea-Betula papyrifera bioclimatic domain whereas the coniferous ecological region belongs to the Picea mariana -moss bioclimatic domain. In each plot, tree composition was described, surficial deposits and drainage were recorded, and fire history was reconstructed using standard dendro-ecological methods. Ordination techniques (Correspondence Analysis and Canonical Correspondence Analysis) were used to describe the successional patterns of forest vegetation and to correlate them with the explanatory variables. The results showed the importance of surficial deposits, the time since fire and the ecoregion in explaining the variation of stand composition. Abies balsamea tends to increase in importance with an increase in time since fire, and this trend is more pronounced in the mixed-wood region. Even when controlling both for surficial deposits and time since fire, differences in successional trends were observed between the two ecoregions. As all the species are present in both ecoregions and as they are all observed further north, our results suggest that both the landscape configuration and fire regime parameters such as fire size and fire intensity are important factors involved in these differences. [source] Environmental and geographic correlates of the taxonomic structure of primate communitiesAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Jason M. Kamilar Abstract Previous research has shown that both environmental and historical factors influence the taxonomic structure of animal communities; yet, the relative importance of these effects is not known for primates. Environmental characteristics shape the possible niches in a community, providing suitable habitats for some species and not others. Therefore, communities found in similar environments should display similar species compositions. Additionally, geography may be viewed as a surrogate for historical processes. For instance, as the geographic distance between communities increases, dispersal between sites is more limited, and the probability of historical vicariance increases. Therefore, communities in close proximity to each other should exhibit similar species compositions. The geographic location, environmental characteristics, and species composition of 168 primate communities were gathered from the literature. Canonical correspondence analyses were conducted to examine the relative effects of geographic distance and environmental variables on the taxonomic structure of communities. In addition, UPGMA cluster analyses were conducted to better visualize the taxonomic similarity of communities. Spatial variables were significant predictors of community structure in all regions. Rainfall patterns explained African, Malagasy, and Neotropical community structure. In addition, maximum temperature was also correlated with community structure in Madagascar and the Neotropics. No climatic variables predicted Asian community structure. These results demonstrate that both historical and environmental factors play a significant role in structuring modern primate communities; yet, the importance of environmental factors depend on the region in question. Am J Phys Anthropol, 2009. © 2008 Wiley-Liss, Inc. [source] Patterns of Floristic Differentiation among Atlantic Forests in Southeastern Brazil and the Influence of Climate,BIOTROPICA, Issue 4b 2000Ary T. Oliveira-Filho ABSTRACT The tree flora of southeastern Brazilian Atlantic forests was investigated according to two main aspects: (a) the variations in floristic composition of bodi rain and semi-deciduous forests were analyzed in terms of geographic and climatic variables by performing multivariate analyses on 125 existing floristic checklists; and (b) the links of both rain and semi-deciduous forests to Amazonian forests and Cerrados (woody savanna) were assessed. All analyses were performed at the species, genus, and family levels. The information obtained for the 125 forest areas was organized into an environmental database containing geographic and climatic records, and a floristic database containing binary presence records for 2532 species, 520 genera, and 106 families. Canonical correspondence analyses (CCA) were utilized to assess the relationship between geographic and climatic variables, and tree flora composition. Venn diagrams and cluster analyses were used to assess the floristic links to Amazonian forests and Cerrados. The following patterns were detected at all three taxonomic levels: (a) the differentiation between rain and semi-deciduous forests is floristically consistent and strongly correlated with rainfall regime, although transitions may be abrupt to gradual; (b) a north,south differentiation exists for both rain and semi-deciduous forests, probably caused by variations in both temperature and rainfall regime; (c) The flora of semi-deciduous forests also changes with increasing distance from the ocean and the associated increasing rainfall seasonality; and (d) elevation and associated temperatures are strongly correlated with the internal differentiation of both rain and semi-deciduous forests. To a considerable extent, the tree flora of semi-deciduous forests is a subset of the rain forest flora, probably extracting species that are able to cope with a longer dry season. There is greater floristic similarity at the species level between Atlantic rain and semi-deciduous forests than between any of these and either Amazonian rain forests or Cerrados. Nevertheless, semi-deciduous forests and Cerrados show stronger links, particularly at the generic and familial levels. Therefore, rhere is little floristic ground for viewing Atlantic rain forests as being closer to their Amazonian counterparts than to the adjacent semi-deciduous forests. The most appropriate view of rain and semi-deciduous forests in southeastern Brazil is that of a continuum in tree species distribution. We suggest that the definition of Atlantic forests should be as comprehensive as that of Amazonian forests. RESUMO A flora arbórea das florestas Atlãnticas do sudeste do Brasil é investigada sob dois aspectos principals: (a) as varia¸ões em composi¸ão florística de florestas ombrófilas e semidecíduas são analisadas sob a ótica de variáveis geográficas e climáticas por meio de análises multivariadas de 125 listagens florísticas existentes na literatura; e (b) os la¸os das florestas ombrófilas e semidecíduas com as florestas Amazõnicas e cerrados são avaliados. Todas análises foram feitas nos níveis de espécie, gênero e família. A informa¸ão obtida para as 125 áreas de floresta foi organizada em um banco de dados ambientais, contendo registros geográficos e climáticos, e um banco de dados florísticos, contendo registros binários de presen¸a para 2532 espécies, 520 gêneros e 106 famílias. Análises de correspondência canõnica (ACC) foram utilizadas para avaliar as rela¸ões entre variáveis geográficas e climáticas e a composi¸ão da flora arbórea. Diagramas de Venn e análises de agrupamento foram utilizados para avaliar os la¸os florísticos com florestas Amazõnicas e cerrados. Os seguintes padrões foram detectados para todos os níveis taxonõmicos: (a) A diferencia¸ão entre florestas ombrófilas e semidecíduas é floristicamente consistente e fortemente correlacionada com o regime de chuvas, embora as transi¸ões possam ser abruptas a graduais; (b) Há uma diferencia¸ão norte-sul tanto para florestas ombrófilas como semidecíduas, provavelmente causada por varia¸ões em temperatura e regime de chuvas; (c) A flora das florestas semidecíduas também muda com a distãncia do oceano e o correspondente aumento da dura¸ão da esta¸ão seca; e (d) Altitude e suas correspondentes varia¸ões de temperatura são fortemente correlacionadas com a diferencia¸ão interna tanto das florestas ombrófilas como semidecíduas. A flora arbórea das florestas semidecíduas é, em boa medida, um sub-conjunto da flora das florestas ombrófilas, provavelmente extraindo espécies capazes de enfrentar uma esta¸ão seca mais prolongada. Há mais similaridade florística, no nível de espécies, entre florestas Atlãnticas ombrófilas e semidecíduas do que entre qualquer destas e as florestas Amazõnicas, ou mesmo os cerrados. No entanto, florestas semidecíduas e cerrados mostram la¸os florísticos mais fortes, particularmente nos níveis de gênero e família. Portanto, há pouco fundamento florístico para se pensar nas florestas ombrófilas Atlãnticas como mais próximas de suas correspondentes Amazõnicas do que de suas vizinhas semidecíduas. A abordagem mais correta para florestas ombrófilas e semidecíduas do sudeste brasileiro é de um contínue de distribui¸ão de espécies. Sugerimos, portanto, que a defini¸ão de florestas Atlãnticas deve ser tão abrangente quanto a das florestas Amazõnicas. [source] Site scores and conditional biplots in canonical correspondence analysisENVIRONMETRICS, Issue 1 2004Jan Graffelman Abstract Canonical correspondence analysis is an important multivariate technique in community ecology. It produces an interesting biplot that summarizes the data matrices involved in the analysis. The method produces two sets of site scores that can be used in a biplot. One set concerns site scores that are weighted averages of the species scores (WA scores), and the other set represents site scores that are linear combinations of the environmental variables (LC scores). We show that the use of both sets of scores in a CCA biplot can be justified. The use of the WA scores leads to the best possible representation of the species data conditional on the representation of the weighted averages. Likewise, the LC scores lead to the best possible representation of the environmental variables, also conditional on the representation of the weighted averages and on the use of a Mahalanobis metric. The eigenvalues obtained in CCA indicate how well the species data are represented when LC scores are used. The quality of representation of the species data when WA scores are used can be computed from the CCA eigenvalues and the variances of the WA scores. Scalar products between WA scores and environmental variable vectors do not form a biplot of the environmental data. Theoretical results are illustrated with Australian data from freshwater ecology. Copyright © 2003 John Wiley & Sons, Ltd. [source] Lake depth rather than fish planktivory determines cladoceran community structure in Faroese lakes , evidence from contemporary data and sedimentsFRESHWATER BIOLOGY, Issue 11 2006SUSANNE LILDAL AMSINCK Summary 1. This study describes the environmental conditions and cladoceran community structure of 29 Faroese lakes with special focus on elucidating the impact of fish planktivory. In addition, long-term changes in biological structure of the Faroese Lake Heygsvatn are investigated. 2. Present-day species richness and community structure of cladocerans were identified from pelagial snapshot samples and from samples of surface sediment (0,1 cm). Multivariate statistical methods were applied to explore cladoceran species distribution relative to measured environmental variables. For Lake Heygsvatn, lake development was inferred by cladoceran-based paleolimnological investigations of a 14C-dated sediment core covering the last ca 5700 years. 3. The 29 study lakes were overall shallow, small-sized, oligotrophic and dominated by brown trout (Salmo trutta). Cladoceran species richness was overall higher in the surface sediment samples than in the snapshot samples. 4. Fish abundance was found to be of only minor importance in shaping cladoceran community and body size structure, presumably because of predominance of the less efficient zooplanktivore brown trout. 5. Canonical correspondence analysis showed maximum lake depth (Zmax) to be the only significant variable in explaining the sedimentary cladoceran species (18 cladoceran taxa, two pelagic, 16 benthic) distribution. Multivariate regression trees revealed benthic taxa to dominate in lakes with Zmax < 4.8 m and pelagic taxa to dominate when Zmax was > 4.8 m. 6. Predictive models to infer Zmax were developed using variance weighted-averaging procedures. These were subsequently applied to subfossil cladoceran assemblages identified from a 14C-dated sediment core from Lake Heygsvatn and showed inferred Zmax to correspond well to the present-day lake depth. A recent increase in inferred Zmax may, however, be an artefact induced by, for instance, eutrophication. [source] Determinants of inselberg floras in arid Nama Karoo landscapesJOURNAL OF BIOGEOGRAPHY, Issue 10 2001Antje Burke Aim This study investigated the relationship between inselberg floras in floristic and functional terms and their correlation with environmental variables at macro-scale and landscape level. Location Four inselberg landscapes in Namibia's arid Nama Karoo in southern Africa were selected. Methods Plant surveys were undertaken over a 3-year period and species composition, growth form and dispersal spectra were used as measures for floristic and functional composition. Canonical correspondence analysis (CCA) was employed as the main tool to explain the perceived patterns. Results Regarding floristic affinities, inselberg floras formed distinct groups per study area and thus geographical position, with strong correlations between inselbergs within a particular study area. Neither growth form nor dispersal spectra closely resembled the pattern that emerged in the ordination of floristic composition. The influence of geographical position lessened when functional rather than floristic measures were introduced in the analysis. Main conclusions (1) On landscape and macro-scale, floristic composition of inselberg floras was largely determined by geographical position, geology, elevation, habitat diversity, rock outcrop in the surrounding and surface area of inselbergs. (2) Environmental variables operating at landscape level had greater influence on functional composition than on floristic composition. (3) Stochastic variables were more important in shaping the flora of these arid Nama Karoo inselbergs than deterministic processes such as niche relations and competition. [source] Turnover in flightless invertebrate species composition over different spatial scales in Afrotemperate forest in the Drakensberg, South AfricaAFRICAN JOURNAL OF ECOLOGY, Issue 3 2009Charmaine Uys Abstract An understanding of species turnover at different spatial scales and the influence of environmental variables including distance are important for conservation planning and management. Ground dwelling, flightless invertebrates have poor dispersal abilities and other taxa may not be effective as surrogates. This is an important consideration for biodiversity conservation in Afrotemperate forests of the Drakensberg Mountains, South Africa, where flightless invertebrates are geographically isolated by the naturally fragmented state of forests. Seventeen Afrotemperate forests in four reserves across the Drakensberg were sampled using soil and leaf litter sampling, pitfall traps, active search quadrats and tree beats. Seventy-two species were recorded, comprising 31 mollusc, nine earthworm, one onychophoran, six centipede, twelve millipede and thirteen ant species. Canonical correspondence analysis indicated that latitude (distance); fire history (disturbance) and mean annual precipitation were the most important factors governing invertebrate assemblage composition. ,sim measurements detected change in species at all spatial scales investigated, but no clear trends were evident. Distance or spatial scale alone does not explain species turnover and community composition. Effective selection of target areas, therefore, requires species level information to identify species of special concern. Résumé Une bonne compréhension de la rotation des espèces à différentes échelles spatiales et de l'influence des variables environnementales, y compris de la distance, est importante pour la planification et la gestion de la conservation. Les invertébrés qui vivent dans le sol, ceux qui ne volent pas, n'ont que de faibles capacités de se disperser, et d'autres taxons peuvent ne pas être des substituts efficaces. Ceci pourrait être une réflexion importante pour la conservation de la biodiversité dans les forêts afro-tempérées des monts Drakensberg, en Afrique du Sud, où des invertébrés qui ne volent pas sont isolés géographiquement par l'état naturellement fragmenté des forêts. On a prélevé des échantillons dans 17 forêts afro-tempérées, dans quatre réserves du Drakensberg, en utilisant des échantillons de sols et de litière de feuilles, des pièges, la recherche active dans des quadrats et le battage d'arbres. On a enregistré 72 espèces comprenant 31 mollusques, neuf vers de terre, un onychophore, six centipèdes, 12 mille-pattes et 13 fourmis. L'analyse canonique des correspondances a indiqué que la latitude (distance), l'historique des feux (perturbations) et les précipitations annuelles moyennes étaient les facteurs les plus importants pour la composition des assemblages d'invertébrés. Des mesures de ,sim ont détecté des changements d'espèces dans toutes les échelles spatiales étudiées, mais aucune tendance nette n'était visible. L'échelle de distance ou d'espace n'explique pas seule la rotation des espèces et la composition de la communauté. La sélection effective de zones cibles requiert donc des informations au niveau des espèces pour pouvoir identifier les espèces dont le statut est particulièrement inquiétant. [source] Relationships between fish assemblages, macrophytes and environmental gradients in the Amazon River floodplainJOURNAL OF FISH BIOLOGY, Issue 3 2003P. Petry During the flood season of 1992,1993, 139 species of fishes were collected from a floodplain lake system in the central Amazon Basin. Fish species distribution was examined relative to abiotic variables in seven vegetation strata on Marchantaria Island, Solimões River. Both environmental variables and species distributions were influenced by a river channel to floodplain-interior gradient. Species diversity was significantly higher in vegetated areas than in unvegetated areas, with deeper water Paspalum repens stands harbouring the highest diversity. As a result, species richness and catches were positively related to habitat complexity, while catch was also negatively related to dissolved oxygen (DO) and water depth. Low DO and shallow waters appeared to act as a refuge from predation. Fish assemblages were related to water chemistry, but species richness was not. Canonical correspondence analysis provided evidence that floodplain fish assemblages formed by the 76 most common species were influenced by physical variables, macrophyte coverage and habitat complexity, which jointly accounted for 67% of the variance of fish species assemblages. Omnivores showed no pattern relative to the river channel to floodplain-interior gradient while detritivores were more likely to be found at interior floodplain sites and piscivores closer to the river. Piscivores could be further separated into three groups, one with seven species associated with free-floating macrophytes in deep water, a second with five species found in shallow waters with rooted grasses and a third with six open water orientated species. The results suggest that fish assemblages in the Amazon floodplain are not random associations of species. [source] Modern distribution of saltmarsh testate amoebae: regional variability of zonation and response to environmental variablesJOURNAL OF QUATERNARY SCIENCE, Issue 5-6 2002Dan J. Charman Abstract Sea-level reconstruction from biological indicators in saltmarsh sediments requires an understanding of the modern ecology of the organisms concerned. Previous work suggested that testate amoebae are a potential new group of organisms to use for sea-level reconstruction, especially combined with diatoms and foraminifera. This paper analyses data from three saltmarshes on the Taf estuary, South Wales, the River Erme, Devon, and at Brancaster, Norfolk (UK) to (i) test for the presence and zonation of testate amoebae in relation to elevation; (ii) examine the similarity of zonation patterns between marshes; and (iii) explore the relationship between assemblage composition and a wider range of environmental variables. In addition we provide an update on the identification of testate amoebae on saltmarshes. Our results confirm that at all sites the primary environmental gradient is tidal inundation. Major changes in taxa along the tidal gradient are similar except for the lowest elevations, where different taxa become dominant at different sites. Canonical correspondence analysis (CCA) shows that assemblage composition is also strongly related to other variables, independent of the tidal position. Salinity, particle size and organic matter content are particularly important, and there is a statistically significant geographical effect on assemblages. Relationships between sea-level and assemblage composition are often stronger for individual sites, suggesting that local data sets should be used for quantitative sea-level reconstructions. However, the combined data set would provide more robust estimates of past sea-level change from fossil data. Other environmental variables explain as much of the variability in species assemblages as tidal parameters and should be considered more often in sea-level reconstructions based on microfossil indicators. Copyright © 2002 John Wiley & Sons, Ltd. [source] Secondary old-field succession in an ecosystem with restrictive soils: does time from abandonment matter?APPLIED VEGETATION SCIENCE, Issue 2 2010E. Martínez-Duro Abstract Question: Our knowledge of secondary old-field succession in Mediterranean environments is extremely poor and is non-existent for restrictive soil conditions. How these ecosystems, such as those on semi-arid gypsum outcrops, recover seems a priority for managing change and for ensuring conservation of specialized and endangered biota. We tested whether reinstallation of gypsum vegetation after cropland abandonment requires: (1) soil physical restructuring and (2) chemical readjustment to enable growth and survival of specialized gypsophilous vegetation, and more specifically how time from abandonment drives such environmental change. Location: We sampled a complete set of old fields on gypsum soils (1,60 yr since abandonment) in Villarrubia de Santiago (Toledo, Spain). Methods: Generalized linear models and model comparisons were used to analyse the effect of several environmental parameters on species abundance and richness. Ordination methods (canonical correspondence analyses and partial canonical correspondence analyses) were undertaken to evaluate compositional variation among the sampled fields. Results: Secondary old-field succession on semi-arid Mediterranean gypsum soils was controlled by a complex set of factors acting relatively independently. Surprisingly, time since abandonment explains only a small proportion of compositional variation (3%). Conversely, soil chemical features independently from time since abandonment are important for explaining differences found in old-field composition. Conclusions: Secondary succession on specialized Mediterranean soils does not follow the widely described "amelioration" process in which soil features and composition are closely related over time. Restrictive soil conditions control both structure and functioning of mature communities and also secondary succession. [source] Fish assemblages as influenced by environmental factors in streams in protected areas of the Czech RepublicECOLOGY OF FRESHWATER FISH, Issue 1 2006M. Humpl Abstract,,, Three streams of comparable size located in different landscape-protected areas were selected for studying the effect of environmental factors on fish assemblages using indirect (detrended correspondence analysis, DCA) and direct (canonical correspondence analysis, CCA) gradient analysis. DCA of species showed well a gradient of assemblage changes in the longitudinal profile. DCA of sites stressed the variability between the fish assemblages of the three streams. This pattern was then confirmed by the highly significant between-stream CCA. In the within-site CCA, environmental factors explained 50.7% variability for presence,absence data and 58.3% for the relative abundance data. The analysis revealed that number of ponds and land use are the most influential factors of the strongest environmental gradient. However, in the partial CCAs, factor substratum type explained the largest proportion of the variability affecting fish in their habitat choice. Generally, presence,absence and relative abundance data of fish gave similar results in both DCA and CCA analyses; the same environmental factors proved to be important in both data type analyses. The environmental factors explain more variability than the regional (between-stream) one. The total proportion of variability explained by the presence,absence data analysis was 71.9% and in the relative abundance analysis even 80.8%. The environmental factors measured during the field survey explain 2.1- and 3.4-times more assemblages' variability than factors measured from a hydrological map. Resumen 1. Tres ríos de tamaño comparable localizados en diferentes áreas de paisaje protegido de la República Checa fueron seleccionados para estudiar el efecto de factores ambientales sobre los ensamblajes de peces. Para ello, utilizando análisis de gradientes indirectos (DCA) y directos (CCA). 2. El DCA para las especies enfatizó la variabilidad entre los ensamblajes de peces de los tres ríos. Este patrón fue confirmado por un CCA altamente significativo. Para la variabilidad dentro de la localidad, un CCA reveló que los factores ambientales explicaron un 50.7% para datos de presencia-ausencia y un 58.3% para las abundancias relativas. 3. Los análisis revelaron que el número de pozas y el uso del suelo fueron los factores de mayor influencia en el gradiente ambiental. Sin embargo, en el CCA parcial, el tipo de sustrato explicó la mayor proporción de la variabilidad que afecta a los peces en la elección de hábitat. 4. Generalmente los datos de presencia-ausencia y abundancia relativa produjeron resultados similares tanto en los análisis DCA como en los CCA; los mismos factores ambientales probaron ser importantes en los análisis de ambos tipos de datos. Los factores ambientales explicaron mas variabilidad que los regionales (entre ríos). La proporción total de variabilidad explicada por el análisis de los datos de presencia-ausencia fue 71.9% mientras que para las abundancias relativas fue de 80.8%. Los factores ambientales medidos durante los muestreos de campo explicaron 2.1 y 3.4 veces mas variabilidad que los factores medidos sobre mapas hidrológicos. [source] Structural diversity of bacterial communities in a heavy metal mineralized granite outcropENVIRONMENTAL MICROBIOLOGY, Issue 3 2006Deirdre Gleeson Summary This laboratory study of a variably mineralized and hydrothermally altered granite outcrop investigated the influences of rock-surface chemistry and heavy metal content on resident bacterial populations. Results indicated that elevated heavy metal concentrations had a profound impact on bacterial community structure, with strong relationships found between certain ribotypes and particular chemical/heavy metal elements. Automated ribosomal intergenic sequence analysis (ARISA) was used to assess the nature and extent of bacterial diversity, and this was combined with chemical analysis and multivariate statistics to identify the main geochemical factors influencing bacterial community structure. A randomization test revealed significant changes in bacterial structure between samples, while canonical correspondence analysis (CCA) related each individual ARISA profile to linear combinations of the chemical variables (mineralogy, major element and heavy metal concentrations) revealing the geochemical factors that correlated with changes in the ARISA data. anova was performed to further explore interactions between individual ribotypes and chemical/heavy metal composition, and revealed that a high proportion of ribotypes correlated significantly with heavy metals. [source] Site scores and conditional biplots in canonical correspondence analysisENVIRONMETRICS, Issue 1 2004Jan Graffelman Abstract Canonical correspondence analysis is an important multivariate technique in community ecology. It produces an interesting biplot that summarizes the data matrices involved in the analysis. The method produces two sets of site scores that can be used in a biplot. One set concerns site scores that are weighted averages of the species scores (WA scores), and the other set represents site scores that are linear combinations of the environmental variables (LC scores). We show that the use of both sets of scores in a CCA biplot can be justified. The use of the WA scores leads to the best possible representation of the species data conditional on the representation of the weighted averages. Likewise, the LC scores lead to the best possible representation of the environmental variables, also conditional on the representation of the weighted averages and on the use of a Mahalanobis metric. The eigenvalues obtained in CCA indicate how well the species data are represented when LC scores are used. The quality of representation of the species data when WA scores are used can be computed from the CCA eigenvalues and the variances of the WA scores. Scalar products between WA scores and environmental variable vectors do not form a biplot of the environmental data. Theoretical results are illustrated with Australian data from freshwater ecology. Copyright © 2003 John Wiley & Sons, Ltd. [source] Bacterial community structure of glacier forefields on siliceous and calcareous bedrockEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2009A. Lazzaro Summary Forefields of retreating glaciers represent unique opportunities to investigate the initial phases of soil formation and microbial interactions with mineral surfaces. An open question concerns the physical and chemical driving-factors affecting the establishment of microbial communities in these young ecosystems. In this study we compared the bacterial community structure of six glacier forefield soils belonging to two contrasting bedrock categories (calcareous and siliceous) through T-RFLP profiling of the 16S rRNA gene. The community profiles were correlated with an array of physical (soil texture, water holding capacity, hours of sunshine, temperature, rainfall and exposure) and chemical (TC, TN, DOC, extractable nutrients and pH) factors using canonical correspondence analysis (CCA). A first comparison of the T-RFLP profiles suggested that the degree of operational taxonomic unit (OTU) diversity of these soils was similar, and that community structure was dominated by ubiquitous taxa. CCA showed that both physical (e.g. hours of sunshine or rainfall) and chemical factors (e.g. SO2,4 or PO3,4) played an equal role in shaping the soil bacterial communities. OTUs unique to specific sites appeared to be strongly influenced by the climatic regime and by texture. Overall, the community structure of the six glacial forefields showed no clear dependence on the bedrock categories. [source] The role of oceanographic conditions and plankton availability in larval fish assemblages off the Catalan coast (NW Mediterranean)FISHERIES OCEANOGRAPHY, Issue 3 2010M. PILAR OLIVAR Abstract In the northwestern Mediterranean, most fish species reproduce in early summer and fewer in the autumn mixing period. This study analyses and compares larval fish assemblages (LFA) in both seasons, and is the first attempt to characterize LFA structure for the autumn period. We analyze horizontal and vertical distribution of fish larvae and the micro- and mesozooplankton biomass and abundance of the main zooplankton groups. The oceanographic situation was analyzed through the study of data from CTD, N,-Shuttle and ADCP surveys. LFA were determined by ordination analyses based on larval abundance, and the relationships between larval assemblages and environmental variables were investigated through canonical correspondence analysis. The importance of some hydrographic variables (temperature, salinity and stability of the water column), current fields (along-shelf and across-shelf transport) and the abundance of zooplankton are discussed as important factors shaping the structure of larval assemblages. In early summer, LFA were mainly structured by a combination of bathymetry and trophic components, although sea surface temperature also played a role in shaping the horizontal larval distributions. In autumn, trophic variables were the main factors influencing the shelf-dwelling species assemblage. Larvae of oceanic species, on the other hand, were not related to trophic variables but were more affected by current fields. [source] Groundfish species diversity and assemblage structure in Icelandic waters during recent years of warmingFISHERIES OCEANOGRAPHY, Issue 1 2010LILJA STEFANSDOTTIR Abstract Elevated ocean temperatures have been predicted to lead to a poleward shift in the latitudinal distribution ranges of fish species. Different responses of fish species to increased temperatures might lead to changes in assemblage structure and local species richness. In this study, the assemblage structure and diversity of groundfish in Icelandic waters were examined using data from a standardized groundfish survey conducted annually in 1996,2007. We used hierarchical cluster analysis to define assemblages in two time periods and canonical correspondence analysis to explore the relationships between the assemblages and temperature, depth, latitude, longitude and year. We further used two estimates of diversity, species richness and the Shannon index. Four major species assemblages were identified. Assemblages in the hydrographically stable deep waters north of the country were consistent during the study, while assemblage structure in the more variable shallow waters underwent some changes. For this period of generally increasing sea temperature, the canonical correspondence analysis also revealed a shift towards species representative of warmer temperatures. Diversity was shown to be highly variable both temporally and spatially, and also to vary with depth and temperature. Species richness increased with temperature and time southwest of the country, but decreased northeast of the country. The different trends detected between the northern and southern areas illustrate the importance of performing analyses at the most appropriate scale. [source] Spatial distribution and overlap between ichthyoplankton and pelagic fish and squids on the southern flank of Georges BankFISHERIES OCEANOGRAPHY, Issue 5 2002Lance P. Garrison Abstract We conducted larval and adult fish surveys on the southern flank of Georges Bank during the spring of two years (1990 and 1995) with contrasting physical conditions. We employed canonical correspondence analysis (CCA) to examine the relationships between physical variables and the spatial distribution of pelagic fish and ichthyoplankton. Surface temperature bottom temperature, and vertical stratification were significant factors affecting larval fish distributions, and there were groups of species with similar responses to these variables. There were also consistent relationships between physical variables and pelagic fish and squid abundances and spatial distributions. Pelagic fish and ichthyoplankton with similar responses to hydrographic variables had high spatial overlap, and variation in hydrographic regimes modulated the strength of this interaction. Pelagic fish and squids are potentially important predators of both larval and juvenile fish on Georges Bank. Hydrographic structure modulates the degree of spatial overlap and therefore likely influences the strength of predator,prey interactions. [source] The relative importance of local conditions and regional processes in structuring aquatic plant communitiesFRESHWATER BIOLOGY, Issue 5 2010ROBERT S. CAPERS Summary 1. The structure of biological communities reflects the influence of both local environmental conditions and processes such as dispersal that create patterns in species' distribution across a region. 2. We extend explicit tests of the relative importance of local environmental conditions and regional spatial processes to aquatic plants, a group traditionally thought to be little limited by dispersal. We used partial canonical correspondence analysis and partial Mantel tests to analyse data from 98 lakes and ponds across Connecticut (northeastern United States). 3. We found that aquatic plant community structure reflects the influence of local conditions (pH, conductivity, water clarity, lake area, maximum depth) as well as regional processes. 4. Only 27% of variation in a presence/absence matrix was explained by environmental conditions and spatial processes such as dispersal. Of the total explained, 45% was related to environmental conditions and 40% to spatial processes. 5. Jaccard similarity declined with Euclidean distance between lakes, even after accounting for the increasing difference in environmental conditions, suggesting that dispersal limitation may influence community composition in the region. 6. The distribution of distances among lakes where species occurred was associated with dispersal-related functional traits, providing additional evidence that dispersal ability varies among species in ways that affect community composition. 7. Although environmental and spatial variables explained a significant amount of variation in community structure, a substantial amount of stochasticity also affects these communities, probably associated with unpredictable colonisation and persistence of the plants. [source] Species co-occurrence, nestedness and guild,environment relationships in stream macroinvertebratesFRESHWATER BIOLOGY, Issue 9 20092Article first published online: 2 JUN 200, JANI HEINO Summary 1. Describing species distribution patterns and the underlying mechanisms is at the heart of ecological research. A number of recent studies have used null model approaches to explore mechanisms behind spatial variation in community structure. 2. However, unexplored questions are the degree to which single guilds of potentially competing stream macroinvertebrate species show: (i) interspecific segregation among-stream sites (i.e. occur together less often than expected by chance), suggesting competitive interactions; (ii) interspecific aggregation (i.e. occur together more often than expected by chance), suggesting similar responses to the environment; (iii) comply with nestedness, suggesting the existence of selective extinctions or colonisations and (iv) show similar environmental relationships. 3. The present analyses showed that guilds of stream macroinvertebrates exhibit non-random co-occurrence patterns that were generally contingent on the weighting of sites by stream size. Despite significant segregation of species, each guild also showed significantly nested patterns. Species richness was correlated with different environmental factors between the guilds, although these correlations were relatively low. By contrast, correlations between the major ordination axes and key environmental variables were slightly stronger in canonical correspondence analysis, and generally the same factors were most strongly correlated with variation in the species composition of each guild. 4. The present findings are the first to show that species within each stream macroinvertebrate guild show significant negative co-occurrence at the among-stream riffle scale. These findings present challenges for future studies that aim to disentangle whether these patterns comply with the habitat checkerboard or the competitive checkerboard explanations. [source] Ecological relationships between stream communities and spatial scale: implications for designing catchment-level monitoring programmesFRESHWATER BIOLOGY, Issue 5 2007RICHARD K. JOHNSON Summary 1. Stream communities are structured by factors acting over multiple spatial and temporal scales. Identifying what factors are driving spatial patterns in stream communities is a central aim of ecology. 2. Here we used two large European data sets of fish, invertebrates, macrophytes, benthic diatoms and environmental data in two stream groups (lowland and mountain) to determine the importance of variables at different spatial scales (geographical, regional, local) on community structure. 3. Both geographical position and ecoregion were selected first in canonical correspondence analysis (CCA), clearly showing the broad spatial gradients covered in the data set. Secondary predictors (after accounting for spatial and/or ecoregion effects) were similar between stream groups and among the four organism groups. In particular, conductivity and N concentration were strong predictors reflecting catchment land use. 4. Using partial CCA, we assessed the individual importance of the three spatial scales on the community structure of the four organism groups in the two stream groups. The majority of among-site variability (22,29%) was accounted for by local scale variables (e.g. water chemistry and substratum type), with regional and spatial variables accounting 11,13% and 5,6%, respectively. Our findings indicate that the four organism groups are responding similarly to the different levels of spatial scale, implying much redundancy which should be consider when implementing studies of bioassessment. [source] An application of canonical correspondence analysis for developing ecological quality assessment metrics for river macrophytesFRESHWATER BIOLOGY, Issue 5 2005IAN DODKINS Summary 1. Aquatic macrophyte composition and abundance is required by the European Union's Water Framework Directive for determining ecological status. Five metrics were produced that can be combined to determine the deviation of aquatic macrophytes from reference conditions in Northern Ireland's rivers. 2. Species optima and niche breadths along silt, nitrate, pH, conductivity and dissolved oxygen gradients were generated from aquatic macrophyte and water quality surveys conducted at 273 sites throughout Northern Ireland using Canonical Correspondence Analysis (CCA). Five metric scores based on these environmental gradients were determined at new monitoring sites using the mean optima of the species occurring at the site, weighted by percentage cover and niche breadth of each species. 3. A preliminary reference network of 32 sites of high physico-chemical and hydromorphological quality, and representative of the range of river types in Northern Ireland, enabled reference metric scores to be produced for each river type. Five unimpacted and twenty impacted sites were used for testing the performance of the metrics. By subtracting reference metric scores from metric scores at a monitoring site measures of ecological impact could be determined along five different impact gradients. Metrics were also combined to give a measure of total ecological change. 4. The metrics system distinguished unimpacted from impacted sites and correctly identified 77% of the known impacts. The metrics distinguished different types of impact, e.g. silt and nitrate. 5. Aquatic macrophyte occurrence and abundance has high natural variability at a site, both temporally and spatially. This method was designed to be sensitive to ecological change whilst reducing noise caused by natural variation. [source] Distribution of rotifer assemblages in North Island, New Zealand, lakes: relationships to environmental and historical factorsFRESHWATER BIOLOGY, Issue 2 2002Ian C. Duggan 1.,The geographical distribution of planktonic rotifer species was investigated in 31 lakes in the North Island of New Zealand. 2.,A total of 78 species was recorded. Species richness, previously thought to be low in New Zealand, was found to be comparable with that of northern temperate lakes with an average of 21.1 species found per lake. The large, deep oligotrophic Lake Taupo had the lowest richness, and the artificial reservoirs the highest. 3.,The distribution of species, investigated using multivariate techniques [Cluster analysis, canonical correspondence analysis (CCA)], was most strongly associated with trophic state gradients. For example, Conochilus unicornis, C. dossuarius and Ascomorpha ovalis were associated with more oligotrophic conditions, and Brachionus budapestinensis, B. calyciflorus and Keratella tropica with more eutrophic conditions. Inorganic turbidity was also of importance in determining rotifer distributions in some shallower lakes. 4.,Some species, for example K. australis and C. exiguus, appear to be limited in distribution by poor dispersal abilities. [source] Effect of soil and physiographic factors on ecological plant groups in the eastern Elborz mountain rangeland of IranGRASSLAND SCIENCE, Issue 2 2010Mohammadreza Tatian Abstract To investigate the cause of differences among ecological plant groups in the east of the Elborz mountain rangeland, the role of edaphical and topographical characteristics was considered. Two ordination techniques, detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA), were used. The values of slope, aspect, altitude and lithology information were provided by Geographic Information System (GIS), and geomorphological land units were determined by intersection of overlaid data layers. Plant sampling was undertaken within nine land units with similar lithology and altitude but which differed in slope and aspect, using 30 randomly selected 1 m2 plots per land unit. Soil samples were taken from two depths (0,20 and 20,50 cm) in each plot. Organic matter, bulk density, texture, calcium carbonate, total nitrogen and available phosphorus and potassium contents were determined. The results indicated that plant species have different responses to edaphical and topographical parameters. The invader species group had a balanced amount of influence from all soil components and topographic factors, whereas the native grasses were located in productive soils, which typically have a low grazing intensity, such as the north facing slopes. Coniferous bushy trees, cushion plants and some shrub plant groups were found on steep slopes with alkaline soils. The broad-leaved bushy trees plant group was abundant in fine texture soils on low and humid slopes. [source] | |||||||||||||||||||||||||||||||