Multivariate Ordination Methods Research Articles

Impactos dos métodos de colheita da cana-de-açúcar sobre a macrofauna do solo em área de produção no Espírito Santo – Brasil

The objective of this study was to evaluate the effects of harvesting methods on the macrofauna, a known indicator of soil quality that detects changes in the system and indicates management alternatives. The experimental design was randomized blocks with six replications, with each block consisting of four parcels that corresponded to treatments green cane (CC), burnt cane (CQ), green cane – burnt cane (CC-Q) and burnt cane – green cane (CQ-C). Samples were collected in February and July 2010. The animals were divided into major taxonomic groups and accounted. Were evaluated ecological indexes (Shannon, Pielou and richness) and average total density of individuals and groups. Data were analyzed by the nonparametric statistical tools by Friedman or Signal test at 5%. To check relationships between soil fauna and environmental variables, was used a multivariate conditional ordination method, the redundancy analysis (RDA). The index richness was more efficient than the total average density to evaluate the influence of cane harvesting systems, with the highest values related to areas harvested without burning. Further, the occurrence of key groups in the areas harvested without burning configures the establishment of a trophic web. There was dominance of the social group Formicidae in all treatments.

Soil preferences and morphological diversity of goldenrods (Solidago L.) from south-western Poland

<p>Invasive plants in their new range can differ from their ancestors, including traits ultimately influencing habitat preferences, competitiveness and dispersal ability. In Europe <em>Solidago</em> species are considered as one of the worst invaders of American origin. In this study the frequency of occurrence of <em>Solidago</em> species, their soil preferences and morphological diversity, in Silesia (south-western Poland, Central Europe) were surveyed. On the basis of phytosociological relevés, made using the Braun-Blanquet method, in 75 plots, we determined the composition of species co-occurring with particular <em>Solidago</em> species. The height of ramets, as well as length and width of inflorescences of <em>Solidago</em> species were measured. We also determined the basic soil properties and noted the presence of trees overshading the ground vegetation. The compositional variation of vegetation and its relation to environmental traits: soil properties (texture, pH, percentage of organic matter, total nitrogen, nitrate, phosphorus, potassium and calcium content) and presence of canopy were analyzed by multivariate ordination methods (CA and CCA). Goldenrod species, in most cases (74.3%) occurred singly, two on one plot – rather rarely (mostly <em>S. canadensis</em> with <em>S. altissima</em>), whereas three <em>Solidago</em> species co-occurred only in three plots. Particular species differed in the height of the plant and inflorescence size, the exception was lack of difference between <em>S. altissima</em> and <em>S. canadensis</em>. <em>S. virgaurea</em> often occurred under trees canopy and the populations were separated from other goldenrod species. The species co-occurring with <em>S. altissima</em> and <em>S. canadensis</em> were the ruderal species, whereas plants from wet meadows occurred in plots with <em>S. gigantea</em>. The distribution of <em>S. graminifolia</em> was very limited, but inside its range it was able to occupy different habitats. The plots, where particular <em>Solidago</em> species occurred, did not differ significantly with respect to soil conditions.</p>

A year in hypoxia: epibenthic community responses to severe oxygen deficit at a subsea observatory in a coastal inlet.

Changes in ocean ventilation driven by climate change result in loss of oxygen in the open ocean that, in turn, affects coastal areas in upwelling zones such as the northeast Pacific. Saanich Inlet, on the west coast of Canada, is a natural seasonally hypoxic fjord where certain continental shelf species occur in extreme hypoxia. One study site on the VENUS cabled subsea network is located in the hypoxic zone at 104 m depth. Photographs of the same 5 m2 area were taken with a remotely-controlled still camera every 2/3 days between October 6th 2009 and October 18th 2010 and examined for community composition, species behaviour and microbial mat features. Instruments located on a near-by platform provided high-resolution measurements of environmental variables. We applied multivariate ordination methods and a principal coordinate analysis of neighbour matrices to determine temporal structures in our dataset. Responses to seasonal hypoxia (0.1–1.27 ml/l) and its high variability on short time-scale (hours) varied among species, and their life stages. During extreme hypoxia, microbial mats developed then disappeared as a hippolytid shrimp, Spirontocaris sica, appeared in high densities (200 m−2) despite oxygen below 0.2 ml/l. The slender sole Lyopsetta exilis was abundant in severe hypoxia and diminished as oxygen increased in the summer. This planktivore may be responding to changes in the depth of the diurnal migration of zooplankton. While the squat lobster Munida quadrispina was common at all times, juveniles disappeared in fluctuating conditions. Despite low oxygen conditions, animal densities were high indicating that the risk from hypoxia is balanced by factors such as food availability and escape from less tolerant predators. As hypoxia increases on the continental shelf, we expect benthic communities to become dominated by low diversity, hypoxia-tolerant species of low commercial significance.

A critical approach to the use of published data for baseline characterisation of marine fish assemblages: An exercise on Portuguese coastal waters

Policy-makers are becoming increasingly aware of the importance of coastal fish communities for the integrity of marine habitats. However, initial assessments are often done prior to any major funding and available published data is sometimes seen as a low-cost approach to this problem. The present work constituted an exercise on marine fish assemblage characterisation, by relying only on published data from mainland Portugal, covering soft substrate areas and near-shore rocky reefs. Regardless of the characterisation itself, this exercise aimed to critically approach these procedures, by pinpointing problems and highlighting achievements. Criteria were defined for the inclusion of published studies and included datasets were standardised in terms of species proportions, spatial and temporal scales. Species were assigned to ecological guilds and all analyses were performed separately for species and guild data. The influence of season, depth and latitude were analysed through multivariate analysis of variance using permutations and distance-based linear models and assemblages were characterised based on multivariate ordination and hierarchical classification methods. Significant differences were found between studies employing different methods in rocky reefs and outliers were not used in assemblage characterisation. Due to limitations in spatial and temporal detail in published data, only a rough, large scale characterisation of assemblage types was accomplished, with datasets divided in rocky reefs, shallow soft-substrate (0–20 m), intermediate soft-substrate (20–100 m) and deep soft substrate (100–200 m). No seasonal differences were detected, but a non-linear relationship with latitude was found in deep soft-substrate assemblages. During the exercise, spatial and temporal scales were forced by the quality of the data and some analyses failed to detect known patterns. Differences between methods, designs and types of data required assumptions to be made regarding data comparability. Overall, the exercise provided a hands-on insight into the use of published data for planning in a coastal management context, pinpointing data comparability, scale and information gaps as severe limitations of these approaches. In order to improve planning and design, some proposed measures were highlighted, such as the establishment of national databases and the use of pilot studies.

Ostracod Assemblages in Relation to Littoral Plant Communities of a Shallow Lake (Lake Świdwie, Poland)

AbstractThe aims of this study included: specifying values of ecological parameters and Ostracoda species characteristic for different types of plant habitats occurring in lake systems, determining the impact of mud presence on the taxonomic structure and density of the ostracods, tracing seasonal changes in the structures of Ostracoda assemblages identifying the species typical of particular seasons. Various types of rushes and underwater meadows were taken into consideration as lake microhabitats. The research was conducted in the shallow Lake Œwidwie (NW Poland). Multivariate (constrained) ordination methods were used to analyse the relationships between species composition and environmental variables. In the lake and its margins 31 species of the Ostracoda were identified. The development of water vegetation during the vegetation season was conducive to growth in ostracod density. The accessibility of mud in plant habitats had a favourable effect on the general density of ostracods. Species which preferred a high mud content in their habitats included: Cypria ophtalmica, C. exsculpta and Physocypria kraepelini. Species typically encountered in underwater meadow habitats were: Cyclocypris ovum and Cypridopsis vidua. Underwater meadows of charophyte were characterized by the highest ostracod density in the whole lake system, with the average of 7860 ind. m–2 and the maximum of 17 470 ind. m–2. Species typically encountered in rush habitats included Notodromas monacha, Dolerocypris fasciata and Metacypris cordata. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

The evolution of waving displays in fiddler crabs (Uca spp., Crustacea: Ocypodidae)

Male fiddler crabs are commonly recognized by the presence of a single massive claw used in a variety of contexts, including territorial defence, agonistic interactions, and courtship behaviour. The most common behavioural context involving these enlarged chelipeds is their use in waving displays, which are remarkably diverse among species. Although the waving display is one of the most obvious behavioural features of male fiddler crabs, little is known about their main evolutionary trends during the diversification of the genus. The present study employed phylogenetic comparative methods to investigate the evolution of waving behaviour in a sample of 19 species of Uca from Central and North America. Digital recordings were used to quantify the temporal dynamics of waving behaviour in each species. Multivariate ordination methods were used to assess whether different elements of the display showed distinct evolutionary dynamics, particularly with respect to body size and the environment where species are most commonly found. Most of the interspecific variation in displays involves differences in the overall waving velocity, with no correspondence to their local environments, nor their body size. Interestingly, despite the strong concentration of variance in the first two ordination axes, there was no statistically significant evidence for phylogenetic signals in their respective scores. These results suggest that the overall structure of waving displays is evolutionarily labile, at the same time as being concentrated in a few particular axes of variation, possibly indicating evolution along lines of least resistance. The approach employed in the present study highlights the utility of phylogenetic comparative methods for elucidating the evolution of complex behavioural characteristics, such as the waving display in male fiddler crabs. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 307–315.

Deriving Plant Functional Types for Amazonian forests for use in vegetation dynamics models

a b s t r a c t Recent advances in our understanding of the linkages between plant physiological and morphological traits suggest a new means by which to define Plant Functional Types (˚) for use in conceptual and mathematical models of vegetation dynamics. In this study we used data from the RAINFOR-network database, aiming to numerically derivefor tropical forest trees by jointly analysing an Amazon-wide dataset of (409) species abundance, species functional traits (10) and site edaphic and climatic conditions across 53 plots. We followed a stepwise procedure of numericaldefinition with increasing complexity, starting from a simple PCA on species functional traits. We subsequently applied a three-table (RLQ) multivariate ordination method in two ways: with and without spatial autocorrelation between plots being taken into account. In all cases the environmental contribution to trait variation had been partialled out. Thus our results link species-specific inherent trait values with associated species abundances along environmental gradients. Our final classification of Amazonian tree species based on foliar dry leaf mass per area (MA), leaf concentrations of C, N, P, Ca, K, Mg, carbon isotopic discrimination (� ), branch xylem density (� X) and maximum tree height (Hmax) yielded four discrete ˚. Thesewere found to represent distinct life-history strategies and can be aligned with previous empirical definitions of tropical tree guilds. In particular, two ecological dimensions are identified: (1) a leaf deployment dimension which co-varies with soil fertility and (2) a stem deployment dimension which co-varies with soil texture. By analysing diameter growth rates of the same trees used to define the fourwe found eachto have a different overall growth pattern. Furthermore, from a Basin-wide forest survey, differences in the relative abundance of the fourwere related to stand level basal area growth and/or turnover rate variations. These new derivedshould enhance our ability to better understand and model the dynamics of the Amazon forest, with the general procedure for plant functional trait definition described here potentially applicable to many other ecosystems.

Spontaneous restoration of target vegetation in old‐fields in a central European landscape: a repeated analysis after three decades

AbstractQuestions(a) What are directions of spontaneous succession; in particular, do target stages (identified as shrubby grassland and semi‐natural deciduous woodland) develop, and if so, which species are involved? (b) Are the target stages predictable? (c) How do species richness and environmental characteristics change during succession? (d) What are the consequences for restoration and landscape management?LocationThe Bohemian Karst Protected Landscape Area, SW of Prague, Czech Republic (49° 52′–50° 00′ N, 14° 03′–14° 21′ E, 251–488 m a.s.l.).MethodsIn a repeated analysis, phytosociological relevés recorded in 4 m × 4 m plots in 58 old‐fields initially surveyed in 1975 were compared to those from 28 still existing fields in 2008–2009. Average Ellenberg indicator values were calculated for each relevé. Aspect and slope were measured and potential radiation calculated. pH was measured from soil samples. Species were grouped according to their affiliation to the phytosociological classes Querco‐Fagetea, Festuco‐Brometea, Trifolio‐Geranietea, Molinio‐Arrhenatheretea, and weedy and ruderal vegetation. Those belonging to the first three classes were considered target species. The data were analysed using multivariate (ordination methods) and univariate statistics.ResultsThe spontaneous succession in old‐fields proceeded towards target stages, either deciduous woodlands or shrubby grasslands. Their establishment can be tentatively predicted by soil pH and early occurrence of grassland species. Except pH, all Ellenberg indicator values changed during succession. pH values (Ellenberg and measured) were higher in shrubby grasslands than in woodlands. The total number of species decreased during succession, the number of target woodland species increased, and target grassland species remained the same in the shrubby grassland stages but decreased in the woodland stages during the past 33 yr of succession.ConclusionsTarget shrubby grasslands, resembling natural steppe‐like communities typical of the region and valuable from a conservation point of view, can be restored by spontaneous succession within a few decades in about one‐third of the studied old‐fields. Other fields developed into deciduous woodland. Restoration of well‐developed target woodland will take longer, but the trend is already obvious, although less desirable nitrophilous woodland might also alternatively develop. Repeating earlier chronosequence studies may provide valuable information useful in restoration ecology and landscape management.

Organic carbon and nitrogen in soil particle-size aggregates under dry tropical forests from Guanacaste, Costa Rica — Implications for within-site soil organic carbon stabilization

Abstract In this study we report results on the soil organic carbon (SOC) pool (0–50 cm) from a chrono-sequence of dry tropical forest (dTf) of increasing age and a yearly burned ancient pasture in the “Sector Santa Rosa” at the “Area de Conservacion Guanacaste” (ACG) in northwestern Costa Rica, where intense human induced land-use modifications has occurred during the past century. The effects of land conversion on soil organic carbon (SOC) have mainly been conducted in the Atlantic humid forests while overlooking dTfs. We quantified the depth distribution of SOC concentration down to 50-cm and in physically separated mineral soil fractions, as these data are scanty from the dTf. Additional objectives were to identify the relationship with selected soil physical and chemical properties, including stabilized SOC fractions by means of multivariate ordination methods. Statistically significant differences were found for the main fixed factor ecosystem for all soil variables analyzed (ANOVA). SOC and N concentrations were significantly higher in the oldest dTf compared to the other dTfs. Soil physical properties like aggregate size distribution and bulk density changed with depth, and varied significantly among the three dTf stands sampled. The multivariate analysis, i.e. between-within class principal component analysis (PCA), revealed a significant ordination of dTfs (P 80 years-old dTfs, i.e., 228.9 and 150.3 Mg C ha− 1, respectively, values similar to those obtained in the Atlantic humid forests of Costa Rica. Comparatively to other studies, soils under dTf at Santa Rosa store a considerable amount of SOC with potentially large CO2 emissions if this ecosystem is not preserved.

Combined effects of local environment and continental biogeography on the distribution of Ostracoda

Summary 1. The relationship between altitudinal gradients on small spatial scales and latitudinal gradients on broader scales has been repeatedly recognised in the biogeography of animals and plants. However, little is known about this topic in the ecology and biogeography of ostracod communities in Mediterranean flowing waters or the factors underlying these spatial patterns. 2. We analysed the ostracod assemblages of near-natural headwater streams in the Betic and Pre-Betic Mountains in the southern Iberian Peninsula to decipher the most important environmental gradients structuring ostracod communities on a local scale. In addition, the European altitudinal and latitudinal distributions of the most commonly found species were analysed with GIS and regression models to compare geographical effects from local to continental scales. 3. Forty sampling sites, distributed among six catchments and ranging in altitude between 150 and 1940 m a.s.l., were sampled seasonally. Limnological and geographical information was also recorded for each sample. Seventeen ostracod species were found, two of which were new findings for the Iberian Peninsula: Potamocypris fulva and Cypria reptans. The most common species were Potamocypris zschokkei, Candona neglecta, Herpetocypris brevicaudata, Cyclocypris ovum, Potamocypris villosa and Pseudocandona albicans. The distribution of these species in 918 European locations was analysed to test the hypothesised change in altitudinal distribution with varying latitude. 4. The best subset of logistic and linear regression models, selected by means of the information-theoretic approach, found that oxygen content and the variables related with substratum and discharge were the most important variables with a negative influence on ostracod presence, abundance and species richness on a local scale. These findings suggest that the negative effect on benthic invertebrates of physical disturbances relates to high flow velocity and turbulences. 5. Multivariate ordination methods show how altitude and water chemistry are the most important variables to explain the distribution of ostracod assemblages on the small spatial scale. On a larger scale, differences in latitudinal distribution throughout Europe were significant for the six most common species found in Granada. In addition, four of these showed significant negative linear relationships between latitude and altitude in Europe, supporting the important effect of climate on local and continental scale distributions. While ostracod biogeographies are still poorly known, our results indicate the influence of Quaternary climate variability on ostracod dynamic colonisation and extinction in Europe in accordance with species-specific temperature and water chemistry preferences.

Plant Functional Traits Show Non-Linear Response to Grazing

The trait-based approach aims to detect functional patterns in vegetation beyond specific sites or taxa. In most cases, plant traits are assumed to be linearly related to environmental gradients such as grazing intensity. To generalize results beyond specific sites, it is important to know to which extent environment-trait relationships are non-linear. Non-linearity can be a source of inconsistency among different studies according to length and studied portion of a gradient. In this study, we test if and to what extent traits relate non-linearly to a grazing gradient using data from a grassland-matorral interface in the Mediterranean rangeland of “La Crau” (SE France). Because quantification of grazing by itinerant sheep flocks is difficult, we use a marker plant, Phillyrea angustifolia, and several independent pasture indicators to estimate grazing intensity. First, we related traits to grazing using a multivariate three-table ordination method (RLQ), which assumes linear reactions of traits. To evaluate the importance of non-linearity, we applied generalized additive models (GAMs) to our data. This revealed that a third of traits studied here showed non-linear relationships to grazing. These non-linear responses cover a large spectrum including seed mass, life form, phenology dispersal- and leaf traits. The high part of non-linear relations compromises a general assumption of linear trait-environment relationships. Future works should therefore more often consider non-linear relationships using methods with no constraints on shape of response, e.g., GAM in the analysis of functional trait studies. In this way, non-linear relationships can reveal new aspects of species and community response to global change and deepen our understanding of trait-environment relations.

Acidophilous oak forests of the Wielkopolska region (West Poland) against the background of Central Europe

Acidophilous oak forests of the Wielkopolska region (West Poland) against the background of Central Europe This monograph gives the phytosociological characteristics of acidophilous oak forests from the class Quercetea robori-petraeae (Aulacomnio androgyni-Quercetum, Molinio caeruleae-Quercetum, and Calamagrostio arundinaceae-Quercetum) and the closely related forest communities from the classes Querco-Fagetea (Potentillo albae-Quercetum and acidophilous forms of Galio sylvatici-Carpinetum) and Vaccinio-Piceetea (Querco roboris-Pinetum and Serratulo-Pinetum) in the Wielkopolska region and adjacent areas. The report is based on 1655 relevés selected from 59 published or unpublished studies. The analysed and revised syntaxa are described in accordance with the International Code of Phytosociological Nomenclature. The distribution of the documented localities of all associations and subassociations in the study area is shown in cartograms on the ATPOL grid (squares of 10 km x 10 km). The classical phytosociological methods are complemented with multivariate ordination methods (detrended correspondence analysis and/or principal component analysis) and analyses taking into account Ellenberg indicator values. The natural geographical and site differentiation of all the plant associations is presented, and stages of degeneration are distinguished in some of them. The separation of degenerated forms and substitute forest communities has allowed a clearer classification of the studied syntaxa. This study shows that the analysed associations can be subdivided into 16 subassociations and 23 variants. For 5 subassociations, nomenclatural types are designated here. The most common association in the study area is Calamagrostio arundinaceae-Quercetum, but most of its relevés represent various stages of degeneration. Among communities from the order Quercetalia roboris, patches of Aulacomnio androgyni-Quercetum and Molinio caeruleae-Quercetum are rare. On the basis of this detailed study, a coherent system of classification of acidophilous oak forests from the order Quercetalia roboris in Central Europe is proposed. The results are important for biodiversity conservation and sustainable forest management.

Spontaneous recovery of an intensively used grassland after cessation of fertilizing

AbstractQuestions: (1) Does a fertilized grassland recover in terms of species composition and species richness after stopping the treatment? (2) Which species contributed most to the changes? (3) Is it realistic to rely upon spontaneous recovery in this and similar cases?Location: A large grassland, located in the western part of the Czech Republic in central Europe, latitude 49° 59′, longitude 12° 45′, altitude 750 m a.s.l.Methods: Experimental plots of 2.5 m × 6.0 m were established in the central part of the grassland in 1968 using a randomized block design with the following variants: unfertilized controls, 80, 160, 240 and 320 kg ha−1 of nitrogen, in four or eight (320 kg) replicates. The fertilization regime was stopped in 1989. Phytosociological relevés of 2 m × 4 m in size were made in 1990, 1994, 1996, 1997, 1999, 2003 and 2006. The data were processed by multivariate ordination methods (DCA, CCA). Differences in the number of species per plot were tested by repeated measures anova and Tukey's HSD test.Results: All plots, including controls, exhibited a distinct trajectory through time, reflecting the rates of fertilizer used and generally changing in the same direction. Both time and nutrients significantly influenced the vegetation pattern. Treatments differed significantly in species richness, especially at the beginning of the observation. Differences in later years were less pronounced, thus a convergence between the treatments was evident.Conclusions: During the 16 years after fertilization ceased, the number of species substantially increased not only in the fertilized plots but also in the controls. Species typical of semi‐natural grasslands predominantly contributed to the increase. Spontaneous recovery after cessation of fertilizing was relatively efficient, but the fertilized plots were small in size and thus rather easily colonized from outside. For interpretation and extrapolation of results from small experimental plots, it is necessary to consider changes in the broader surroundings.

Composition, distribution, and diversity of pelagic fishes around the Canary Islands, Eastern Central Atlantic

Oceanic islands of volcanic origin have a narrow shelf and a steep slope that should lead to considerable spatial overlap among coastal and oceanic fauna. During six pelagic surveys in the Canarian archipelago, Eastern Central Atlantic, over 65,000 fishes belonging to 211 species were collected at depths between 8 and 1035 m. The mesopelagic families of the lanternfishes (Myctophidae) and the bristlemouths (Gonostomatidae) accounted for about 50% of all specimens. By multivariate classification and ordination methods four different assemblages associated with mesopelagic, epipelagic–oceanic or coastal habitats could be identified. Two of these assemblages were coastal, differing in the proportion of meso- and epipelagic species. These data indicate intense horizontal migrations of mesopelagic fishes (mainly Myctophidae) into the neritic realm and increased interactions between coastal and oceanic habitats. Alpha diversity indices were higher and dominance was lower in oceanic habitats compared to the coastal realm. No marked differences among oceanographically similar areas of the entire archipelago were found. Beta diversity as a measure of similarity among sites or samples revealed variabilities between areas south of Gran Canaria and Fuerteventura islands. A considerable heterogeneity in species distribution was found off SE Fuerteventura in an area with high hydrographic variability. Therefore, both topography and hydrography are important factors influencing the distribution and abundance of pelagic fishes in this oceanic archipelago.

Structural attributes of three forest types in central Spain and Landsat ETM+ information evaluated with redundancy analysis

Structural attributes of forest, such as canopy crown closure, stand height, stem density and basal area, derived from the third Spanish National Forest Inventory (IFN‐3) were used in combination with spectral information derived from Landsat Enhanced Thematic Mapper Plus (ETM+) imagery and topographic information to evaluate their relationships. To deal with the variability found in the literature, three different types of vegetation, dominated by conifers, evergreen sclerophyll and broad‐leaved deciduous trees, were analysed. In addition, the analyses were performed using three sets of plots filtered to be successively more homogeneous. A multivariate canonical ordination method, redundancy analysis (RDA), was used to enable the simultaneous evaluation of the two data sets and provide a useful graphical output highlighting the relationships between response (structural attributes) and explanatory (spectral and topographic) variables. Rank correlation analyses were also performed. The low percentage of explained variance at the multivariate analyses and low rank correlation coefficients made it difficult to derive practical empirical models. The strong influence of vegetation type on the results was confirmed, given that each type was sensitive to a different kind of spectral information. Finally, the results did not allow validation of the hypothesis that the relationship should be better when using a more homogeneous set of plots.

Stability of gene contributions and identification of outliers in multivariate analysis of microarray data

BackgroundMultivariate ordination methods are powerful tools for the exploration of complex data structures present in microarray data. These methods have several advantages compared to common gene-by-gene approaches. However, due to their exploratory nature, multivariate ordination methods do not allow direct statistical testing of the stability of genes.ResultsIn this study, we developed a computationally efficient algorithm for: i) the assessment of the significance of gene contributions and ii) the identification of sample outliers in multivariate analysis of microarray data. The approach is based on the use of resampling methods including bootstrapping and jackknifing. A statistical package of R functions was developed. This package includes tools for both inferring the statistical significance of gene contributions and identifying outliers among samples.ConclusionThe methodology was successfully applied to three published data sets with varying levels of signal intensities. Its relevance was compared with alternative methods. Overall, it proved to be particularly effective for the evaluation of the stability of microarray data.

Effects of beach nourishment and groynes building on population and community descriptors of mobile arthropodofauna

Abstract For decades beach nourishment and groyne building have been used to combat sandy beach erosion, but their effects on sandy beach macrofauna are often neglected. Here, we analysed the effects of beach nourishment and groyne building on a sandy beach within the San Rossore-Migliarino-Massaciuccoli Regional Park (a natural park in Tuscany, Italy) on two different levels of organization: the abundance of the crustacean amphipod Talitrus saltator (population level) and community descriptors of the sandy beach arthropod fauna (community level), with emphasis on supralittoral species. Samples were taken bimonthly from September 2004 to January 2006 using pitfall traps. T. saltator abundance was described by generalized linear models (GLMs) and arthropodofauna community descriptors were estimated by species number, diversity indexes and ordered with multivariate ordination methods. The abundance of T. saltator in different seasons was influenced by the month of sampling during the autumn–winter season and by beach width, substrate penetrability and the “species number” biotic factor during the spring–summer season. The abundance models revealed no direct effects of beach nourishment. T. saltator was shown to be both a typifying and discriminating species, confirming its key role in the community of sandy beaches. The arthropodofauna community showed sensitivity to the substrate grain size and quality changes generated by beach nourishment, as the community composition changed at the nourished sites in line with seasonal dynamics. Human actions to stabilise the shoreline therefore emerged as a driving environmental feature, altering the beach's physical characteristics and consequently its fauna on different organizational levels: it was shown to have a direct effect on the arthropodofauna community structure and on sandhopper population abundance by determining habitat availability.

Analysis of T-RFLP data using analysis of variance and ordination methods: A comparative study

The analysis of T-RFLP data has developed considerably over the last decade, but there remains a lack of consensus about which statistical analyses offer the best means for finding trends in these data. In this study, we empirically tested and theoretically compared ten diverse T-RFLP datasets derived from soil microbial communities using the more common ordination methods in the literature: principal component analysis (PCA), nonmetric multidimensional scaling (NMS) with Sørensen, Jaccard and Euclidean distance measures, correspondence analysis (CA), detrended correspondence analysis (DCA) and a technique new to T-RFLP data analysis, the Additive Main Effects and Multiplicative Interaction (AMMI) model. Our objectives were i) to determine the distribution of variation in T-RFLP datasets using analysis of variance (ANOVA), ii) to determine the more robust and informative multivariate ordination methods for analyzing T-RFLP data, and iii) to compare the methods based on theoretical considerations. For the 10 datasets examined in this study, ANOVA revealed that the variation from Environment main effects was always small, variation from T-RFs main effects was large, and variation from T-RF × Environment (T × E) interactions was intermediate. Larger variation due to T × E indicated larger differences in microbial communities between environments/treatments and thus demonstrated the utility of ANOVA to provide an objective assessment of community dissimilarity. The comparison of statistical methods typically yielded similar empirical results. AMMI, T-RF-centered PCA, and DCA were the most robust methods in terms of producing ordinations that consistently reached a consensus with other methods. In datasets with high sample heterogeneity, NMS analyses with Sørensen and Jaccard distance were the most sensitive for recovery of complex gradients. The theoretical comparison showed that some methods hold distinct advantages for T-RFLP analysis, such as estimations of variation captured, realistic or minimal assumptions about the data, reduced weight placed on rare T-RFs, and uniqueness of solutions. Our results lead us to recommend that method selection be guided by T-RFLP dataset complexity and the outlined theoretical criteria. Finally, we recommend using binary or relativized peak height data with soil-based T-RFLP data for ordination-based exploratory microbial analyses.

Subtidal macrozoobenthos communities from northern Chile during and post El Niño 1997–1998

Despite a large amount of climatic and oceanographic information dealing with the recurring climate phenomenon El Nino (EN) and its well known impact on diversity of marine benthic communities, most published data are rather descriptive and consequently our understanding of the underlying mechanisms and processes that drive community structure during EN are still very scarce. In this study, we address two questions on the effects of EN on macrozoobenthic communities: (1) how does EN affect species diversity of the communities in northern Chile? and (2) is EN a phenomenon that restarts community assembling processes by affecting species interactions in northern Chile? To answer these questions, we compared species diversity and co-occurrence patterns of soft-bottoms macrozoobenthos communities from the continental shelf off northern Chile during (March 1998) and after (September 1998) the strong EN event 1997–1998. The methods used varied from species diversity and species co-occurrence analyses to multivariate ordination methods. Our results indicate that EN positively affects diversity of macrozoobenthos communities in the study area, increasing the species richness and diversity and decreasing the species dominance. EN represents a strong disturbance that affects species interactions that rule the species assembling processes in shallow-water, sea-bottom environments.

GIS and ordination techniques for evaluation of environmental impacts in informal settlements: A case study from Cuiabá, central Brazil

This study evaluates the environmental impacts caused by informal occupation in the city of Cuiabá, Mato Grosso, Brazil. In 10 selected districts, an assessment of 35 environmental indicators was conducted, evaluating secondary data as well as field survey results, air photo interpretation and geographical information system (GIS) analysis. A matrix approach was then applied to quantify the magnitude and relevance of 13 types of impacts on the following environmental components: surface water, soil, flora/fauna, air, land use and life quality. Impacts were analyzed in the spatial context of four main classes of municipal zoning. Redundancy analysis (RDA), a multivariate ordination method, was applied to evaluate the dependency of impacts from environmental and socio-economical factors. Total impact scores were the highest in areas devoted to environmental preservation according to municipal zoning, indicating a limited ability of authorities to control informal occupation processes and their impacts on the environment. Indicator analysis showed strong impacts along the stream network in areas susceptible to episodic flooding. RDA indicates that age and district organization have a significantly important impact in the sampled districts; they were found to be as important in ordination as environmental factors such as geo-technical units.