Principal Coordinates Of Neighbour Matrices Research Articles

Particulate Organic Matter Distribution along the Lower Amazon River: Addressing Aquatic Ecology Concepts Using Fatty Acids

One of the greatest challenges in understanding the Amazon basin functioning is to ascertain the role played by floodplains in the organic matter (OM) cycle, crucial for a large spectrum of ecological mechanisms. Fatty acids (FAs) were combined with environmental descriptors and analyzed through multivariate and spatial tools (asymmetric eigenvector maps, AEM and principal coordinates of neighbor matrices, PCNM). This challenge allowed investigating the distribution of suspended particulate organic matter (SPOM), in order to trace its seasonal origin and quality, along a 800 km section of the Amazon river-floodplain system. Statistical analysis confirmed that large amounts of saturated FAs (15:0, 18:0, 24:0, 25:0 and 26:0), an indication of refractory OM, were concomitantly recorded with high pCO2 in rivers, during the high water season (HW). Contrastingly, FAs marker which may be attributed in this ecosystem to aquatic plants (18:2ω6 and 18:3ω3) and cyanobacteria (16:1ω7), were correlated with higher O2, chlorophyll a and pheopigments in floodplains, due to a high primary production during low waters (LW). Decreasing concentrations of unsaturated FAs, that characterize labile OM, were recorded during HW, from upstream to downstream. Furthermore, using PCNM and AEM spatial methods, FAs compositions of SPOM displayed an upstream-downstream gradient during HW, which was attributed to OM retention and the extent of flooded forest in floodplains. Discrimination of OM quality between the Amazon River and floodplains corroborate higher autotrophic production in the latter and transfer of OM to rivers at LW season. Together, these gradients demonstrate the validity of FAs as predictors of spatial and temporal changes in OM quality. These spatial and temporal trends are explained by 1) downstream change in landscape morphology as predicted by the River Continuum Concept; 2) enhanced primary production during LW when the water level decreased and its residence time increased as predicted by the Flood Pulse Concept.

Spatial structure of the helminth parasite communities of the tonguefish, Symphurus plagiusa, from the Campeche coast, southern Mexico

The goals of this paper were to determine whether the helminth communities of the blackcheek tonguefish, Symphurus plagiusa, exhibit a spatial structure and, if so, to determine the relative influence of selected environmental and spatial variables. The parasite communities of tonguefish and environmental data (e.g., temperature, salinity, oxygen) were sampled monthly over a network of 37 stations over 1year (February 2006 to January 2007). Analysis of similarities (ANOSIM), non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) were used. Spatial variables were generated using the analysis of principal coordinates of neighbour matrices (PCNM) method. A total of 1,010 flatfishes and nine helminth taxa were collected. For the environmental variables, hierarchical cluster analyses produced groups of stations associated with the Yucatan dry, rainy and winter seasons. At the infracommunity level, there was no group formation as indicated by ANOSIM and NMDS nor association with environmental or spatial variables. At the component community level, there was significant group formation, and RDA analyses of core, satellite and all species produced significant associations with environmental variables. However, model fit improved substantially (from 17–52% to 49–83% of explained variance) when the spatial variables (variables generated with PCNM method) were added. Thus, the helminth component communities of S. plagiusa were affected by associated environmental variables and unknown ecological processes captured by the spatial variables acting at different spatial scales over time. In contrast, at the infracommunity level there was apparently a very fine spatial grain, where the numerical dominance of core species resulted in biased group formation.

Partitioning the variation of woody plant β‐diversity in a landscape of secondary tropical dry forests across spatial scales

AbstractQuestionWhat is the relative importance of forest successional age, environmental heterogeneity, landscape structure and spatial structure of sampling sites on β‐diversity of tropical dry forests (TDF)? How do the magnitude of β‐diversity and the relative influence of factors, processes and mechanisms driving β‐diversity differ at different spatial grains? What are the effects of stand age on β‐diversity?LocationYucatán Peninsula, México.MethodsFloristic composition was obtained from a hierarchical survey performed in 276 sites distributed across 23 sampling landscapes (SL) (12 sites per SL). Land‐cover classes were derived from the classification of multi‐spectral SPOT 5 satellite imagery. We calculated landscape metrics of patch type for each SL, and characterized local soil conditions for each sampling site. A principal coordinates of neighbour matrices (PCNM) analysis was performed to estimate spatial variables, and partial redundancy analysis was used to decompose variation into spatial, stand age and landscape structure components.ResultsThe magnitude of β‐diversity varied with spatial scale (grain size), and was larger at the local than at the landscape grain. The magnitude of β‐diversity also decreased slightly but significantly with successional age. There were significant differences in species composition among vegetation classes. Environmental factors (local soil conditions, as well as landscape structure) and spatial structure both contributed to woody plant β‐diversity in our TDF landscape, but their relative importance was scale‐dependent. At the local grain size, both the environment (mainly soil conditions) and the spatial structure strongly affected β‐diversity, while at the landscape grain, environmental factors (variation in soil conditions, as well as landscape configuration) played a more prominent role.ConclusionsThe magnitude of β‐diversity decreased with increasing spatial grain and successional age, while the relative importance of mechanisms influencing β‐diversity was scale‐dependent: both niche partitioning and dispersal limitation affect β‐diversity at the local grain size, while niche partitioning prevails at the landscape grain.

Multiscale characterization of spatial relationships among oxycline depth, macrozooplankton, and forage fish off Peru using geostatistics, principal coordinates of neighbour matrices (PCNMs), and wavelets

Upwelling ecosystems are particularly heterogeneous and present intense mesoscale (tens of kilometres) and submesoscale (hundreds of metres to kilometres) activity that are expected to drive the distribution of the organisms and thus their interactions. Here we addressed the impact of the physical forcing in the northern Humboldt Current system off Peru, which is characterized by the presence of an intense and shallow oxygen minimum zone and used the variability of the depth of the oxycline as a proxy of the physical forcing that impacts the epipelagic communities. We analyzed simultaneous high-resolution acoustic observations of the oxycline depth, the biomass in macrozooplankton, and the biomass in pelagic fish. Three complementary methodologies were considered: (i) geostatistical methods and correlation tests, (ii) principal coordinates of neighbour matrices, and (iii) wavelet analysis. Our results highlight the relevance of a multimethod framework to characterize the multiscale relationships between marine ecosystem components. We also provided evidence that the submesoscale-to-mesoscale variability of the oxycline depth drives the distribution of macrozooplankton, which further structures the distribution of forage fish in a bottom-up cascade.

Dispersal limitation is stronger in communities of microorganisms than macroorganisms across Central European cities

AbstractAim It is generally believed that communities of small organisms, or those with small propagules, are structured mainly by local niche‐based processes, and less by dispersal limitation. Conversely, weaker environmental and stronger spatial structure, indicating dispersal limitation, are expected to occur more frequently in communities of large organisms. However, this hypothesis has rarely been tested by comparing spatial and environmental effects across groups of organisms of different size (or with different size of propagules) sampled at the same set of sites. Here, we test it in urban environments.Location Thirty‐two cities in 10 countries of Central Europe and Benelux.Methods We compared effects of spatial location and climate on species composition of different groups of organisms sampled in corresponding types of urban habitats. The studied groups were: (1) subaerial cyanobacteria and algae, (2) vascular plants, (3) land snails; and subgroups of vascular plants with different life form and dispersal mode, namely: (4) herbs, (5) animal‐dispersed trees and shrubs, and (6) wind‐dispersed trees and shrubs. Data were analysed by variation partitioning based on redundancy analysis (RDA) with principal coordinates of neighbour matrices (PCNM). Eighteen PCNM eigenvectors (expressing spatial effects) and mean annual temperature, July–January temperature difference and annual precipitation sum (expressing environmental effects) were used as explanatory variables.Results Pure effects of climate on species composition, indicating niche‐based processes, were not significant for any group or subgroup of the studied organisms. In contrast, pure effects of space, indicating dispersal limitation, were significant for all groups and subgroups except herbs. Surprisingly, the community of cyanobacteria/algae possessed much stronger spatial structure independent of climate than communities of larger organisms, although cyanobacteria/algae had the lowest beta diversity among the studied cities.Main conclusions We hypothesize that the community of subaerial cyanobacteria/algae is structured by natural processes which involve dispersal limitation, whereas communities of urban plants and snails are influenced by human‐assisted dispersal of their propagules between cities, which results in weaker dispersal limitation. Our study indicates that dispersal vectors can be more important for community structure than size of organisms or of their propagules.

Impacts of space, local environment and habitat connectivity on macrophyte communities in conservation lakes

AbstractAim To assess the relative impacts of spatial, local environmental and habitat connectivity on the structure of aquatic macrophyte communities in lakes designated for their conservation value.Location Selected lakes of conservation importance all over Scotland, representing a wide variety of lake habitat types and associated macrophyte communities.Methods Local environmental variables and species occurrence were measured in the field. Spatial variables were generated using principal coordinates of neighbour matrices (PCNM) analysis. Connectivity between each lake and its neighbours was defined as either (i) all lakes within a radius of 5, 10, 25, 50, 75 or 100 km; (ii) all lakes in same river system; or (iii) all lakes in the same catchment and upstream of the lake. Using variance partitioning within canonical correspondence analysis, the relative impact of E = local environment, S = space and C = lake connectivity was compared on submerged (n = 119 lakes) and emergent (n = 96 lakes) macrophyte assemblages.Results Local environmental conditions, such as total phosphorus, alkalinity/conductivity and the presence of invasive species, as well as spatial gradients were key drivers of observed variation in macrophyte communities; e.g., for submerged macrophytes, a combination of local to moderate factors relating to water chemistry and broad‐scale gradients reflecting elevation and climate are important. Spatially structured environmental variables explained a large portion of observed variation.Main conclusions Our findings confirmed the need to manage local environmental pressures such as eutrophication, but suggested that the traditional catchment approach was insufficient. The spatial aggregation of environmental and connectivity factors indicated that a landscape scale approach should be used in lake management to augment the risk assessment to conservation species from the deterioration of suitable lake sites over broad biogeographic areas.

Native and alien floras in urban habitats: a comparison across 32 cities of central Europe

ABSTRACTAim To determine relative effects of habitat type, climate and spatial pattern on species richness and composition of native and alien plant assemblages in central European cities.Location Central Europe, Belgium and the Netherlands.Methods The diversity of native and alien flora was analysed in 32 cities. In each city, plant species were recorded in seven 1‐ha plots that represented seven urban habitat types with specific disturbance regimes. Plants were classified into native species, archaeophytes (introduced before ad 1500) and neophytes (introduced later). Two sets of explanatory variables were obtained for each city: climatic data and all‐scale spatial variables generated by analysis of principal coordinates of neighbour matrices. For each group of species, the effect of habitat type, climate and spatial variables on variation in species composition was determined by variation partitioning. Responses of individual plant species to climatic variables were tested using a set of binomial regression models. Effects of climatic variables on the proportion of alien species were determined by linear regression.Results In all cities, 562 native plant species, 188 archaeophytes and 386 neophytes were recorded. Proportions of alien species varied among urban habitats. The proportion of native species decreased with increasing range and mean annual temperature, and increased with increasing precipitation. In contrast, proportions of archaeophytes and neophytes increased with mean annual temperature. However, spatial pattern explained a larger proportion of variation in species composition of the urban flora than climate. Archaeophytes were more uniformly distributed across the studied cities than the native species and neophytes. Urban habitats rich in native species also tended to be rich in archaeophytes and neophytes.Main conclusions Species richness and composition of central European urban floras are significantly affected by urban habitat types, climate and spatial pattern. Native species, archaeophytes and neophytes differ in their response to these factors.

Topography related spatial distribution of dominant tree species in a tropical seasonal rain forest in China

The degree to which variation in species distribution is predictable from topographic variation is of considerable current interest. In this paper, canonical correspondence analysis (CCA), linear regression and principal coordinates of neighbour matrices (PCNM) models were used to explain the variation in the distributions of the 13 dominant species in a 20-ha tropical rain-forest plot in China. The results showed that: (1) Tree distribution maps show that some species are mainly found in the gullies of the plot, whereas others occur on the slopes. Which indicates topographic variables are important factors for the distribution pattern of species. (2) Both linear regression and CCA results show that convexity and elevation are the most important variables effecting distribution of trees. For saplings, elevation, convexity and aspect explain 15.3%, 9.0% and 10.1% of the total variation of species abundance. For poles, elevation and convexity explain 19.3% and 11.4% respectively. However, only 5.3% of the total variation is explained for adults. (3) The PCNM results showed that topography alone explained 20%, 24% and 5% of the total variation of species abundance for saplings, poles and adults, respectively. Overall evidence for topographic control of the tropical tree distribution is strong, but the explanatory power of topographic variables was a small part of the total of variation.

Comparison of novel and standard methods for analysing patterns of plant death in designed field experiments

SUMMARYThe present paper compares standard and novel methods for analysing aggregated patterns of plant death in designed field experiments; these methods include binomial (BN), beta-binomial (BBN), logistic-normal-binomial (LNB), BN models with random blocks, BN models with smooth-scale spatial components and principal coordinates of neighbour matrices (PCNM). PCNM is a relatively new technique used in ecology to determine how much observed variability can be explained by spatial and environmental variables, and has not yet been applied to agricultural studies. The survival data of two pasture species, collected from a designed field experiment that was replicated at multiple locations, were used. First, the occurrence of overdispersion was tested using the BN and BBN distributions. Goodness-of-fit tests proved that the BBN model provided a better description (better fit) of the observed data in some cases than did the BN distribution, indicating overdispersion was present. When overdispersion was not present, the BN distribution was adequate to describe the data, and the use of the BBN distribution was superfluous. It is then shown that the PCNM approach, the BN model with smooth-scale spatial components and the LNB model were able to account for some of the variation as spatial variability, thus reducing the species effect compared with that explained under the standard BN model. The amount of variation among species according to the BN model and the BN model with random blocks was similar. Therefore, it is argued that the novel PCNM approach warrants further testing when exploring the spatial variability in designed experiments in agriculture and using LNB, PCNM and BN with smooth-scale spatial components may provide better predictions of species effects than do other, more conventional, approaches.

Environmental control and spatial structures in peatland vegetation

Question: What are the relative influences of environment and space in structuring the plant composition in a peatland complex? Location: Lakkasuo, southern boreal zone, Finland. Method: We used principal coordinates of neighbour matrices (PCNM) to model spatial structures in the plant composition of a peatland complex comprising ombrotrophic and minerotrophic, open and forested areas. We used redundancy analyses (RDA) and variation partitioning to assess the relative influences of chemical variables (peat and water characteristics), physical variables (hydrology, soil properties, shade), as well as broad-scale (>350 m) and medium-scale (100–350 m) spatial structures on vegetation assemblages. Results: We identified five different significant spatial patterns circumscribing (1) the minerotrophic–ombrotrophic gradient; (2) dry ombrotrophic and wet minerotrophic areas; (3) open and shaded areas; (4) dry open/shaded and wet patches within the ombrotrophic areas; and (5) dry open patches and dry forested patches. With spatial structures and environmental variables, we were able to model 30% of the variability in plant composition in the peatland complex, 13% of which was attributable to spatial structures alone. Conclusions: We demonstrated that in the peatland complex, the spatial dependence processes were more important at the broadest scale, and found that patterns at a medium scale might reflect finer-scale patterns that were not investigated here. Spatial autocorrelation in vegetation composition in the peatland complex appeared to be driven by Sphagnum species. Our results emphasize that spatial modelling should be routinely implemented in studies looking at species composition, since they significantly increase the explained proportion of variance.

Determinants of spider species richness in coastal dunes along a gradient of mediterraneity

Abstract. 1. The Iberian Peninsula is one of the most relevant areas in terms of species richness, rarity and endemism in the Mediterranean Basin. Using spiders as a model, we studied the relative importance of environmental and non‐environmental spatial variation along a gradient of mediterraneity on the western coast of the Iberian Peninsula.2. We performed a spatially explicit analysis to evaluate the contribution of pure environmental and pure spatial effects and their shared influence on spider species richness by variation partitioning and principal coordinates of neighbour matrices (PCNM). We dissect the spatial variation of species richness into additive scale‐specific models through PCNM analysis and estimate the relative importance of environmental variables for each model.3. Variation partitioning revealed that 72.8% of species richness variation could be explained by the environmental (climate and dune stability) and spatial variables. Most of this variation (51.3%) corresponds to the environmental spatially structured component.4. The influence of environmental variables was scale‐dependent. At the broadest scales, the latitudinal‐climatic gradient was the dominant factor that influenced spider species richness variation. At the finest scale, stability of the dune system was the most important component.5. In conclusion, spider species richness patterns were determined mostly by spatially structured environmental variation. More importantly, this study shows that different environmental factors act at multiple scales. Hence, our results reinforce the importance of the incorporation of both local and broad‐scale factors when examining species richness patterns.

Modelling the effect of directional spatial ecological processes at different scales

During the last 20 years, ecologists discovered the importance of including spatial relationships in models of species distributions. Among the latest developments in modelling how species are spatially structured are eigenfunction-based spatial filtering methods such as Moran's eigenvector maps (MEM) and principal coordinates of neighbour matrices (PCNM). Although these methods are very powerful and flexible, they are only suited to study distributions resulting from non-directional spatial processes. The asymmetric eigenvector map (AEM) framework, a new eigenfunction-based spatial filtering method, fills this theoretical gap. AEM was specifically designed to model spatial structures hypothesized to be produced by directional spatial processes. Water currents, prevailing wind on mountainsides, river networks, and glaciations at historical time scales are some of the situations where AEM can be used. This paper presents three applications of the method illustrating different combinations of: sampling schemes (regular and irregular), data types (univariate and multivariate), and spatial scales (metres, kilometres, and hundreds of kilometres). The applications include the distribution of a crustacean (Atya) in a river, bacterial production in a lake, and the distribution of the copepodite stages of a crustacean on the Atlantic oceanic shelf. In each application, a comparison is made between AEM, MEM, and PCNM. No environmental components were included in the comparisons. AEM was a strong predictor in all cases, explaining 59.8% for Atya distribution, 51.4% of the bacterial production variation, and 38.4% for the copepodite distributions. AEM outperformed MEM and PCNM in these applications, offering a powerful and more appropriate tool for spatial modelling of species distributions under directional forcing and leading to a better understanding of the processes at work in these systems.

Determinants of beta diversity of spiders in coastal dunes along a gradient of mediterraneity

AbstractAim The Mediterranean Basin is recognized for its high levels of species richness, rarity and endemicity. Our main aim was to evaluate the relative effects of environmental and spatial variables and their scale‐specific importance on beta diversity patterns along a gradient of mediterraneity, using spiders as a model group.Location This study was carried out in 18 coastal dune sites along the Portuguese Atlantic coast. This area encompasses 445 km and comprises two distinct biogeographic regions, Eurosiberian (northern coast) and Mediterranean (centre and south).Methods A forward selection procedure was carried out to select environmental and spatial variables responsible for determining beta diversity patterns. Variation partitioning and principal coordinates of neighbour matrices (PCNM) were used to estimate the contribution of pure environmental and pure spatial effects and their shared influence on beta diversity patterns and to estimate the relative importance of environmental structured variation and pure spatial variation at multiple spatial scales.Results Climate, ground vegetation dune cover and area were selected by a forward selection procedure. The same procedure identified three PCNM variables, all corresponding to large and medium spatial scales. Variation partitioning revealed that 46.1% of the variation of beta diversity patterns was explained by a combination of environmental and PCNM variables. Most of this variation (42.5%) corresponded to spatial variation (environmental spatially structured and pure spatial). Climate and vegetation structure influences were predominant at the PCNM1 and PCNM3 scales, while area was more important at the intermediate PCNM2 scale.Main conclusions Our study revealed that beta diversity of spiders was primarily controlled by a broad‐scale gradient of mediterraneity. The relative importance of environmental variables on the spider assemblage composition varied with spatial scale. This study highlights the need of considering the scale‐specific influence of niche and neutral processes on beta diversity patterns.

Water table response to an experimental alley farming trial: dissecting the spatial and temporal structure of the data

Clearing vegetation for traditional agriculture diminishes native habitat and reduces plant transpiration, leading to increased groundwater recharge and onset of dryland salinization due to rising groundwater and mobilization of salt stores in the soil profile. This change in hydrology and salinity can also negatively affect biodiversity in many semiarid regions. Alternating native perennial tree belts with mono-species agriculture within the tree belt alleys is one possible system that can provide recharge control and recover some of the ecosystem services of degraded agricultural landscapes. To assess the effect of this agroforestry technique on groundwater levels, an alley farming trial was established in 1995, incorporating different combinations of belt width, alley width, and revegetation density. Transects of piezometers within each design have been monitored from October 1995 to January 2008. The data set consisted of 70 piezometers monitored on 39 dates. Two trends were observed within the raw data: An increase in water table depth with time and an increase in the range of depths monitored at the site were clearly discernible. However, simple hydrograph analysis of the data has proved unsuccessful at distinguishing the effect of the tree belts on the water table morphology. The statistical techniques employed in this paper to show the effect of the experiment on the water table were variation partitioning, principal coordinates of neighbor matrices (PCNM), and canonical redundancy analysis (RDA). The environmental variables (alley farming design, distance of piezometer from the tree belt, and percentage vegetation cover including edge effect) explained 20-30% of the variation of the transformed and detrended data for the entire site. The spatial PCNM variables explained a further 20-30% of the variation. Partitioning of the site into a northern and southern block increased the proportion of explained variation for the plots in the northern block. The spatial PCNM variables and vegetation cover remained the most significant variables. The PCNM analysis revealed no spatial pattern that could be attributed to the trial. The high proportion of unexplained variation may be due to site variables that have not been considered in this study.

Partitioning temperate plant community structure at different scales

Three stem-mapped field plots, each representing a specific forest developmental stage, were established in a temperate forest in Northeastern China: a young secondary conifer and broadleaved mixed forest (YSF), an old secondary conifer and broadleaved mixed forest (OSF), and an old-growth Korean pine and broad-leaf forest (OGF). The focus of this study is to test an environmental control hypothesis. The spatial variations of community structure (species diversity, forest density and size differentiation) were partitioned into pure environment, pure space, and spatially-structured environmental processes in the three research plots. The principal coordinates of neighbor matrices (PCNMs) method was included in the procedure of variation decomposition with respect to spatial and environmental components. The significant PCNM variables could be directly interpreted in terms of spatial scales. The results indicate that the explanatory power of the soil data was much greater in the secondary forests (YSF and/or OSF) than in the old-growth forest regarding species diversity, forest density and size differentiation. Nearly half (48.35% and 44.86%) of the variation of species richness was explained by soil properties in the young secondary forest and the old secondary forest, respectively. However, only 4.87% of that variation was explained by soil properties in the old-growth forest. Over 14% of the variation of the tree size differentiation was explained by soil properties in two secondary forests, and only 4.23% in the old-growth forest. In this study, the spatial variation of species richness and size differentiation was related to environmental variables at multiple scales. Soil variables had a significant effect on species richness and size differentiation at broader scales in the secondary forests, but mainly at medium and fine scales in the old-growth forest. The results challenge the commonly held assumption that tree distributions simply reflect patterns of seed dispersal at local scales.

Plant species richness–environment relationships across the Subantarctic–Patagonian transition zone

AbstractAim To evaluate the relative importance of climate, productivity, environmental heterogeneity, biotic associations and habitat use by cattle to account for the species richness of trees, shrubs and herbs across the Subantarctic–Patagonian transition.Location An area of c. 150 × 150 km, within the transition zone between the Subantarctic and Patagonian subregions on the eastern slope of the Andes (c. 39–42° S, 70–72° W).Methods All vascular plants found at each one of 50 (10 × 10 m) sampling plots were counted to estimate the local tree, shrub and herb species richness. Path analysis was used to evaluate the relationship between the richness of the three life‐forms and plant cover, dried litter biomass, mean annual temperature, annual precipitation, daily temperature range, substrate heterogeneity and number of faecal pats. Principal coordinates of neighbour matrices was used to model the spatial autocorrelation of the data.Results Total plant species richness showed a unimodal pattern of spatial variation across the transition. Richness responded positively to indirect effects of precipitation mediated through plant cover, but there was a negative overall effect of precipitation on richness towards the west of the transition, most strongly for trees. An increase in substrate heterogeneity promoted a local increase in herb and shrub richness; the richness of trees increased in sites with steeper slopes. Canopy closure had a direct negative impact on herb richness; it also increased the local accumulation of litter, which negatively affected shrub and herb richness. The impact of habitat use by cattle negatively affected herb richness in areas to the east of the biogeographical transition.Main conclusions We suggest that the importance of indirect climatic effects mediated by vegetation cover can account for species richness patterns across this transition, most strongly for woody species, which supports the productivity hypothesis. The southern temperate forests towards the west may represent a deviation from the predictions of the water–energy dynamics hypothesis. Dissimilar spatial patterns of variation in the richness of woody and herbaceous species, and their different responses to climatic and heterogeneity variables across the transition, suggest that plant life‐form influences the plant species richness–environment relationships.

Community surveys through space and time: testing the space–time interaction in the absence of replication

In order to test hypotheses about changes in the environment induced by man, including climatic change, ecologists are sampling portions of the environment repeatedly across time. This paper describes a method for testing a space-time interaction in repeated ecological survey data, when there is no replication at the level of individual sampling units (sites). This methodological development is important for the analysis of long-term monitoring data, including systems under anthropogenic influence. In these systems, an interaction may indicate that the spatial structure of community composition has changed in the course of time or that the temporal evolution is not the same at all sites. This paper describes ANOVA models corresponding to the steps leading to a solution to the problem, which is based on the representation of space and time by principal coordinates of neighbor matrices (PCNM eigenfunctions) in the ANOVA. Numerical simulations showed that ANOVA Model 5 was the model of choice for the analysis of the space-time interaction because it always had correct rates of Type I error, and its power was always equal to or higher than those of other possible models of analysis. If the hypothesis of absence of interaction is not rejected, one cannot conclude that a change has occurred in the spatial structure of the response data across time; one should follow the ordinary rules of two-way ANOVA if testing the significance of the main factors is of interest. If the hypothesis of absence of interaction is rejected, one should model the spatial structure of each time period in a separate way. One can also conduct a single test involving a separate model of the spatial structure for each time period. This paper presents two applications to real ecological data.

Classic metapopulations are rare among common beetle species from a naturally fragmented landscape

1. The general importance of metacommunity and metapopulation theories is poorly understood because few studies have examined responses of the suite of species that occupy the same fragmented landscape. In this study, we examined the importance of spatial ecological theories using a large-scale, naturally fragmented landscape. 2. We measured the occurrence and abundance of 44 common beetle species in 31 natural rainforest fragments in Tasmania, Australia. We tested for an effect on beetle distribution of geographic variables (patch area, patch isolation and amount of surrounding habitat) and of environmental variables based on plant species, after first accounting for spatial autocorrelation using principal coordinates of neighbour matrices. The environmental variables described a productivity gradient and a post-fire succession from eucalypt-dominated forest to late-successional rainforest. 3. Few species had distributions consistent with a metapopulation. However, the amount of surrounding habitat and patch isolation influenced the occurrence or abundance of 30% of beetle species, implying that dispersal into or out of patches was an important process. 4. Three species showed a distribution that could arise by interactions with dominant competitors or predators with higher occurrence in small patches. 5. Environmental effects were more commonly observed than spatial effects. Twenty-three per cent of species showed evidence of habitat-driven, deterministic metapopulations. Furthermore, almost half of the species were influenced by the plant succession or productivity gradient, including effects at the within-patch, patch and regional scales. The beetle succession involved an increase in the frequency of many species, and the addition of new species, with little evidence of species turnover. Niche-related ecological theory such as the species-sorting metacommunity theory was therefore the most broadly applicable concept. 6. We conclude that classic and source-sink metapopulations are probably rare in this large-scale, naturally fragmented system, although dispersal processes like those occurring in metapopulations may have a substantial influence on community composition. However, deterministic processes (niche specialisation, species-sorting metacommunities and deterministic metapopulations) drive the occurrence or frequency of the majority of species. We urge further research into the prevalence of spatial ecological processes in large-scale natural ecosystems to expand our understanding of the processes that may be important in nature.

The relations between ‘standard’ fluvial habitat variables and turbulent flow at multiple scales in morphological units of a gravel‐bed river

AbstractFluvial fish habitat is often characterized by highly turbulent flow conditions. Several laboratory experiments suggest that unpredictable turbulent fluctuations can increase the swimming energy costs of fish. At the scale of fish habitat models, it can be hypothesized that turbulence can be captured by the combined effects of the standard habitat variables: depth, velocity and substrate. However, recent studies conducted at the reach scale suggest that turbulent properties are more controlled by the large‐scale bed morphology than by individual roughness elements. In this study, we investigate the spatial structure of turbulent flow and the potential relationships between ‘standard’ habitat variables and turbulent flow properties in pools and riffles of a shallow gravel‐bed river. The study explores these relations at multiple spatial scales. Mean turbulent properties and turbulent flow structures statistics were computed from 1932 near bed velocity time series sampled with acoustic Doppler velocimeters on a regular grid in four morphological units (two pools and two riffles) presenting a gradient of complexity. We used a novel multivariate variation partitioning analysis involving principal coordinates of neighbour matrices (PCNM) to partition turbulent flow properties into six significant spatial scales (VF: 0.35, F: 0.75, M: 1.25, L: 2, XL: 2.5 and XXL: 3 m). Between 45 and 70% of the variance of the turbulent flow properties were explained by the spatial PCNM. In the four units, turbulent properties exhibited a spatial dependence across the entire range of scales. However, the proportion of variation explained by the larger‐scaled PCNMs was higher in the most homogeneous units. In general, the spatial dependence of turbulent flow was lower in the riffles than in the pools, where the mean flow velocity was slower. The capacity of ‘standard’ fish habitat variables to explain turbulent properties was relatively low, especially in the smaller scales, but varied greatly between the units. From a practical point of view, this level of complexity suggests that turbulence should be considered as a ‘distinct’ ecological variable within the range of spatial scales included in this study. Further research should attempt to link the spatial scales of turbulent flow variability to benthic organism patchiness and fish habitat use. Copyright © 2009 John Wiley & Sons, Ltd.

Beetle abundance–environment relationships at the Subantarctic–Patagonian transition zone

Abstract. The spatial variation in the abundance of individuals may be associated with the variation in environmental variables. The productivity hypothesis proposes that climate affects plant productivity, which may limit the abundance of beetles. The thermal‐limitation hypothesis proposes the direct effect of ambient temperature may limit beetle abundance. We analysed the abundance of epigaeic beetles at the Subantarctic–Patagonian transition to test for these abundance–environment relationships. We collected beetles using 450 pitfall traps within a ~150 × 150 km area representative of the Subantarctic–Patagonian transition. We used path analysis to evaluate the relationships between beetle abundance and plant cover, litter biomass, averaged minimum and daily temperature range, and mean annual precipitation. We used principal coordinates of neighbour matrices to model the spatial autocorrelation of the data. The abundance of beetles increased strongly with tree canopy cover and less strongly with herb cover. The increase in shrub cover had a positive effect on beetle abundance in areas to the east of the transition, within the scrubland‐steppe, but it has a negative effect on beetle abundance in areas to the west of the transition, within the forests. The association between beetle abundance and minimum daily temperature was negative or weak throughout. Increased temperature variation had a negative effect on beetle abundance. We suggest that indirect positive climatic effects mediated through plant cover are important to account for the variation in beetle abundance, which favours the productivity hypothesis. Thermal limitation may operate locally through variation in daily temperature range.