Principal Coordinates Of Neighbour Matrices Research Articles

Microhabitat variation affects the understory community assembly of a neotropical rainforest

Deterministic and stochastic processes combine with biotic interactions in community assembly. Stochasticity and biotic interactions are thought to operate on fine scales, and determinism on coarse scales. Would determinism be detected on a fine scale in an understory community of a tropical rainforest? We measured the altitude, index of convexity (IC), slope, and canopy openness, counted the individuals and species and calculated Simpson's dominance index of plants with height ≥ 30 cm and DBH < 5 cm for each of 50 randomly drawn 3 × 3 m plots from a one-hectare grid. We used redundancy analysis and spatial modeling with principal coordinates of neighbor matrices to assess how much of the community variation each variable explained. The same was done for each set of plots with 20%, 60%, and 20% respectively of the lower, intermediate, and higher values of the microrelief variables. Most of the community variation remained unexplained, but the effect of the microrelief variables was significant. IC had the highest contribution and was four times higher in the plots with 20% higher values, stressing the increasing importance of determinism towards the higher extremes of the variable's local range. Species richness decreased and dominance increased in convex plots (high IC), and the most abundant species differed between concave and convex plots. Microrelief variation can act as a local filter with a growing influence towards the extremes of the local range of microenvironmental variables in the community space. Niche-based processes rely on the strength of the environmental filter.

Contrasting spatial distribution of pioneer versus non‐pioneer saplings in a Taiwanese forest: A multiple scale approach

AbstractDispersal limitation and environmental filtering were recognized as the main dispersal‐based and niche‐based processes responsible for community assembly. These interactions usually leave more spatial signatures in sapling communities and create detectable spatial patterns in different functional types of species. We investigated saplings of pioneer and non‐pioneer species, which facilitated an understanding of species co‐existence and biodiversity recovery. Based upon mapped tree data in the subtropical evergreen broad‐leaved forest dynamics plot in Taiwan, we endeavored to: (1) determine the different spatial scales contributing to distribution patterns of pioneer and non‐pioneer saplings; (2) understand how dispersal limitation affects distribution of pioneer and non‐pioneer saplings; and (3) evaluate the degree to which the different environmental factors explain variation in species composition in pioneer and non‐pioneer saplings. We used the principal coordinates of neighbor matrices (PCNM) method, and variation partitioning to disentangle the contributions of these processes. Fine‐scale spatial patterns were more important for pioneer than for non‐pioneer saplings. Dispersal limitation was the main process influencing the spatial distribution of the non‐pioneer saplings. Environmental filtering was also an important process regulating the spatial distribution of saplings for both functional types, especially for pioneer saplings. Disturbance effects contributed to fine‐scale spatial variation in pioneer saplings, whereas topographic and soil effects contributed to broad and medium scale spatial variation in non‐pioneer saplings. It was evident that different spatial patterns of saplings of different functional types served to facilitate tree regeneration and maintain species co‐existence in this subtropical broad‐leaved forest.

Diversidade beta de Ephemeroptera, Plecoptera e Trichoptera ao longo de múltiplas escalas espaciais nas corredeiras do rio Xingu

Abstract: Aim Additive diversity partitioning has been used to explain the accumulation of diversity at different spatial scales with relative success. In lotic ecosystems, the spatial extent is extremely relevant in studies of diversity accumulation, because it encompasses environmental variation that causes changes in the observed communities. Despite of previous knowledge on the effect of extent on biological communities and diversity accumulation, little is known about the topic in aquatic insect communities in large rivers. In this context, we studied the effect of spatial extent and environmental variation on diversity components, alpha and beta, in Ephemeroptera, Plecoptera and Trichoptera (EPT) groups in Xingu River rapids. Methods The sampling was carried out in October 2015 in the dry period of the region, in nine rapids in the Xingu, Bacajá and Iriri rivers. At each collection site, five Surber samples were taken. We also recorded pH, dissolved oxygen, electrical conductivity, water temperature, and geographic coordinates. We used additive diversity partitioning to separate the diversity components α and β. For the spatial component, we generated the spatial filters using PCNM (Principal Coordinates of Neighbour Matrices) and partitioned the variance between space and environment using partial Redundancy Analysis (pRDA). Results We collected 12,249 individuals in 27 genera within 11 families in the EPT orders. The greatest accumulation of diversity was observed among rapids of the river, when the β diversity in this spatial extent was greater than the expected. The spatial structure was an indirect effect at this extent, since it is a relevant drive to environmental variables. Conclusions The results indicate that the effect of spatial extent on rapids is a contributing factor in the diversity components of aquatic insect communities in large river rapids. To the conservation and management of this environment is necessary cover as many rapids as possible, since the preservation of only a few rapids can mean a substantial loss of regional diversity.

Spatial autocorrelation shapes liana distribution better than topography and host tree properties in a subtropical evergreen broadleaved forest in SW China

AbstractLianas are an important component of subtropical forests, but the mechanisms underlying their spatial distribution patterns have received relatively little attention. Here, we selected 12 most abundant liana species, constituting up to 96.9% of the total liana stems, in a 20‐ha plot in a subtropical evergreen broadleaved forest at 2472–2628 m elevation in SW China. Combining data on topography (convexity, slope, aspect, and elevation) and host trees (density and size) of the plot, we addressed how liana distribution is shaped by host tree properties, topography and spatial autocorrelation by using principal coordinates of neighbor matrices (PCNM) analysis. We found that lianas had an aggregated distribution based on the Ripley's K function. At the community level, PCNM analysis showed that spatial autocorrelation explained 43% variance in liana spatial distribution. Host trees and topography explained 4% and 18% of the variance, but less than 1% variance after taking spatial autocorrelation into consideration. A similar trend was found at the species level. These results indicate that spatial autocorrelation might be the most important factor shaping liana spatial distribution in subtropical forest at high elevation.

Spatio‐temporal analyses show conflicting evidence of the role of an invasive minnow in the decline of an endangered desert fish endemic to the south‐western U.S.A.

Abstract Invasive species are often blamed for the declines of native species, although this is often based on anecdotal or incomplete evidence. In the Virgin River (U.S.A.), the red shiner minnow (Cyprinella lutrensis) has been identified as a major factor in woundfin (Plagopterus argentissimus) decline, a critically endangered endemic minnow. We assessed the evidence for the hypothesis that negative interactions between these two fish drove this decline. We tested three predictions: (1) spatial and temporal patterns were significant predictors of assemblage structure; (2) red shiner would show opposite spatial and temporal patterns to native species; and (3) woundfin would show site‐specific decreases in abundance following red shiner invasion. We used a long‐term (28 years) dataset of fish abundances in the Virgin River at 10 regularly monitored sites to test our predictions. Using principal coordinates of neighbour matrices with redundancy analysis, we tested our first two predictions by identifying the temporal and spatial structure of the fish assemblages and comparing the patterns of native fish species to those of the invasive fish species. To test our third prediction, we used a breakpoint analysis of site‐specific population data to determine if woundfin showed stable populations prior to red shiner invasion, followed by declines after invasion. We found that 42% of variation in fish abundances in the river could be explained by spatial patterns, and 12% by temporal patterns. Red shiner showed opposite spatial and temporal patterns to woundfin (but not to other native species), and abundances of red shiner and woundfin were negatively correlated, yielding correlative evidence of negative interactions between red shiner and woundfin. However, our breakpoint analysis did not show the expected patterns and woundfin declined even in sites that did not experience red shiner invasion pointing to alternate mechanisms of decline such as effects of poor water quality. Our analyses provided correlative but conflicting evidence of red shiner influence on woundfin but were unable to identify a definitive causal mechanism of woundfin decline. We discuss two possible explanations for the contemporary woundfin decline and red shiner invasion: displacement of woundfin via negative interactions, or replacement of woundfin by red shiner in a niche already vacated by woundfin due to environmental or anthropogenic disturbances. This study demonstrates that the dynamics between native and non‐native species may not be straightforward and can be complicated by other factors such as anthropogenic activities and environmental changes. This research highlights that long‐term monitoring is essential to untangling interactions between native and invasive species to develop effective conservation methods that address underlying causes of decline.

Dispersal limitation, soil, and fire affect functional properties of tropical secondary forests on abandoned cattle ranching landscapes

Forest age is a major predictor of secondary forest functional properties and through the chronosequence approach continues to be a principal focus in local, landscape, and regional-scale studies of secondary succession. Recent work has shown that patterns of temporal change in functional properties differ markedly between wet and seasonally dry lowland forests, suggesting that decreasing light and increasing water availability, respectively, are the main drivers of successional change. Meanwhile, however, the potentially marked effects of anthropogenic factors (especially fire), soils, climate, and dispersal limitation on the variation of forest characteristics over landscapes remain poorly understood. We studied the functional properties of seasonally dry secondary forests 5–35 years after pasture abandonment on the Nicoya Peninsula, Costa Rica. We measured 11 functional traits for 63 dominant tree and palm species in 52 plots of 0.12 ha. We used linear regression and variation partitioning to determine the relative importance of soil, climate, site use, fire history, spatial factors, and forest age in the determination of community weighted mean (CWM) trait values. CWM leaf trait and stem trait spectra of the 52 plots were orthogonal in a PCA ordination. Our seasonal forest hypothesis, that forest functional properties become more acquisitive with age as suggested by other authors, was not supported, perhaps because our chronosequence was relatively short. Our fire tolerance hypothesis was that bark thickness, wood specific gravity and resprouting capacity would increase with time of exposure to fires. This hypothesis was not supported for bark thickness. Rather, our results suggest that wood specific gravity and resprouting capacity are better predictors of fire tolerance. Also, our results suggest that >10 years of exposure to fire generates changes in forest fire tolerance strategies from high CWM bark thickness to high wood specific gravity. Finally, we tested our dispersal limitation hypothesis, that spatial variables, expressed as principal coordinates of neighbor matrices (PCNM) eigenfunctions, predict variation in forest functional properties, using variation partitioning analysis with matrices of climate, soil, anthropogenic and spatial variables. The results (overall model R2 = 0.46) indicated that spatial variables, followed by soil (acidity, depth, and extractable Mn), are the best overall predictors of forest functional traits values, supporting this hypothesis. Overall, fire, dispersal limitation and soil characteristics explain the functional properties of these secondary forests, with no effect of age in the 5–35 years range. This indicates a critical need for sampling designs and analytical approaches that take into account all these factors to advance understanding of tropical seasonal forest recovery at the landscape scale.

Spatial and environmental factors contributing to phytoplankton biogeography and biodiversity in mountain ponds across a large geographic area

Exploring phytoplankton biodiversity and biogeographic patterns, and the factors that control them, can help to understand the structure and function of aquatic ecosystems. We selected mountain ponds with minimal anthropogenic disturbance to reveal the biogeographic patterns of phytoplankton and to assess the influence of spatial and environmental factors on phytoplankton biodiversity. On a large regional scale, the phytoplankton communities in the mountain ponds showed geographic patterns—the community composition differed between eastern and western areas. A total of seven phyla and 73 genera were identified. Alpha diversity indices did not significantly correlate with nutrient concentrations. Environmental factors and principal coordinates of neighbour matrices together explained 28.5% of the total variation in phytoplankton community composition in the 41 ponds, with each uniquely explaining 3.0% and 14.4% of the total variation, respectively. Therefore, compared with environmental factors, spatial factors predominantly contributed to the distribution of phytoplankton across the study area. With increasing trophic status, the relative influence of spatial factors decreased, while that of environmental factors increased.

How Iberian are we? Mediterranean climate determines structure and endemicity of spider communities in Iberian oak forests

Understanding the causes behind species richness and endemicity is fundamental to explain biodiversity and assist conservation management, especially in biodiversity hotspots like the Mediterranean Basin. Here we investigate the patterns in Iberian forest spider communities and the processes behind their assembly, by testing hypotheses about the effects of climate and habitat on species richness, endemicity and structure of communities at different spatial scales, and about how microhabitat and dispersal affect the level of endemicity of species. We studied 16 spider communities in Iberian Quercus forests from different climatic zones, applying a standardised sampling protocol. We examined the contribution of habitat, climate, and geography to the differences in the composition of spider communities across spatial scales using distance-based redundancy analysis models (dbRDA) and principal coordinates of neighbour matrices (PCNM). We assessed the effects of the same variables on the endemicity of communities (measured by a weighted index), and tested the correlation between the microhabitat and the ballooning frequency (obtained from bibliography), and the endemicity of species through generalised linear models. Spider communities formed two groups—one southern and one northern—based on similarity in species composition. Precipitation and temperature were inversely related with the number of species while geography and forest type explained the compositional similarities between communities at different spatial scales. Endemicity of communities increased with temperature and decreased with precipitation, whereas species endemicity decreased with ballooning frequency. Our findings illustrate how niche-related processes may drive spider diversity while dispersal determines species distribution and identity and, ultimately, community composition. From a conservation viewpoint, when maximising species richness is incompatible with prioritising endemicity, the criteria to follow may depend on the geographic scale at which decisions are made.

Effect of environmental gradients, habitat continuity and spatial structure on vascular plant species richness in semi-natural grasslands

European semi-natural grasslands host numerous and diverse living organisms within a relatively small area; therefore, conservation of these habitats is crucial to maintain high biodiversity in agricultural areas. The aim of this study was to examine the effects of environment, habitat continuity and spatial structure on semi-natural grassland species richness (SR) at the regional extent. SR and characteristic SR (CHSR) were calculated in 709 georeferenced vegetation plots obtained from the Polish Vegetation Database. For each vegetation plot, (1) environmental variables representing climate, topography, soil characteristics (e.g. pH and physical soil properties), landscape and anthropogenic pressure; (2) habitat continuity in time and (3) variables reflecting the spatial structure of vegetation plots using principal coordinates of neighbour matrices were measured. Environmental data were measured at four different spatial scales (buffers of 0.05-, 0.5-, 2.5- and 5-km radii surrounding each vegetation plot). Boosted regression trees were generated to explore the relationships of SR and CHSR with predictors. Variables associated with anthropogenic pressure, landscape structure and soil characteristics operating in the 0.5- and 5-km buffers significantly improved SR and CHSR model. However, effects of individual predictors on SR and CHSR were not predominant. Habitat continuity and topographic heterogeneity operating in the 0.05-km buffer exclusively improved CHSR model. The results suggest that neutral processes (dispersion limitation, local management history and/or stochastic events) reflected by spatial variables are strongly related to SR and CHSR. Patterns observed herein may also exist in other agriculture-dominated regions in temperate Europe. This knowledge will contribute to effective conservation of valuable habitats over large spatial areas.

Drivers of plant species composition in alder-dominated forests with contrasting connectivity

The effects of local and regional environmental variables as well as spatial gradients on the plant species composition of two types of alder-dominated forests (riparian forests and alder carrs) with contrasting connectivity were studied across the Western Carpathians from Hungary through Slovakia to Poland. We used large vegetation (240 sampling plots) and environmental (24 variables) datasets, which were accompanied by spatial variables represented by principal coordinates of neighbour matrices. Canonical correspondence analysis (CCA) of the two datasets revealed 13 and 29 variables with significant effects on variation in species composition of alder carrs and riparian alder forests, which jointly explained 41.2% and 36.4% of the variability, respectively. Altitude was the most important factor explaining 7.7% of the variability in the species composition of alder carrs and 8.2% in riparian alder forests. Variation partitioning in CCA revealed that local variables were crucial drivers for species composition patterns in alder carrs, while spatial processes unrelated to the measured environmental variables shaped the vegetation structure of riparian forests.

Spatial and environmental factors predict the composition of non-native fish assemblages in Neotropical reservoirs

Hydropower dams are one of the largest sources of anthropogenic impacts on freshwater systems in the world. In addition to the modifications in environmental dynamics (i.e., fish migration barrier, water flow reduction, depth increase, flood regulation), the novel environments are favorable to the dissemination of non-native species in the basin. The lack of native species adapted to the changed environment creates occupations opportunity (i.e., available resources) for non-native species, which end up finding in these environments ideal areas to complete their life cycle. Thus, the aim of the work was identify which reservoir characteristics provide as well benefits for non-native fish species. Specifically, we tested the hypothesis that the spatial structure, reservoir productivity and morphology, and chronological characteristics are factors related to the composition and abundance of non-native fish species in reservoir. Using novel statistical techniques (Principal coordinates of neighbour matrices and Distance-based linear models), it was possible to identify the spatial patterns and to understand how the characteristics of the reservoirs influence the composition of the abundance of these species. Our results show that some reservoir characteristics provide benefits to non-native fish species, thus being localities within the hydrologic basins that can be considered as sources of non-native fish species propagules. In general, our results showed that larger and older reservoirs have a greater abundance of non-native fish species. Also, it was possible to identify spatial patterns, where in smaller scales neighboring reservoir tend to be more similar as to the composition and abundances of non-native fish species and this similarity can reach basin level.

Everything is not everywhere: can marine compartments shape phytoplankton assemblages?

The idea that 'everything is everywhere, but the environment selects' has been seminal in microbial biogeography, and marine phytoplankton is one of the prototypical groups used to illustrate this. The typical argument has been that phytoplankton is ubiquitous, but that distinct assemblages form under environmental selection. It is well established that phytoplankton assemblages vary considerably between coastal ecosystems. However, the relative roles of compartmentalization of regional seas and site-specific environmental conditions in shaping assemblage structures have not been specifically examined. We collected data from coastal embayments that fall within two different water compartments within the same regional sea and are characterized by highly localized environmental pressures. We used principal coordinates of neighbour matrices (PCNM) and asymmetric eigenvector maps (AEM) models to partition the effects that spatial structures, environmental conditions and their overlap had on the variation in assemblage composition. Our models explained a high percentage of variation in assemblage composition (59-65%) and showed that spatial structure consistent with marine compartmentalization played a more important role than local environmental conditions. At least during the study period, surface currents connecting sites within the two compartments failed to generate sufficient dispersal to offset the impact of differences due to compartmentalization. In other words, our findings suggest that, even for a prototypical cosmopolitan group, everything is not everywhere.

Different ecological processes determined the alpha and beta components of taxonomic, functional, and phylogenetic diversity for plant communities in dryland regions of Northwest China.

Drylands account for more than 30% of China’s terrestrial area, while the ecological drivers of taxonomic (TD), functional (FD) and phylogenetic (PD) diversity in dryland regions have not been explored simultaneously. Therefore, we selected 36 plots of desert and 32 plots of grassland (10 × 10 m) from a typical dryland region of northwest China. We calculated the alpha and beta components of TD, FD and PD for 68 dryland plant communities using Rao quadratic entropy index, which included 233 plant species. Redundancy analyses and variation partitioning analyses were used to explore the relative influence of environmental and spatial factors on the above three facets of diversity, at the alpha and beta scales. We found that soil, climate, topography and spatial structures (principal coordinates of neighbor matrices) were significantly correlated with TD, FD and PD at both alpha and beta scales, implying that these diversity patterns are shaped by contemporary environment and spatial processes together. However, we also found that alpha diversity was predominantly regulated by spatial structure, whereas beta diversity was largely determined by environmental variables. Among environmental factors, TD was most strongly correlated with climatic factors at the alpha scale, while with soil factors at the beta scale. FD was only significantly correlated with soil factors at the alpha scale, but with altitude, soil and climatic factors at the beta scale. In contrast, PD was more strongly correlated with altitude at the alpha scale, but with soil factors at the beta scale. Environment and space explained a smaller portion of variance in PD than in TD and FD. These results provide robust evidence that the ecological drivers of biodiversity differ among different scales and facets of diversity. Future research that focuses on the comparisons among TD, FD and PD would likely provide new insights into elucidating the underlying community assembly.

Local-scale determinants of arboreal spider beta diversity in a temperate forest: roles of tree architecture, spatial distance, and dispersal capacity.

Spiders are a functionally important taxon in forest ecosystems, but the determinants of arboreal spider beta diversity are poorly understood at the local scale. We examined spider assemblages in 324 European beech (Fagus sylvatica) trees of varying sizes across three forest stands in Würzburg (Germany) to disentangle the roles of tree architecture, spatial distance, and dispersal capacity on spider turnover across individual trees. A large proportion of tree pairs (66%) showed higher compositional dissimilarity in spider assemblages than expected by chance, suggesting prominent roles of habitat specialization and/or dispersal limitation. Trees with higher dissimilarity in DBH and canopy volume, and to a lesser extent in foliage cover, supported more dissimilar spider assemblages, suggesting that tree architecture comprised a relevant environmental gradient of sorting spider species. Variation partitioning revealed that 28.4% of the variation in beta diversity was jointly explained by tree architecture, spatial distance (measured by principal coordinates of neighbor matrices) and dispersal capacity (quantified by ballooning propensity). Among these, dispersal capacity accounted for a comparable proportion as spatial distance did (6.8% vs. 5.9%). Beta diversity did not significantly differ between high- and low-vagility groups, but beta diversity in species with high vagility was more strongly determined by spatially structured environmental variation. Altogether, both niche specialization, along the environmental gradient defined by tree architecture, and dispersal limitation are responsible for structuring arboreal spider assemblages. High dispersal capacity of spiders appears to reinforce the role of niche-related processes.

PARTIÇÃO DA VARIAÇÃO FLORÍSTICO-ESTRUTURAL DO COMPONENTE ARBÓREO EM UMA FLORESTA OMBRÓFILA MISTA ALUVIAL NO SUL DO BRASIL

Objetivou-se avaliar a influência da estruturação espacial e de variáveis ambientais sobre a organização florístico-estrutural do componente arbóreo em uma Floresta Ombrófila Mista Aluvial no sul do Brasil. Para isso, foram alocadas 48 parcelas de 200 m2 no remanescente amostrado, localizado em Lages-SC. Todos os indivíduos dentro das parcelas com diâmetro na altura do peito (DAP) igual ou superior a 5 cm foram identificados. Foram mensuradas variáveis ambientais e espaciais em cada parcela. Os dados foram analisados por meio de Correlograma de Mantel, Particionamento da Variância, Análises de Redundância, análise de Coordenadas Principais de Matrizes Vizinhas e testes de correlação. Foram amostrados 1.462 indivíduos pertencentes a 66 espécies. Conjuntamente, as variáveis ambientais e espaciais explicaram 24,13% da variação total, sendo que a maior parte (15,22%) se encontrou espacialmente estruturada. Dentre as variáveis ambientais, a topografia (desnível máximo) e a fertilidade do solo (soma de bases e P) foram significativas. Conclui-se que o componente arbóreo está organizado na forma de um gradiente florístico-estrutural. Ainda, os resultados sugerem que o regime de inundação do rio e a presença de zonas de maior encharcamento do solo foram relevantes na definição de micro-hábitat, que influenciaram na distribuição das espécies.

Relating species richness to the structure of continuous landscapes: alternative methodological approaches

AbstractNumerous studies have focused on the relationship between landscape structure and plant diversity based on the patch‐mosaic landscape paradigm, by deriving structural data from classified images. Since the use of discrete classes poses limitations for predicting biodiversity patterns in complex, low human‐impacted ecosystems, two alternative methods have been used to analyze changes of landscape attributes in a continuum: moving‐window metrics and surface metrics (image texture). Here, we compare these two approaches for predicting richness of all plant species, legume species, legume trees, legume shrubs, legume forbs, and legume climbers across a tropical landscape in Mexico, based on the records of vascular plants in 250 10 × 10 m plots. Multiple regression and variance partitioning methods were used to analyze the effects of the two landscape descriptors (moving‐window and surface metrics), scale (400‐ and 200‐m moving‐window sides), and space (based on the extraction of principal coordinates of neighbor matrices’ vectors) on species richness. The predictive power of all metrics was relatively small for total species richness, but generally higher for legume species. For legume forbs, surface metrics‐based models indicated a direct association between species richness and landscape homogeneity. Moving‐window metrics were highly sensitive to the biological group and to spatial scale, likely due to a leftover effect of image classification procedures. Conversely, surface metrics were more independent from scale and taxonomy. Attempts to predict species richness in highly diverse, low human‐impacted tropical ecosystems more rapidly and accurately should better rely on surface metrics rather than on moving‐window metrics, in line with the continuous landscape paradigm.

Uncoupling the complexity of forest soil variation: Influence of terrain indices, spectral indices, and spatial variability

Growing concern over climate and management induced changes to soil nutrient status has prompted interest in understanding the spatial distribution of forest soil properties. Recent advancements in remotely sensed geospatial technologies are providing an increasing array of data sources (e.g., LiDAR, hyper-spectral imagery) relating to forest biophysical properties. While these data sources have the potential to improve spatial predictions of forest soil properties, considerable uncertainty exists regarding which remotely sensed (RS) indices are correlated to soil variability and what underlying pedogenic processes connect them. The main objective of this study was to identify and interpret RS indices that account for soil variability within a 2300ha forested watershed. Redundancy analysis (RDA) and variation partitioning methods were used to uncouple the complexity of soil–environmental relationships. Thirty-two soil pedons were described, sampled, characterized and analyzed for 22 soil properties within the 0–50cm soil depth interval. A suite of environmental covariates, comprised of LiDAR derived canopy metrics, land-surface and hydrologic terrain indices, broad-band remotely sensed indices (GeoEye-1), and narrow-band hyper-spectral indices (HyMap), were used as covariates in our RDA models. Principal coordinates of neighbor matrices (PCNM) was used to disentangle the contribution of spatial autocorrelation among sampling locations to the total variance explained by our RDA models. Two groups of soil properties were identified using discriminate analysis of principal components, with each soil property group (SPG) relating to different pedogenic processes occurring with the watershed (SPG1: organic matter-metal cycling; SPG2: base-cation cycling). Our results show there was a relatively strong correspondence between soil properties and terrain/spectral indices; with 61% and 81% of the total variance explained by the first four RDA axes for SPG1 and SPG2, respectively. Variation partitioning analysis revealed that both SPG1 and SPG2 were most strongly related to terrain and canopy indices; although spectral indices were also important, especially for SGP2. Variation in the types of RS indices correlated to each SPG results from variation in the degree to which each environmental covariate relates to the pedogenic process(es) driving soil property development. The approach used in this study can help improve our understanding of soil spatial variability through identifying the most significant environmental covariates related to soil variation. Given the growing demands placed upon forest ecosystems (e.g., timber, recreation, carbon sequestration), improved knowledge of soil variability and the factors that affect the soil resource is essential to facilitate more effective forest management.

Soil microbial communities along the route of a venturous cycling trip

The purpose of the present study is not solely scientific but arose from a rare fusion of art and science during a venturesome bicycle trip from Austria (Europe) to Laos (Asia). The artist Wolfgang Burtscher produced every-day dirt tire imprints on papers (tripmarks) to document his journey (www.tripmarks.at) Contributing to public awareness in this International Year of Soils 2015 we took a closer look at the dirt forming these pieces of art, namely to investigate the inherent microbial life. As such, we benefited from minute soil samples along a global transect, which permitted the classical hypothesis on microbial cosmopolitanism to be evaluated. DNA from 0.1g soil was extracted and amplified with specific primers for fungi and actinobacteria to obtain denaturing gradient gel (DGGE) fingerprinting patterns. Spatial variables were generated by applying trend surface analysis and principal coordinates of neighbour matrices. Canonical correspondence analysis was also used to check for driving factors.Our results show that microbial variability is primarily being influenced by environmental rather than spatial patterns. Clearly distinct communities in the soils of distant sampling sites were formed for actinobacteria but not for fungi. Furthermore, cosmopolitan phylotypes with relative abundances as high as 80.5% (fungi) and 74.0% (actinobacteria) were detected. These findings show that Eurasian soil microbial communities follow environmental rather than spatial constraints. For the artist, these results emphasize the broad diversity of microorganisms present on his tripmarks joining the facet of the beauty and variety of life with his dirty tire imprints.

Different roles of environmental variables and spatial factors in structuring stream benthic diatom and macroinvertebrate in Yangtze River Delta, China

Exploring the relative contribution of spatial factors and environmental variables in shaping communities is of widespread interest in biodiversity conservation and environmental management. Stream communities are hierarchically regulated by environmental variables over multiple spatial scales, and the reaction of different organisms to stressors are still equivocal. We sampled both macroinvertebrates and diatom at 80 sites and additional 10 sites for macroinvertebrates, field measured and laboratory analyzed environmental variables, from the tributaries of Qiantang River, Yangtze River Delta China in 2011. We used PCNM (principal coordinates of neighbor matrices) to generate spatial predictors. We applied redundancy analysis and variation partitioning procedures to identify key spatial and environmental factors, and to quantify their relative roles in shaping diatom and macroinvertebrate assemblages. Our results demonstrated the role of spatial and environmental variables differed in shaping benthic diatom and macroinvertebrate. Diatom assemblage variations were better explained by spatial factors, however macroinvertebrate assemblage variations were better explained by environmental variables. In terms of environmental variables, catchment scale variables (e.g., land use estimators, land use diversity) played the primary role in determining the patterns of both diatom and macroinvertebrate assemblages, whereas the influence of reach-scale variables (e.g., pH, substrates, and nutrients) appeared less. However, nutrients were the stronger factors influencing benthic diatom, whereas physical habitat (e.g., substrates) played more important role than water chemistry in structuring macroinvertebrates. Our results provided more evidence to the incorporation of spatial factors interpreting spatial patterns of stream organisms, and highlighted the useful of multiple organisms and environmental variables at different spatial scales in diagnosing mechanism of stream degradation and in building a sound stream conditions monitoring program for Yangtze River Delta.

Spatial autocorrelation in fitness affects the estimation of natural selection in the wild

Summary Natural selection is typically estimated in the wild using Lande and Arnold's multiple regression approach. Despite its utility for evolutionary ecologists, this method is subject to the classical assumptions of multiple regressions, which could result in potential analytical problems. In particular, spatial autocorrelation in fitness violates the assumption of residuals independence. Although widespread in the wild, the consequences of this effect have yet to be investigated in the context of Lande and Arnold's regression and resulting selection estimation. Here we first described four spatially explicit models that allow to control for spatial autocorrelation in residuals of the Lande and Arnold's regression: a generalized least square (GLS) model with a distance‐based exponential covariance function, two simultaneous autoregressive models (SAR, the lagged‐response model (SAR‐lag) and the spatial error model (SAR‐err)) and a 5‐step procedure using the principal coordinates of neighbour matrices (PCNM) method based on the extraction of spatial descriptors. We then compared the four spatially explicit models of selection to non‐spatial models for three life‐history traits recorded over 6 years in a wild blue tit (Cyanistes caeruleus) population. We also compared the performance of the four spatially explicit models of selection using a simulation approach. Our analyses revealed strong spatial autocorrelation in residuals of selection models, which was completely described by the two SAR and the PCNM models, while only partially described by the GLS model. The magnitude of selection gradients and differentials decreased systematically in the 4 spatially explicit models while the degree of fit of these models increased (except for the GLS model). Moreover, we showed using simulations that the selection coefficients extracted from the SAR‐lag model were systematically biased compared to those extracted from the GLS, SAR‐err and PCNM models. We hereby showed that spatial autocorrelation in fitness can severely affect selection differentials and gradients, even at a relatively small spatial scale. By using geostatistical models such as PCNM or SAR‐err models, it is possible to control for this spatial autocorrelation. Finally, since spatial autocorrelation is closely linked to spatial environmental variation, this approach can also be used to explore environmental components of covariance between fitness and traits.