Spatial Patterns Of Community Composition Research Articles

The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds

AbstractAimHow community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge of microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, their most influential drivers and their spatial scale dependence.LocationCzech Republic.Time periodPresent.Taxa studiedFungi.MethodsWe analysed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition and climate) in fungi using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.ResultsWe found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance–decay relationships, and their community composition was driven mainly by vegetation and dispersal at local scales but, at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.Main conclusionsOur results underscore the remarkable variation in the community ecology of fungi, which seems to range well‐known patterns both from the macro‐ and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro‐ and macroorganisms.

Herpetofauna das áreas protegidas da Caatinga VIII: Um inventário atualizado para a região da Serra das Confusões com novos dados da Serra Vermelha, Piauí, Brazil

Abstract It is repeatedly stressed the need to characterize the extant biodiversity in tropical ecosystems. However, inventory studies are still progressing slowly in dry ecosystems, leading to the underestimation of their true biodiversity and hindering conservation efforts. In this study, we present primary and secondary data, along with an updated list of amphibians and reptiles from two localities in the São Francisco-Gurguéia region in Piauí. Additionally, we compare the species composition between nine areas within the Caatinga, which were sampled using standardized methods over the past ten years, to examine broader spatial patterns of community composition. To survey reptiles and amphibians, we employed similar methods and sampling efforts in two areas within the Serra das Confusões National Park (SCNP) region. Our surveys recorded a total of 73 species of amphibians and reptiles, of which 24 are new distribution records for the SCNP region. Consequently, our findings increase the known herpetofauna in the region to 94 species. Despite their proximity, the two sites in the SCNP region exhibited only 42% similarity in species composition, and they differed significantly from other areas within the Caatinga. Furthermore, even the closer Caatinga areas presented differences in species composition, highlighting the necessity to evaluate biodiversity across the landscape and contribute to understanding biogeographic patterns.

Revealing perturbation responses with limited observations of biological communities

Restrictions in empirical research of biological communities have limited our understanding of the combined influence of environmental variability and system structure on community composition. Spatial patterns of community composition in less accessible systems, such as marine benthos, can often not be explained by many factors beyond the direct impact of the environment on community members. We present a method that combines commonly collected data of community composition with analyses of qualitative mathematical models, to assess not only direct impacts of environmental variability, but also the propagation of impacts through complex interaction networks. Transformed spatial data of community composition describe the community members’ observed similarity of response to an external input. The output of qualitative mathematical models describes the community members’ predicted similarity of response to input entering the system through any of its variables. A statistically significant agreement between the observed and any of the predicted response similarities indicates the respective system variable as a likely gateway for environmental variability into the system. The method is applied to benthic macroinvertebrate communities in the Rance estuary (Brittany, France). Organisms identified as likely gateways have traits that agree with their predicted response to documented spatially and temporally structured environmental variability. We suggest use of this novel framework for more comprehensive identification of environmental drivers of community change, including gateway community members and cascades of environmentally driven change through community structure.

Quantitative assessment of fish larvae community composition in spawning areas using metabarcoding of bulk samples.

Accurate assessment of larval community composition in spawning areas is essential for fisheries management and conservation but is often hampered by the cryptic nature of many larvae, which renders them difficult to identify morphologically. Metabarcoding is a rapid and cost-effective method to monitor early life stages for management and environmental impact assessment purposes but its quantitative capability is under discussion. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve quantification accuracy (relative abundance estimates), the amount of tissue for each specimen was standardized and mitochondrial primers (12S gene) with conserved binding sites were used. Relative family abundance estimated from metabarcoding reads and morphological assessment were positively correlated, as well as taxon richness (RS =0.81, P=0.007) and diversity (RS =0.90, P=0.002). Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments. Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient, and faster alternative to morphological methods that can be applied to terrestrial and aquatic habitats.

Community structure of woody plants on islands along a bioclimatic gradient

Understanding patterns of community structure and the causes for their variation can be furthered by comparative biogeographic analyses of island biotas. We used woody plant data at the local scale to investigate variations in species rarity, alpha, beta, and gamma diversity within and between three islands from the oceanic archipelagoes of Azores, Canaries and Mascarene. We used standardized protocols to sample ten 50 m × 50 m forest plots in each of the three islands with contrasting climate and regional species pools: Terceira (Azores), Tenerife (Canaries), and Reunion (Mascarene Islands). Occupancy frequency distributions and species abundance distributions were used to investigate rarity. The partitioning of beta diversity in a distance-decay framework was used to test for spatial patterns of community composition. Rarity was much more pronounced in the highly diverse islands of Tenerife and Reunion than in the regionally poorer island of Terceira. The number of species rose faster with increasing sample area in both Tenerife and Reunion. The slope of the species rank abundance curve was steeper in Terceira whereas the richer island assemblages approached a lognormal model. Compositional changes according to spatial distance were mostly due to replacement of species in Terceira and Reunion. Our results point to important differences in the community structure of Terceira, which is the less diverse and temperate region in comparison to Tenerife and Reunion which are highly diverse.

Seasonal, interannual, and spatial patterns of community composition over the eastern Bering Sea shelf in cold years. Part I: zooplankton

Seasonal, interannual, and spatial patterns of community composition over the eastern Bering Sea shelf in cold years. Part I: zooplankton

Seasonal, interannual, and spatial patterns of community composition over the eastern Bering Sea shelf in cold years. Part II: ichthyoplankton and juvenile fish

AbstractClimate-mediated oceanographic changes have led to protracted periods of above- or below-average water temperatures over the eastern Bering Sea shelf since the early 2000s. Ecosystem components, from phytoplankton to marine birds, have shown dichotomous responses to these temperature stanzas. Understanding within-stanza responses is fundamental to modelling efforts that project ecosystem responses under future climate scenarios. This study describes fish communities associated with Walleye Pollock during the age-0 period and also examines within-stanza homogeneity of assemblages. Spatial patterns of assemblage structure are compared with pre-defined ecoregions and environmental indices are assessed to determine potential mechanisms that delineate species assemblages. Walleye Pollock, rockfishes, Sand Lance, and Northern Rock Sole contributed to spring assemblages in every year. Assemblages were delineated by across-shelf gradients in 2008 and 2010 while 2009 assemblages showed less spatial structure. In summer, the diversity of fish assemblages increased across years but early-stage juvenile Walleye Pollock represented a small portion of the total abundance in 2009. Environmental gradients were related to fish assemblages, but patterns were along-shelf in 2008 and across-shelf in 2010. In fall, late-stage juvenile Walleye Pollock dominated the catch in 2008, but did not typify any assemblage in 2009. Overall, patterns of assemblage structure were not consistent with pre-defined ecoregions. Assemblage structure in 2009 was unique and indicates that within-stanza variability may complicate modelling projections based on ecosystem-level responses to climate changes.

Characterizing ontogenetic habitat shifts in marine fishes: advancing nascent methods for marine spatial management.

Niche requirements and habitat resource partitioning by conspecific fishes of different sizes are significant knowledge gaps in the species distribution modelling domain. Management actions and operations are typically concentrated on static habitats, or specific areas of interest, without considering movement patterns of species associated with ontogenetic shifts in habitat usage. Generalized additive models were used to model the body-length-habitat relationships of six fish species. These models were used to identify subsets of environmental parameters that drive and explain the continuous length-habitat relationships for each of the study species, which vary in their degree of ecological and/or commercial importance. Continuous predictive maps of the length distributions for each of the six study species across approximately 200km2 of the study area were created from these models. The spatial patterns in habitat partitioning by individuals of different body lengths for all six study species provide strong evidence for ontogenetic shifts. This highlights the importance of considering ontogenetic processes for marine spatial management. Importantly, predictive hotspot maps were created that identify potential areas that accumulate individuals of similar life stages of multiple species (e.g., multispecies nursery areas). In circumstances where limited resources are available for monitoring and management of fish resources, predictive modelling is a valuable tool for studying previously overlooked processes such as ontogenetic habitat shifts. Predictive modelling provides crucial information that elucidates spatial patterns in community composition across mosaics of benthic habitats. This novel technique can contribute to the spatial management of coastal fish and fisheries by identifying areas that are important for different life history stages of multiple fish species.

Sgdm: An R Package for Performing Sparse Generalized Dissimilarity Modelling with Tools for gdm

Global biodiversity change creates a need for standardized monitoring methods. Modelling and mapping spatial patterns of community composition using high-dimensional remotely sensed data requires adapted methods adequate to such datasets. Sparse generalized dissimilarity modelling is designed to deal with high dimensional datasets, such as time series or hyperspectral remote sensing data. In this manuscript we present sgdm, an R package for performing sparse generalized dissimilarity modelling (SGDM). The package includes some general tools that add functionality to both generalized dissimilarity modelling and sparse generalized dissimilarity modelling. It also includes an exemplary dataset that allows for the application of SGDM for mapping the spatial patterns of tree communities in a region of natural vegetation in the Brazilian Cerrado.

Spatial patterns of genetic diversity, community composition and occurrence of native and non-native amphipods in naturally replicated tributary streams.

BackgroundWorldwide, natural communities are invaded by non-native species, with potentially devastating effects on the native communities. A large part of past research aimed at finding traits and characteristics of the invading species or the invaded community explaining observed invasions. Only recently, the focus shifted on the spatial patterns during invasions per se. Empirical data, however, are limited, as invasions are often unique incidences of a complex spatio-temporal process. In order to identify generalities of invasion patterns, we studied 13 naturally replicated tributary streams draining into Lake Constance, and studied the occurrence of native and non-native amphipods along linear transects from the stream outlets to the upstream headwater reaches.ResultsWe found repeated spatial patterns of community composition and the occurrence of native and non-native amphipod species across two different years. Specifically, occurrence as well as abundance of two non-native amphipod species decreased from the stream outlets at the lake site towards upstream headwater reaches. Populations of the most common native amphipod species were largest at the uppermost headwater reaches. All populations of this native species, however, showed significant signals of recent genetic bottlenecks, irrespective of the stream position and occurrence of non-native species. Contrary to our expectations, this native species also showed no longitudinal genetic differentiation within individual tributaries as postulated for headwater versus outlet populations.ConclusionsOur results indicate that invasions of river-systems may overall follow predictable patterns on the level of spatial distributions and community composition. However, effects of invading organisms on the genetic diversity and genetic structure of native populations observed at larger scales may not necessarily be directly reflected at the scale of smaller tributaries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12898-016-0079-7) contains supplementary material, which is available to authorized users.

Long‐term change and spatial variation in butterfly communities over an elevational gradient: driven by climate, buffered by habitat

AbstractAimEfforts to adapt conservation to climate change are hampered by a scarcity of studies of community‐level ecological responses. We examined temporal (40 years) and spatial (1700 m elevational gradient) variation in butterfly communities, aiming to test whether the composition of communities in terms of species' thermal envelopes tracked regional warming, and whether local habitat influenced community responses to climate variation.LocationSierra de Guadarrama (central Spain).MethodsButterfly assemblages were sampled at sites between 550 and 2250 m elevation, in 1967–1973 and 2006–2012. Changes in community composition over time and space were evaluated using the community temperature index, or CTI, which reflects for local assemblages the balance between species whose geographic ranges occupy regions of low vs. high temperatures. We used multiple regressions and an information‐theoretic approach to test: (1) whether relationships of CTI with elevation or temperature remained consistent after an estimated 1.78 °C regional warming; and (2) how spatial variation in CTI was related to air temperature and land cover.ResultsCommunity temperature index decreased consistently with increasing elevation and increased after 40 years of warming, as communities were increasingly composed by species with warmer geographic ranges. Long‐term CTI change represented a c. 160 m uphill shift in community thermal composition, whereas isotherms shifted 307 m upwards. In 2006–2012, CTI was influenced positively by temperature, and negatively by forest and meadow cover.Main conclusionsVariation in community composition over space and time suggested a role of climate in structuring butterfly assemblages. Despite this, changing spatial patterns of community composition (CTI) did not appear to keep pace with climate change. In addition, lower values of CTI recorded for sites with greater forest and meadow/pasture cover suggested a role for local habitat in buffering the effects of climate change on community composition.

Coral reef community composition in the context of disturbance history on the Great Barrier Reef, Australia.

Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into the future.

Delineating ecological regions in marine systems: Integrating physical structure and community composition to inform spatial management in the eastern Bering Sea

Characterizing spatial structure and delineating meaningful spatial boundaries have useful applications to understanding regional dynamics in marine systems, and are integral to ecosystem approaches to fisheries management. Physical structure and drivers combine with biological responses and interactions to organize marine systems in unique ways at multiple scales. We apply multivariate statistical methods to define spatially coherent ecological units or ecoregions in the eastern Bering Sea. We also illustrate a practical approach to integrate data on species distribution, habitat structure and physical forcing mechanisms to distinguish areas with distinct biogeography as one means to define management units in large marine ecosystems. We use random forests to quantify the relative importance of habitat and environmental variables to the distribution of individual species, and to quantify shifts in multispecies assemblages or community composition along environmental gradients. Threshold shifts in community composition are used to identify regions with distinct physical and biological attributes, and to evaluate the relative importance of predictor variables to determining regional boundaries. Depth, bottom temperature and frontal boundaries were dominant factors delineating distinct biological communities in this system, with a latitudinal divide at approximately 60°N. Our results indicate that distinct climatic periods will shift habitat gradients and that dynamic physical variables such as temperature and stratification are important to understanding temporal stability of ecoregion boundaries. We note distinct distribution patterns among functional guilds and also evidence for resource partitioning among individual species within each guild. By integrating physical and biological data to determine spatial patterns in community composition, we partition ecosystems along ecologically significant gradients. This may provide a basis for defining spatial management units or serve as a baseline index for analyses of structural shifts in the physical environment, species abundance and distribution, and community dynamics over time.

Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton

We sampled 100 small lakes in Finland for bacterio‐, phyto‐, and zooplankton. The lakes were located in five drainage systems, 20 lakes for each system. We tested two main predictions: that the correlation between community similarity and geographical distance (spatial distance decay) is stronger at the across‐drainage than at the within‐drainage system scale, and that spatial distance decay is strongest for zooplankton and weakest for bacteria. We used a combination of direct ordination, multivariate statistical tests, and distance‐based approaches to examine spatial patterns in our data. Our analyses confirmed both of our predictions. Spatial distance decay was scale‐dependent; communities were overall weakly spatially structured within the drainage systems, yet distance decay was significant for all planktonic groups across drainage systems. Spatial distance decay was stronger for zooplankton, with higher slopes and shorter halving distances, than for phytoplankton and bacteria. These results provide evidence that distance decay of similarity is related to study scale, environment, and organism characteristics. Planktonic communities may be controlled by both dispersal‐driven assembly and local ecological determinism, with the balance between these two forces depending on study scale.

Biogeographical patterns of freshwater micro‐ and macroorganisms: a comparison between phytoplankton, zooplankton and fish in the eastern Mediterranean

AbstractAim We investigated the biogeographical patterns of phytoplankton, zooplankton and fish in freshwater ecosystems. We tested whether spatial distance or environmental heterogeneity act as potential factors controlling community composition.Location Northern and central Greece, eastern Mediterranean.Method Data on 310 phytoplankton, 72 zooplankton and 37 fish species were collected from seven freshwater systems. Species occurrence data were used to generate similarity matrices describing community composition. We performed Mantel tests to compare spatial patterns in community composition of phytoplankton, zooplankton and fish. Next, we examined the correlation between geographical distance and the degree of similarity in community composition. The analysis was repeated for different taxonomic, trophic and size‐based groups of the microorganisms studied. We assessed different environmental variables (topographic and limnological) as predictors of community composition.Results Phytoplankton community composition showed a strong positive correlation with environmental heterogeneity but was not correlated with the geographical distance between systems. Zooplankton community composition was unrelated to geographical distance and was only weakly correlated with environmental variables. In contrast, fish community similarity decayed significantly with distance. We found no relationship along all pairwise comparisons of the compositional matrices of the three groups. The pairwise comparisons of the different taxonomic, trophic and size‐based groups of the microorganism communities studied were in accordance with the results for the entire microorganism community.Main conclusions Our results support the proposition that the biogeography of microorganisms does not demonstrate a distance–decay pattern and further suggest that, in reality, the drivers of distribution depend on the specific community examined. In contrast, the biogeography of macroorganisms was affected by geographical distance. These differences reflect the dispersal abilities of the different organisms. The microorganisms exhibit passive dispersal through the air, with local environmental conditions structuring their community composition. On the other hand, for macroorganisms such as fish, the terrestrial environment could pose barriers to their dispersal; with fish structuring distinctive communities over greater distances. Overall, we suggest that the biogeography of freshwater phytoplankton and zooplankton reflects contemporary environmental conditions, while the biogeographical patterns for fish inhabiting the same systems are related to factors affecting their dispersal ability.

Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment

ABSTRACTGeneralized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large‐scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate‐change impact assessment.

Spatial patterns and coexistence mechanisms in systems with unidirectional flow

River ecosystems are the prime example of environments where unidirectional flow influences the dispersal of individuals. Spatial patterns of community composition and species replacement emerge from complex interplays of hydrological, geochemical, biological, and ecological factors. Local processes affecting algal dynamics are well understood, but a mechanistic basis for large scale emerging patterns is lacking. To understand how these patterns could emerge in rivers, we analyze a reaction–advection–diffusion model for two competitors in heterogeneous environments. The model supports waves that invade upstream up to a well-defined “upstream invasion limit”. We discuss how these waves are produced and present their key properties. We suggest that patterns of species replacement and coexistence along spatial axes reflect stalled waves, produced from diffusion, advection, and species interactions. Emergent spatial scales are plausible given parameter estimates for periphyton. Our results apply to other systems with unidirectional flow such as prevailing winds or climate-change scenarios.

Benthic diatom communities in boreal streams: community structure in relation to environmental and spatial gradients

An important goal for community ecology is the characterization and prediction of changes in community patterns along environmental gradients. We aimed to identify the major environmental correlates of diatom distribution patterns in boreal running waters. We classified 197 stream sites based on their diatom flora. Direct ordination methods were then used to identify the key environmental determinants of this diatom‐based stream typology. Finally, we tested whether a regional classification scheme based on terrestrial landscapes (ecoregions) provides a reasonable framework for a regional grouping of streams based on their diatom flora. Two‐way indicator species analysis produced 13 site groups, which were primarily separated by chemical variables, mainly conductivity, total P and water colour. In partial CCA, the environmental and spatial factors accounted for 38% and 24%, respectively, of explained variation in community composition. A high proportion (almost 40%) of variation explained by the combined effect (spatially‐structured environmental) indicated that diatom communities of boreal streams incorporate a strong spatial component. At the level of subecoregions, classification strength was almost equally strong for all sites as for near‐pristine reference sites only. Procrustes analysis indicated that spatial factors and patterns in diatom community structure were strongly concordant. Our data support the argument that diatom communities are strongly spatially structured, with distinctly different communities in different parts of the country. Because of the strong spatial patterns of community composition, bioassessment programs utilising lotic diatoms would clearly benefit from regional stratification. A combination of regional stratification and the prediction of assemblage structure from local environmental features might provide the most robust framework for diatom‐based assessment of the biological integrity of boreal streams.

Spatial and temporal variations in a community of nektobenthic invertebrates from Moreton Bay, Queensland

The temporal and spatial patterns in community composition, number of species and number of individuals were described and related to abiotic factors. During warmer months, nocturnal periods had more species and individuals than diurnal periods and a changed community composition. Burrowing in the sediment during daytime caused these changes and probably serves to reduce both predation and energy expenditure. Diel differences were reduced or absent in winter when the community was depauperate. Monthly patterns were highly positively correlated with temperature but not with salinity. These patterns were affected by summer migrations of juveniles from very shallow nursery areas. The deepest site varied least over time and was also the most individualistic in community composition. Numbers of species and individuals were both positively correlated with distance offshore and depth during most months. These factors probably reflect relative marine influence and environmental stability. The dynamic nature of the community is illustrated by the fact that interaction terms in factorial anovas were always significant and thus no spatial or temporal pattern was consistent.