Nestedness Values Research Articles

Metacommunity structures of dormant and active zooplankton in two distant mediterranean regions

Abstract Temporary ponds are small‐sized limnic systems that dry periodically. The length of the wet phase defines the hydroregime and determines community assembly in temporary ponds. Zooplankton species have adapted to desiccation by adopting some dormant strategies, such as the formation of resting stages. Hatching from resting stages is a source of recolonization after drought events and the composition of hatching taxa is also influenced by hydroregime. We compared metacommunity structure and composition of the dormant sub‐community (resting stages); the pioneer active sub‐community (fauna present immediately after inundation of ponds); and the cumulative active sub‐community (fauna present at the initial, middle and final phases of hydroperiod) in a set of temporary ponds with semipermanent and seasonal hydroregimes in two areas with mediterranean climate: central Chile and eastern Spain. We aimed to determine the influence of hydroregime and identify whether metacommunity patterns are consistent between regions sharing a mediterranean climate. We selected five semipermanent and five seasonal ponds in each region to sample sediments and active zooplankton sub‐communities. By combining hatching experiments from the sediments with direct counts of active zooplankton from the field samples, we gathered data on both dormant and active sub‐communities to build unweighted bipartite networks of species occurrences in each pond. The obtained networks were analysed to determine seasonal trends in structural features of the metacommunities (diversity, nestedness and modularity) and their relation to hydroregime (semipermanent and seasonal) and geographical location (Chile and Spain). We observed consistent differences in community structure when comparing sub‐communities at different successional stages (dormant, pioneer active and cumulative active) and with different hydroregimes (semipermanent vs. seasonal). Both α‐ and γ‐diversity showed a consistent trend, being highest in cumulative active sub‐communities and lowest in dormant ones, and were consistently higher in seasonal ponds, regardless of the region. In addition, β‐diversity was higher in the pioneer active sub‐community in both regions, with no significant differences between hydroregimes. The species composition of cumulative active sub‐communities were less heterogeneous than that of the pioneer and dormant ones. No consistent patterns were found in modularity and nestedness values across sub‐communities and hydroregimes. In agreement with our hypotheses, we observed a gradual accumulation of taxa as well as community homogenization over time in both regions. Contrary to our expectations, hydroregime did not affect these patterns and, surprisingly, shorter hydroperiods exhibited higher regional diversity. Our results suggest that hydroregime as a single variable does not have a strong explanatory power for metacommunity assembly of temporary ponds. Therefore, a more comprehensive theory is needed to anticipate the effects of the upcoming hydroperiod shortening.

Maxnodf: An R package for fair and fast comparisons of nestedness between networks

Abstract Nestedness is a widespread pattern in mutualistic networks that has high ecological and evolutionary importance due to its role in enhancing species persistence and community stability. Nestedness measures tend to be correlated with fundamental properties of networks, such as size and connectance, and so nestedness values must be normalised to enable fair comparisons between different ecological communities. Current approaches, such as using null‐corrected nestedness values and z‐scores, suffer from extensive statistical issues. Thus a new approach called NODFc was recently proposed, where nestedness is expressed relative to network size, connectance and the maximum nestedness that could be achieved in a particular network. While this approach is demonstrably effective in overcoming the issues of collinearity with basic network properties, it is computationally intensive to calculate, and current approaches are too slow to be practical for many types of analysis, or for analysing large networks. We developed three highly optimised algorithms, based on greedy, hill climbing and simulated annealing approaches, for calculation of NODFc, spread along a speed‐quality continuum. Users thus have the choice between a fast algorithm with a less accurate estimate, a slower algorithm with a more accurate estimate and an intermediate option. We outline the package and its implementation, as well as provide comparative performance benchmarking and two example analyses. We show that maxnodf enables speed increases of hundreds of times faster than existing approaches, with large networks seeing the biggest improvements. For example, for a large network with 3,000 links, computation time was reduced from 50 min using the fastest existing algorithm to 11 s using maxnodf. maxnodf makes correctly normalised nestedness measures feasible for complex analyses of even large networks. Analyses that would previously take weeks to complete can now be finished in hours or even seconds. Given evidence that correctly normalising nestedness values can significantly change the conclusions of ecological studies, we believe this package will usher in necessary widespread use of appropriate comparative nestedness statistics.

Spatiotemporal patterns of β-diversity of flower chafer beetles in urban park and natural reserve sites in Brazilian Cerrado

Understanding the drivers underlying spatial and temporal changes of species distribution is a major and urgent challenge, given the scenario of increased climate and land use changes. The creation and maintenance of urban parks is an efficient conservation strategy in urbanized landscapes. In this study, we explore how spatiotemporal β-diversity components of turnover and nestedness of flower chafer beetles are influenced by climate conditions in urban park and natural reserve sites in Brazilian Cerrado, one of the largest, richest and possibly the most threatened tropical savannah on the Planet. We sampled flower chafer beetles using aerial fruit-baited traps, every 2 weeks from January to December 2014, in six ‘natural reserve’ sites (outside the urban matrix) and four ‘urban park’ sites (within the urban matrix) in Brazilian Cerrado. Our results highlighted four main findings: (i) spatially, ‘natural reserve’ and ‘urban park’ sites presented similar values of dissimilarity and substitution of flower chafer beetles but ‘urban park’ sites had higher nestedness values than ‘natural reserve’ sites; (ii) temporally, ‘natural reserve’ and ‘urban park’ sites presented similar values of dissimilarity, turnover, and nestedness; (iii) average β-diversity, turnover and nestedness values did not differ between dry and rainy seasons in both ‘natural reserve’ and ‘urban park’ sites; and (iv) none of the climatic variables influenced the temporal variation in β-diversity and its components of flower chafer beetles. Therefore, most of spatiotemporal changes in β-diversity patterns of flower chafer beetles are not related to urbanization effects or changes in climatic variables in Brazilian Cerrado. This group of insects seems to respond more to environmental and climatic filters with changes in richness, abundance, and species composition than changes in β-diversity patterns.

Invasive crayfish alter the long‐term functional biodiversity of lotic macroinvertebrate communities

Abstract Invasive species represent one of the primary threats to global biodiversity. Despite acknowledged implications for taxonomic properties of ecological communities following invasion, functional measures remain poorly understood. We examined the long‐term implications of invasion by a crayfish species, Pacifastacus leniusculus, on functional alpha and beta diversity properties of lotic macroinvertebrate communities in three English regions. The dataset comprised 477 samples collected predominantly between 1990 and 2013. Unlike many invasion studies, we employed before and after invasion comparisons, in association with control rivers not invaded by crayfish. Functional richness and divergence metrics displayed the strongest responses to invasion, highlighting that P. leniusculus may alter the range of functional niches and extreme trait values (likely reflecting resistance and resilience mechanisms) displayed by macroinvertebrate communities. Interestingly, in one region, biodiversity gains seen in control rivers were not mirrored in invaded rivers, potentially suggesting that invasion inhibited ecological improvements. Invasion by signal crayfish resulted in functional compositional changes in two of the three English regions studied, with these rivers yielding greater ecological differences between pre‐ and post‐invasion periods relative to control rivers. This change was primarily driven by higher nestedness values in invaded rivers, with communities containing functional subsets relative to control rivers. The third region demonstrated no functional compositional changes or alterations in functional beta diversity associated with invasion. Our findings indicated that in most instances, the functional properties of macroinvertebrate communities responded to crayfish invasion and may therefore represent a complementary means to monitor the ecological condition of lotic ecosystems. Given their spatial transferability, functional traits could provide a platform to guide regional management practices in the face of biological invasions. A free Plain Language Summary can be found within the Supporting Information of this article.

Diversidad espacial del ensamblaje de escarabajos coprófagos (Coleoptera: Scarabaeinae) en cinco ecoregiones de Sucre, costa Caribe Colombiana

La biodiversidad cambia en el espacio-tiempo generando gradientes complejos. Estos gradientes afectan la estructura de las comunidades creando dos posibles patrones de recambio espacial, reemplazo o anidamiento. Existen pocos estudios que busquen analizar los cambios de la diversidad a lo largo de gradientes ambientales en la región Caribe de Colombia. Buscando entender estos cambios, se realizó un muestreo en cinco ecorregiones del Caribe colombiano (Golfo de Morrosquillo, Montes de María, Sabanas, San Jorge y La Mojana) usando a los escarabajos coprófagos como un grupo bioindicador. En cada región se estableció un transecto lineal con 20 trampas de caída cebadas con excremento. Se evaluaron las diferencias en la abundancia, riqueza, Shannon-índice, equidad y grupos funcionales entre ecorregiones y condiciones ambientales. Un total de 923 individuos pertenecientes a 27 especies fue recolectado. La tribu Deltochilini y el género Canthon fueron los más diversos. La especie más abundante fue Silvicanthon aequinoctialis. Se encontraron diferencias significativas en los parámetros medidos entre las ecorregiones. La diversidad Beta presenta un claro patrón espacial demostrando un alto recambio y un bajo anidamiento. Los Montes de María presentaron la mayor diversidad, asociada con la conservación de fragmentos de bosque. Es fundamental generar estrategias de conservación y crear un nuevo Parque Nacional Natural para los Montes de María, previniendo el impacto negativo causado por la expansión de la frontera agrícola y ganadera. Finalmente, este estudio representa un primer esfuerzo para entender los patrones espaciales de los escarabajos coprófagos en el Caribe colombiano, relacionando los gradientes ambientales con la dinámica espacial de la diversidad.

Mimicking the nested structures of ecosystems in the design of industrial water networks

Abstract The sustainability of industrial practices is a growing point of emphasis in the research and business communities demanding effective systems-level solutions. Eco-Industrial Parks (EIPs), networks of co-located industries connected through mutually beneficial collaborations are a popular systems-level solution but have experienced highly variable degrees of success. Nestedness, a structure prevalent in mutualistic networks found in nature is our design focus for improved outcomes. This paper investigates how ecologically-similar nestedness values in EIPs relate to reductions of freshwater imports. The results indicate a range of nestedness values that support water conservation and critical thresholds for maximizing capital investments.

Beware greedy algorithms.

To fairly compare the nestedness of ecological networks, a network's observed nestedness can be divided by its maximum nestedness. The authors show that a greedy algorithm does not find networks' maximum nestedness values. Simulated annealing achieved much better results, laying the foundation for future development of even more sophisticated algorithms.

Evaluation of macrobenthic community responses to dredging through a multimetric approach: Effective or apparent recovery?

Macrobenthic responses to dredging activities were evaluated in a mesotidal coastal lagoon (Ria Formosa – South Portugal). Four areas (2 dredged and 2 non-dredged) were analysed along different dredging situations (pre-dredging, during dredge 1, during dredge 2 and post-dredging). Beyond the evaluation of sediment descriptors and classical ecological indicators (number of species and abundance), the beta diversity component (partitioned into turnover and nestedness) was used to detect dredging effects on macrobenthic communities, together with a multivariate analysis (both quantitative and qualitative) including the ecological status assessment. Results confirmed the limitations of alpha diversity indicators in detecting dredging effects in naturally stressed systems, given the absence of clear patterns regarding number of species, abundance and equitability among areas and dredging situations. Moreover, post-dredging presented a higher number of species compared to pre-dredging, suggesting a positive disequilibrium induced by these activities. In contrast, partitioned beta diversity analysis revealed higher nestedness values at dredged areas, while turnover clearly prevailed at non-dredged ones. Such results suggest an effective impact of dredging on these communities, namely through the decrease of rarer species after sediment removal. This qualitative analysis, based on presence-absence data (Sorensen dissimilarity), was complemented by multivariate analysis (SIMPER and PERMANOVA) based on quantitative data (Bray-Curtis dissimilarity), highlighting the importance of adopting both approaches to detect dredging impacts on benthic communities. Lower effectiveness was found for M-AMBI index when evaluating benthic Ecological Status, since the apparent absence of organic matter and sediment composition shifts induced by dredging, together with the noticeable high diversity even during dredging situations, strongly limited the analysis. The multimetric approach here proposed can contribute to detect dredging effects on lagoonal benthic communities by disentangling the responses caused by dredging from those resulting from the system natural dynamics.

Climatic variables drive temporal patterns of α and β diversities of dung beetles.

Understanding the mechanisms underpinning spatiotemporal diversity patterns of biological communities is a major goal of ecology. We aimed to test two ecological hypotheses: (i) temporal patterns of β-diversity will mostly be driven by nestedness, with a loss of species from summer to winter, and (ii) nestedness values will correlate with climatic variables instead of turnover values, indicating either a loss of species during winter or a gain of species during summer. We sampled dung beetles using standardized sampling protocols along a year in four Atlantic forest sites: two at the northwest and two at the central region of Rio Grande do Sul state, southern Brazil. We partitioned temporal patterns of β-diversity into turnover and nestedness in order to investigate if community changes are driven by species substitution or gain/loss across time. Our results highlighted five main findings: (i) dung beetle composition varied more with sites than site geographic position; (ii) there was almost one and a half 'true' dung beetle assemblages regarding the spatial distribution of species weighed by abundance; (iii) we found a positive influence of mean temperature and a negative influence of relative humidity on both species richness and abundance; (iv) both spatial and temporal dissimilarity among sites were dominated by species replacement, while the relative importance of nestedness was higher in temporal than spatial patterns; (v) there was an effect of precipitation and relative humidity on temporal patterns of β-diversity components, but these effects were site-dependent. Contrary to our expectations, the β-diversity component of turnover dominated both spatial and temporal patterns in dung beetle dissimilarity among sites and months. Distinct climatic variables affected differently the α-diversity and β-diversity components of dung beetle assemblages. Partitioning β-diversity into temporal components is a promising approach to unveil patterns of the community dynamics and to produce insights on mechanisms underlying such patterns.

The restoration of tropical seed dispersal networks

Human activities have led to the loss of habitats and biodiversity in the Atlantic Rain Forest in Brazil. Ecological restoration aims to rebuild this biome and should include not only the reinstatement of species but also the reestablishment of complex ecological interactions and the ecological functions that they provide. One such function is seed dispersal, which is provided by the interactions between animal frugivores and plants. We studied seed dispersal networks in 3 different tropical forest sites restored 15, 25, and 57 years ago; temporal scales rarely observed in restoration studies. We investigated changes in network structure (nestedness, modularity, and network specialization) in these communities over restoration time. Although network size and the number of interactions increased with time since restoration, the networks were composed of generalist birds, and the large frugivores remained absent. Contrary to our expectations though, species richness was highest in the 25‐year‐old site, maybe due to the higher number of species used in the planting. Nestedness values were low in all 3 networks, but the highest nestedness was observed in the intermediate‐aged site. However, the oldest network was significantly modular and showed higher complementary specialization. These results suggest that 57 years after restoration, the complexity of mutualistic interactions in seed dispersal networks has increased, this enhancing ecosystem function in the Atlantic forest.

Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint.

Nurse abundance determines plant facilitation networks of subtropical forest-grassland ecotone

The theory of complex networks has been recently used to explain ecological associations between nurses and seedlings in plant facilitation systems. The structure of these networks is potentially affected by morphological, ecological and evolutionary factors that can determine the facilitative interactions. In the present study, we evaluate the role of the projected crown area of the nurse plant, the dispersal syndrome, the abundance and the phylogeny relationships with seedlings as drivers of network structure in facilitation networks. To test these parameters, we used an ecotonal forest–grassland system in southern Brazil that experienced historical forest expansion over the grassland in the last few centuries. In two State Parks, Guartelá (GUA) and Vila Velha (VVL), we sampled tree species (nurses and seedlings) along four transects parallel to the forest edge, with five sampling stations along each transect. Tree seedlings (height >0.3 m) were sampled below the nurse's crown (i.e. isolated woody plants, height >1.5 m) and over the grassland area. A total of 160 nurses and 358 seedlings were sampled. Seedling abundance and richness were greater below a nurse's crown than on open grassland. Nurse abundance was the best predictor of the observed interaction matrix. Probabilistic matrices based on abundance, abundance and phylogeny, and dominance were able to predict the observed nestedness values, and they were also closest to the observed connectance, although all of the probabilistic matrices have underestimated this property. Specialization was predicted by abundance and phylogeny, abundance and projected crown area drivers for VVL, and the abundance based models were closest to the predicted specialization for GUA. The result of a similar pattern in predictability between sites indicates that the influences of morphology and evolutionary and ecological processes over the facilitation interactions are equivalent on a regional scale. Woody plant abundance was a key factor for the facilitation networks, driving forest expansion along the subtropical forest–grassland ecotone.

Drivers of tree diversity in tropical rain forests: new insights from a comparison between littoral and hilly landscapes of Central Africa

AbstractAimOur aim was to document African rain forest tree diversity patterns to test whether they support one of the following hypotheses: the structure of tree species diversity is at equilibrium and mostly driven by neutral processes (H0); the structure of tree species diversity results from Pleistocene forest cover dynamics (H1); or the structure of tree species diversity results from ecological sorting along environmental gradients (H2).LocationWest Central Africa: the hilly region of Gabon, a putative Pleistocene forest refuge, and the adjacent flat littoral region, putatively colonized by forests from the hilly region after the last glaciation.MethodsWe used 103 standardized 0.1‐ha tree plots distributed among five landscapes in the two regions. We partitioned the tree diversity within and among plots at a local and regional scale using the Hurlbert effective number of species framework. The explanatory power of geographical and elevational distances on species turnover was tested. At the landscape scale, we partitioned the beta diversity into nestedness and turnover components.ResultsMean alpha and gamma diversities were much higher in the hilly region, where differences in elevation explained a significant part of species turnover. Substantial species turnover correlated with geographical distance also occurred in the littoral region despite its low elevational heterogeneity. Floristic turnover between plots from different regions remained stable whatever the elevational/geographical distances. At the regional scale, species replacement remained the main contributor to beta diversity (low nestedness values).Main conclusionsThe heterogeneous distribution of alpha and gamma diversity, similar levels of species turnover among plots and the low contribution of the nestedness component to beta diversity between hilly and littoral landscapes do not support hypotheses H0 and H1. The combined impacts of limited dispersal and ecological sorting along environmental gradients (H2) can explain patterns within regions. The marked floristic discontinuity between regions could reflect contrasting histories (two distinct refugia) although the role of contrasting environments cannot be discounted.

Analysis of nestedness in freshwater assemblages—patterns across species and trophic levels

Nestedness measures the degree to which species assemblages are proper subsets of larger assemblages within a metacommunity. We analyzed nestedness in 20 freshwater data sets, each for a single metacommunity within a drainage basin. First, we examined the degree of nestedness across local assemblages and identified major environmental correlates of nestedness at sites. Second, we examined whether nestedness showed concordance among trophic levels. Third, we examined whether nested and idiosyncratic species (i.e., species that have unpredictable gaps in their distribution) differed ecologically and showed dissimilar distribution patterns along geographical and environmental gradients. Degrees of nestedness, obtained using a metric by Almeida-Neto et al. (2008), ranged from 22.9 to 57.0, with 11 matrices showing significant nestedness. Lake bacteria had a higher degree of nestedness than did phyto- or zooplankton. The degree of nestedness was related mainly to water temperature, conductivity, and trophic status of the water, results suggesting that habitat quality may be an important predictor of nestedness, but was only weakly concordant among trophic levels within metacommunities. However, averaged across all metacommunities, nestedness values between phytoplankton and zooplankton and between phytoplankton and bacteria were positively correlated. Nested and idiosyncratic species did not differ in their spatial and environmental distribution patterns. Freshwater planktonic assemblages were characterized by a relatively low degree of nestedness. The low congruence in nestedness among trophic levels suggests that assemblages typically show independent gradients of nestedness. This result indicates that assemblages respond dissimilarly to driving forces, such as habitat quality, or that nestedness in freshwaters might be related to stochastic colonization. Conserving only the most diverse sites may not protect rare species because of the relatively low degree of nestedness in fresh waters.

From sampling stations to archipelagos: investigating aspects of the assemblage of insular biota

ABSTRACTAim To investigate the formation of nestedness and species co‐occurrence patterns at the local (sampling station), the intermediate (island group), and the archipelago scale.Location The study used data on the distribution of terrestrial isopods on 20 islands of the central Aegean (Greece). These islands are assigned to two distinct subgroups (Kyklades and Eastern islands).Methods The Nestedness Temperature Calculator was used to obtain nestedness values and maximally nested matrices, the EcoSim7 software and a modified version of Sanderson (2000) method were used for the analysis of species co‐occurrences. Idiosyncratic temperatures of species and the order of species placement in the maximally nested matrices were used for further comparisons among spatial scales. The relationships of nestedness values with beta‐diversity, habitat diversity and a number of ecological factors recorded for each sampling station were also investigated.Results Significant nestedness was found at all spatial scales. Levels of nestedness were not related to beta‐diversity or habitat diversity. Nestedness values were similar among spatial scales, but they were affected by matrix size. The species that contributed most to the nested patterns within single islands were not the same as those that produce nestedness at the archipelago scale. There was significant variation in the frequency of species occurrence among islands and among spatial scales. There was no direct effect of ecological factors on the shaping of patterns of nestedness within individual islands, but habitat heterogeneity was crucial for the existence of such patterns. Positive associations among species prevailed at all scales when species per station were considered, while negative associations prevailed in the species per island matrices. All associations resulted from the habitat structure of sampling stations and from particularities of geographical distributions.Conclusions There was no clear‐cut distinction between nestedness patterns among spatial scales, even though different species, and partially different factors, contributed to the formation of these patterns in each case. There was a core of species that contributed to the formation of nested patterns at all spatial scales, while the patterns of species associations suggested that biotic interactions are not an important causal factor. The results of this study suggest that locally rare species cannot be widespread at a higher spatial scale, while locally common species can have a restricted distribution.