Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,556
datasets available to search
ShareScore release 0.9.0
Dataset results
2,556 results for “assemblages”
Data from: Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems
Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 A.D. were selected to perform Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st Century samples was clearly different than those of mid-19th Century. This compositional change was correlated to shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in paleolimnological studies to include key microbial community characteristics of great scientific and social interest.
Data from: Taxonomic and phylogenetic determinants of functional composition of Bolivian bat assemblages
Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.
Data from: Edge-mediated compositional and functional decay of tree assemblages in Amazonian forest islands after 26 years of isolation
1.Islands formed upstream of mega hydroelectric dams are excellent experimental landscapes to assess the impacts of habitat fragmentation on biodiversity. We examined the effects of plot-, patch- and landscape-scale variables on the patterns of floristic diversity across 34 forest islands that had experienced 26 years of isolation since the creation of the 4,437 km2 Balbina Hydroelectric Reservoir of central Brazilian Amazonia. In addition, three undisturbed continuous forest sites in neighbouring mainland areas were also sampled across a comparable elevational gradient. 2.We identified all live trees ≥10 cm DBH at species level within a total of 87 quarter-hectare forest plots and conducted a comprehensive compilation of functional attributes of each tree species. We then examined species-area relationships (SARs) and the additional effects of patch and landscape scale metrics on patterns of tree assemblage heterogeneity, both in terms of taxonomic and functional diversity. 3.Despite a clearly positive SAR, edge-mediated forest disturbance was the single most important driver of species composition and abundance within islands. Our results suggest that non-random floristic transitions within island plots followed a predictable pattern, with different life-history traits either penalizing or rewarding local persistence of different functional groups. Distance to edges mediated the probability of tree mortality induced by windfalls and episodic surface fires, clearly resulting in faster species turnover and unidirectional changes in guild structure within small islands where light-wooded fast-growing pioneers largely replaced heavy-wooded species of the old-growth flora. 3.Synthesis ─ Following a simultaneous 26-year post-isolation history, we disentangle the effects of habitat loss and insularization on tree assemblages within a large set of Amazonian 'true' forest islands, of variable sizes, sharing a uniform open-water matrix. Area effects are expressed via a response to edge effects, with trees in smaller islands being more vulnerable to edge-related surface fires and windthrows. Additionally, forest edge effects can be a powerful driver of non-random floristic transitions across islands within the Balbina archipelago via a process of rapid pioneer proliferation, drastically affecting both the taxonomic and functional composition of insular tree communities. Finally, our results indicate that detrimental effects of forest fragmentation induced by hydroelectric dams are considerably stronger than those of forest patches embedded within a terrestrial vegetation matrix.
Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits. Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum. Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.
Data from: Traits that allow bats of tropical lowland origin to conquer mountains: bat assemblages along elevational gradients in the South American Atlantic Forest
Aim: This study aims to contribute to the identification of ecological determinants of tropical moist forest montane biodiversity, analyzing changes in the structure of bat assemblages along an elevational gradient and testing the role of species traits shaping those assemblages. Location: Mountain ranges in the Brazilian Atlantic Forest. Methods: We compiled a dataset with the composition of phyllostomid bat assemblages at 32 forested sites, ranging from 60m to 1960m a.s.l. We quantified how abundance and diversity changed along this elevational gradient, and assessed the capacity of each species to be present and abundant at each elevation, identifying traits that may influence that capacity. Results: Abundance and species diversity declined markedly with increasing elevation. Tolerance to low temperatures, low habitat specialization, and cave roosting facilitated success at higher elevations. Owing to trait filtering, and to changes in resource availability with elevation, assemblages were progressively dominated by a smaller number of mostly generalist species as elevation increased. Higher elevations harbor only a subset of the species that are present in the lowland forest, with no mountain specialized species. Main conclusions: High mountains harbor phyllostomid assemblages that are impoverished subsets of those at lower elevations. Phyllostomids have a tropical origin and may thus have a low potential to adapt to montane forest environments, which possibly explains the observed climatic trait filtering. Habitat filtering is also important, keeping forest specialists mostly at lowest elevations. Protected areas in the Atlantic Forest are mostly limited to mountains. While these areas are clearly important to protect biodiversity, including phyllostomid assemblages, it is now critical to protect and restore the few remnants of lower elevation Atlantic Forest where higher productivity and resource levels, increased complexity of vertical structure, and fewer climatic constraints favor the success of a wider range of phyllostomid bat species of tropical origin.
Population asynchrony alone does not explain stability in species rich soil animal assemblages: the stabilising role of forest age on oribatid mite communities
<p>1. The importance of microbial and plant communities in the control of the diversity and structure of soil animal communities has been clarified over the last decade. Previous research focused on abiotic factors, niche separation and spatial patterns. Significant gaps still exist in our knowledge of the factors that control the stability of these communities over time.</p> <p>2. We analysed a nine-year data set form the national Long-term Ecological Research Network of Latvia. We focused on 117 oribatid species from three Scots pine forests of different age (<40 yrs, 65 yrs, and >150 yrs) and structure. For each forest type, 100 samples were collected each year, providing very high replication and long of time series for a soil community. We assessed different aspects of stability: we used a dynamic null model, parametrised on observed growth rates, to test the hypothesis that asynchrony in species populations stabilises total community size; we also analysed alpha and beta diversity over time to test the hypothesis that temporal variation in species composition and relative abundances is controlled by forest attributes.</p> <p>3. Real communities can be more stable than their stochastic counterparts if species are asynchronous, confirming for the first time the role of asynchrony in stabilising soil communities. Yet, while some real communities were more stable and had higher abundance and growth rates than others, they were not necessarily more asynchronous than the less stable communities. Species composition and relative abundances were also less variable in the more stable communities.</p> <p>4. Species asynchrony generally stabilises species rich communities but is not sufficient to explain different levels of stability between forests. Forest age is a key factor explaining different levels of overyielding and so stability. Data suggests that both asynchrony and high diversity of microhabitat structure of Scots pine forests promote stability of soil animal communities.</p>
Data from: Colour lightness of dragonfly assemblages across North America and Europe
Dark-coloured ectotherms absorb energy from the environment at higher rates than light-coloured ectotherms. The thermal melanism hypothesis (TMH) states that this physical mechanism links the colour lightness of the body surfaces of ectotherms to their thermal environment and hence to their geographical distribution. Studies on different insect taxa in Europe found support for this prediction of the TMH. However, whether these results hold also for other biogeographical regions remains unclear. Here, we quantify and map the colour lightness of dragonfly species in North America and directly compare our results to previously published findings for Europe. We estimated the colour lightness of 152 North American dragonfly species from published illustrations, compiled their distribution data from the literature and combined all these data with six biologically relevant environmental variables. We evaluated the importance of phylogenetic autocorrelation for the spatial variation of mean colour lightness of dragonfly assemblages (grid cells of approximately 50 km × 50 km size) by repeating all analyses also for the phylogenetically predicted component of the colour lightness of species and the species-specific deviation from this prediction. We also accounted for spatial autocorrelation with autoregressive error models. All statistical approaches showed that dragonfly assemblages from both continents consistently tended to be darker coloured in regions with cold climates and lighter coloured in regions with warm climates. Regression slopes, however, were significantly less steep, and the amount of variance explained by environmental variables was lower for North America than for Europe. Our results highlight the importance of colour lightness for the distribution of dragonfly species, but they also indicate that idiosyncrasies of the continents modify the general pattern.
Data from: Response diversity in Mediterranean coralligenous assemblages facing climate change: Insights from a multispecific thermotolerance experiment
Climate change threatens coastal benthic communities on a global scale. However, the potential effects of ongoing warming on mesophotic temperate reefs at the community level remain poorly understood. Investigating how different members of these communities will respond to the future expected environmental conditions is, therefore, key to anticipating their future trajectories and developing specific management and conservation strategies. Here, we examined the responses of some of the main components of the highly diverse Mediterranean coralligenous assemblages to thermal stress. We performed thermotolerance experiments with different temperature treatments (from 26 to 29°C) with 10 species from different phyla (three anthozoans, six sponges and one ascidian) and different structural roles. Overall, we observed species‐specific contrasting responses to warming regardless of phyla or growth form. Moreover, the responses ranged from highly resistant species to sensitive species and were mostly in agreement with previous field observations from mass mortality events (MMEs) linked to Mediterranean marine heat waves. Our results unravel the diversity of responses to warming in coralligenous outcrops and suggest the presence of potential winners and losers in the face of climate change. Finally, this study highlights the importance of accounting for species‐specific vulnerabilities and response diversity when forecasting the future trajectories of temperate benthic communities in a warming ocean.
Nutrient deposition on Arctic fox dens creates atypical tundra plant assemblages at the edge of the Arctic
<p class="CxSpFirst"><span><span><span><span><span><span><span><span><span><span><span><i>Questions</i>: In most ecosystems, some organisms can be considered ecosystem engineers because they modify their physical environment in a way that can affect many other organisms. Nutrient deposition may be extremely important as an ecosystem engineering activity in nutrient-limited environments, but this mechanism remains understudied. In low-Arctic tundra, a region characterized by continuous permafrost, low-nutrient soils, and slow nutrient turnover, Arctic foxes (<i>Vulpes lagopus</i>) concentrate nutrients on their dens through fecal deposition and feeding their young. This nutrient concentration enhances productivity in patches on the landscape, likely creating a unique habitat for a variety of plants, and could have cascading effects on the distribution and diversity of vegetation on the tundra. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="CxSpMiddle"><span><span><span><span><span><span><span><span><span><span><span><i>Location</i>: Low-Arctic tundra in Wapusk National Park, Manitoba, Canada</span></span></span></span></span></span></span></span></span></span></span></p> <p class="CxSpMiddle"><span><span><span><span><span><span><span><span><span><span><span><i>Methods</i>: We quantified differences in vegetation composition between 20 fox dens and adjacent control sites. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="CxSpMiddle"><span><span><span><span><span><span><span><span><span><span><span><i>Results</i>: Plant growth form differed greatly between dens, which were dominated by deciduous grasses near the coast and erect shrubs farther from the coast, and control sites, which were dominated by evergreen prostrate shrubs. Dens also had more forb cover and less cover of lichens, mosses, and sedges. Species composition also varied greatly between control and den areas, with 17 of the 20 species found in at least 10% of the sampled sites being indicator species for dens or control sites. </span></span></span></span></span></span></span></span></span></span></span></p> <p><i>Conclusions</i><span><span><span><span><span><span><span><span><span><span><span>: By providing habitat for plants reliant on higher nutrient availability not typical of tundra heath, Arctic foxes enhance the biodiversity of the region. These erect plants may also help create new habitat by retaining snow on normally windswept beach ridges. Overall, this study illustrates the broader impacts of predators on diversity and community composition through mechanisms other than predation.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Drivers of phylogenetic assemblage structure of the Furnariides, a widespread clade of lowland Neotropical birds
Species co-occurrence in local assemblages is shaped by different processes at different spatial and temporal scales. Here we focus on historical explanations and examine the phylogenetic structure of local assemblages of the Furnariides clade (Aves: Passeriformes), assessing the influence of diversification rates on the assembly and species co-occurrence within those assemblages. Using 120 local assemblages across Bolivia and Argentina and a nearly complete phylogeny for the clade, we analyzed assemblage phylogenetic structure applying a recently developed model (DAMOCLES) accounting for the historical processes of speciation, colonization and local extinction. We also evaluated how diversification rates determine species co-occurrence. We found that the assembly of Furnariides assemblages can largely be explained by speciation, colonization and local extinction without invoking current local species interactions. Phylogenetic structure of open habitat assemblages mainly showed clustering, characterized by faster rates of colonization and local extinction than in forest habitats, whereas forest habitat assemblages were congruent with the model's equal rates expectation, thus highlighting the influence of habitat preferences on assembly and co-occurrence patterns. Our results suggest that historical processes are sufficient to explain local assemblage phylogenetic structure, while there is little evidence for species ecological interactions in avian assemblage diversity and composition.
Regional assemblages shaped by historical and contemporary factors: evidence from a species-rich insect group
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the complex diversity patterns is one of the main aims of community ecology. It is important to take both historical and contemporary factors into account in investigating the potential roles in assembling diversity patterns. Here, We compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State-Speciation and Extinction model to track the origins of these patterns. We subsequently estimate diversification rates of the two moth assemblages. Finally, we explored the effects of contemporary ecological factors on diversity patterns.<b> </b>From 7788 specimens we identified to 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Overall, moths in YS mountains showed higher species diversity and phylogenetic diversity than in TH mountains. Ancestral range analysis indicated YS as the origin. Significant historical dispersals from YS to TH mountains were detected. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow, were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we showed that a combined analysis of diversity patterns at multiples scales, including community, population and species levels, incorporating both historical and contemporary factors, are very informative for understanding factors of shaping diversity patterns.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Environmental constraints on the compositional and phylogenetic beta-diversity of tropical forest snake assemblages
The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of ectothermic species may be determined by the partitioning of the climatic niche, since ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche. Conversely, ectotherms facing dry summers would have fewer opportunities to climatic niche partitioning and other processes rather than environmental filtering would mediate species coexistence. We used 218 snake assemblages to quantify the compositional (CBD) and phylogenetic (PBD) beta-diversity of snakes in the Atlantic Forest (AF) hotspot. We identify two AF regions with distinct climatological regimes: dry summers in the northern-AF and rainy summers in the southern-AF. While accounting for the influence of multiscale spatial processes, we disentangle the relative contribution of thermal, water-related, and topographic conditions in structuring the CBD and PBD of snake assemblages, and determine the extent in which snake assemblages under distinct climatological regimes are affected by environmental filtering. Thermal conditions best explain CBD and PBD of snakes for the whole AF, whereas water-related factors best explain the structure of snake assemblages within a same climatological regime. CBD and PBD patterns are similarly explained by spatial factors but snake assemblages facing dry summers are more affected by spatial processes operating at fine to intermediate spatial scale whereas those assemblages in regions with rainy summers have a stronger signature of coarser-scale processes. As expected, environmental filtering plays a stronger role in southern-AF than northern-AF, and the synergism between thermal and water-related conditions is the key cause behind this difference. Differences in climatological regimes within the tropics may affect processes mediating species coexistence. The role of broad-scale gradients (e.g. temperature, precipitation) in structuring tropical ectothermic assemblages is greater in regions with rainy summers where climatic niche partitioning is more likely. Our findings highlight the potential stronger role of biotic interactions and neutral processes in structuring ectothermic assemblages facing changes towards warmer and dryer climates.
Data from: Impact of a hurricane on the herpetofaunal assemblages of a successional chronosequence in a tropical dry forest
Land‐use change is the main cause of deforestation and degradation of tropical forest in Mexico. Frequently, these lands are abandoned leading to a mosaic of natural vegetation in secondary succession. Further degradation of the natural vegetation in these lands could be exacerbated by stochastic catastrophic events such as hurricanes. Information on the impact of human disturbance parallel to natural disturbance has not yet been evaluated for faunal assemblages in tropical dry forests. To evaluate the response of herpetofaunal assemblages to the interaction of human and natural disturbances, we used information of pre‐ and post‐hurricane herpetofaunal assemblages inhabiting different successional stages (pasture, early forest, young forest, intermediate forest, and old growth forest) of dry forest. Herpetofaunal assemblages were surveyed in all successional stages two years before and two years after the hurricane Jova that hit the Pacific Coast of Mexico on October 2011. We registered 4093 individuals of 61 species. Overall, there were only slight effects of successional stage, hurricane Jova or the interaction between them on abundance, observed species richness and diversity of the herpetofauna. However, we found marked changes in estimated richness and composition of frogs, lizards, and snakes among successional stages in response to hurricane Jova. Modifications in vegetation structure as result of hurricane pass promoted particular changes in each successional stage and taxonomic group (anurans, lizards, and snakes). Secondary forests at different stages of succession may attenuate the negative effects of an intense, short‐duration, and low‐frequency natural disturbance such as hurricane Jova on successional herpetofaunal trajectories and species turnover.
Data from: Food and specific macronutrient limitation in an assemblage of predatory beetles
Habitats vary in food resources with carnivores often being prey limited, but it is unclear whether habitats facilitate a nutritionally balanced diet. Two paradigms in nutritional ecology, ecological stoichiometry and nutritional geometry, predict that carnivores are limited mainly by protein or lipid, respectively. Using the carabid beetle Anchomenus dorsalis and 10 other predatory beetles from agricultural fields, we developed and tested two simple procedures for quantifying macronutrient-specific habitat conditions without requiring information about the natural prey. Both procedures assume that predators forage for nutrients rather than specific prey. Our results show that 10 of 11 species were food limited. Five species were lipid limited and one species was protein limited in the field. Co-existing predator species showed considerable segregation of fundamental macronutritional niches. A linear relationship between specific nutrient limitation and the target lipid:protein (L:P) intake ratio indicates that species with high L:P target are more protein limited while species with low L:P target are more lipid limited. The study illustrates how species within a natural assemblage vary in nutritional niche and in specific nutrient limitation.
Figure 1 in Effects of physical and chemical factors on Ephemeroptera (Insecta) assemblages in an urban river of the eastern Colombian Llanos
Figure 1. Geographical location of the Ocoa river basin and sampling stations.
Data from: How do seasonality, substrate, and management history influence macrofungal fruiting assemblages in a central Amazonian Forest?
Worldwide, fungal richness peaks in tropical forest biomes where they are the primary drivers of decomposition. Understanding how environmental and anthropogenic factors influence tropical macrofungal fruiting patterns should provide insight as to how, for example, climate change and deforestation may impact their long-term demographic stability and evolutionary potential. However, in Amazonia no studies have yet to disentangle the effects of substrate, seasonality and forest history on phenology. Here, we quantitate spatial and temporal variation in community structure of fruiting macrofungi in relation to these factors at a long-term forest management research site in central Amazonia: the Biomass and Nutrients of Tropical Rain Forest (BIONTE's). Basidiome surveys of four substrate classes (leaves, soil, branches and trunks) were conducted along 250 m2 transects in primary and secondary (managed) forests, between 2012–13. From the 669 basidiomes collected, 290 taxa were identified of which 44 percent were restricted to primary and 36 percent to secondary forests. Although species-accumulation curves did not asymptote, rarefaction analyses and Fisher's alpha indicate contrasting differences in richness among forests in relation to substrate type. For example, leaf litter basidiome richness was higher in secondary forests, whereas the contrary was observed for soil communities, suggesting that variation in fruiting patterns in relation to disturbance is substrate-dependent possibly due to differences in necromass quality and/or understory micro-climates. Furthermore, secondary forests harbored significantly lower basidiome richness and abundance in dry months, suggesting synergistic impacts of seasonality and management history on fruiting regimes.
Data from: Leaf-litter decomposition and macroinvertebrate assemblages along an urban stream gradient in Puerto Rico
Urbanization is a major land use form that has large impacts on ecosystems. Urban development in the watershed impacts stream ecosystems by increasing nutrient and organic matter loads, altering hydrology, and reducing biodiversity. Puerto Rico is an ideal location to assess and monitor the effects of urbanization on streams, because it is increasingly urbanized and streams do not receive inputs of untreated sewage, characteristic of many other tropical urban areas. The objective of this study was to determine how leaf-litter decomposition and aquatic macroinvertebrate assemblages varied along a tropical urban gradient. We conducted the study in the Río Piedras watershed, San Juan Metropolitan Area, in six low order streams that formed an urban gradient ranging from 10 to 70% urban land cover. At each stream, we placed six 5g leaf bags of Ficus longifolia in three different pools and collected one bag on each sampling date. Decomposition rates were fast in forested streams (range 0.021 – 0.039 day-1) and decreased with increasing urbanization (range 0.007 – 0.008 day-1). Rates were strongly and negatively correlated with percent impervious surface cover (R= 0.81, p=0.01). Functional feeding group diversity was higher in forested streams, with the presence of shredders. Decomposition rates were significantly and positively correlated with functional feeding group diversity and abundance (R= 0.66, p= 0.04). Overall, our results show that urbanization affected the environment and macroinvertebrate diversity resulting in large negative effects on stream ecosystem function.
Data from: Seascapes as drivers of herbivore assemblages in coral reef ecosystems
Herbivorous fish maintain a critical ecosystem function on coral reefs by grazing algae and maintaining highly productive algal turf assemblages. Current paradigms implicate habitat complexity, predation and primary productivity as major drivers of the distribution and abundance of herbivorous fish, yet little is known about the relative contribution of these factors. Here, we compare bottom-up and top-down drivers of notional herbivore assemblages across an environmental gradient of wave exposure in the Palau archipelago. We surveyed herbivore assemblages at reef slopes (6 - 9m) across 18 sites, and quantified proxies of top-down control (predator biomass, habitat complexity) and bottom-up drivers (net primary production, nutrients) at each site. Despite substantial variability in herbivore biomass throughout the archipelago (6 to 65 g m-2), general additive models indicate that neither top-down nor bottom-up drivers significantly predicted biomass or density of herbivores among sites. In contrast to expectations, herbivore biomass was highest at sites with high predator biomass, low structural complexity and low benthic productivity. Rather, the highest biomass of herbivores was associated with shallow, tidally emergent, productive reef flats located adjacent to steep vertical walls ('drop-offs'). The emergent nature of this neighbouring habitat precluded occupation by territorial fishes, and multiple species of herbivores were observed to make foraging runs into this habitat once tidally inundated. We hypothesize that this habitat configuration provides an important cross-habitat resource subsidy. Multivariate ordination and permutation of herbivore communities revealed strong evidence for biogeographic partitioning throughout the archipelago (western, south-western, inner eastern and outer eastern clusters), contributing to an emerging picture that the habitat heterogeneity of seascapes can overwhelm the effects of conventional top-down and bottom-up structuring of herbivory on coral reefs.
Data from: Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants
Microbial communities in plant roots provide critical links between above and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities we designed a trap-plant bioassay experiment. Replicate Populus, Quercus, and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of 4 loci (i.e. 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.
Data from: Insect wing loss is tightly linked to the treeline: evidence from a diverse stonefly assemblage
The secondary loss of flight in previously winged insect lineages has long fascinated biologists. Habitat stability and isolation are thought to play important roles in driving wing reduction (Roff 1990, 1994), with exposure to high winds suggested to accelerate this process (Darwin 1859), although the role exposure plays in insect wing loss has never been empirically demonstrated. Here we assess fine-scale distributional records from a diverse regional stonefly assemblage, to demonstrate a widespread association between wing loss and the treeline in New Zealand. The observed pattern suggests that exposure plays a crucial role driving wing loss in alpine insects.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.