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552 results for “species abundance”
Data from: Odonate species occupancy frequency distribution and abundance – occupancy relationship patterns in temporal and permanent water bodies in a subtropical area
<p>This paper investigates species richness and species occupancy frequency distributions (SOFD) as well as patterns of abundance-occupancy relationship (SAOR) in Odonata (dragonflies and damselflies) in a subtropical area. A total of 82 species and 1983 individuals were noted from 73 permanent and temporal water bodies (lakes and ponds) in the Pampa biome in southern Brazil. Odonate species occupancy ranged from 1 to 54. There were few widely distributed generalist species and several specialist species with a restricted distribution. About 70% of the species occurred in less than 10% of the water bodies, yielding a surprisingly high number of rare species, often making up the majority of the communities. No difference in species richness was found between temporal and permanent water bodies. Both temporal and permanent water bodies had odonate assemblages that fitted best with the unimodal satellite SOFD pattern. It seems that unimodal satellite SOFD pattern frequently occurred in the aquatic habitats. The SAOR pattern was positive and did not differ between permanent and temporal water bodies. Our results are consistent with a niche-based model rather than a metapopulation dynamics model.</p>
Figure 9 in Abundance, reproduction, and feeding of three species of British terrestrial planarians: Observations over 4 years
Figure 9. Microplana terrestris. The number of hatchlings emerging from 13 viable cocoons.
Figure 2 in Abundance, reproduction, and feeding of three species of British terrestrial planarians: Observations over 4 years
Figure 2. The vegetable plots. Planks are placed around the perimeter.
Temporal stability in species richness but reordering in species abundances within avian assemblages of a Tropical Andes conservation hot spot
<p>As the pace of environmental change increases, there is an urgent need for quantitative data revealing the temporal dynamics of local communities in tropical areas. Here we quantify the stability of avian assemblages in the highly threatened, but poorly studied, Andean biodiversity hot spot. We evaluated the temporal variation in species richness and community composition of local bird assemblages in three habitat types (native forest, introduced forest, native shrub) using a unique, relatively long-term data series from Cajas National Park and Mazán Reserve in the Southern Andes of Ecuador. We sampled birds with mist nets using a standardized protocol over 11 years, from 2006 to 2016. Species richness remained stable over time across habitats, but community composition changed in the native forest. In particular, we observed taxonomic reordering in the native forest, in which the evenness in the distribution of abundances of taxa decreased over time. This finding is consistent with other studies where species richness remained constant over time while community composition changed. Our study highlights the value of long-term studies in the tropical Andes as we show that species composition of birds in a montane forest is changing, consistent with global trends in biodiversity change.</p>
Predicting species abundance by implementing the ecological niche theory
<p>Species are not uniformly distributed across the landscape. For every species, there should be few favoured sites where abundance is high and many other sites of lower suitability where abundance is low. Consequently, local abundance could be thought of as a natural expression of species response to local conditions. The correlation between abundance and environmental suitability has been well documented, and a recent meta-analysis has suggested that this relationship could be a generality. Despite the importance and potential implication of the abundance-suitability relationship, its predictive power for meaningful extrapolations has been surprisingly poorly explored. In this study, we showed how a highly predictable trend can be extracted from the abundance-suitability relationship, accurately predicting the variation in species abundance at a high spatial resolution. We produced high-quality environmental suitability estimations for 50 endemic species to the Australian Wet Tropics. Environmental suitability derived from species distribution models was related to observed abundance estimated using data from 29 years of uninterrupted monitoring effort. We used the fitted relationship to accurately predict abundance at a fine scale across the species range. Our results showed that the abundance-suitability relationship was strong for endemic species in the Australian Wet Tropics. The predictive power of our models was high, explaining, on average, 55% of the deviance across taxa. Despite interspecific variation in the strength of the abundance-suitability relationship associated with potential intrinsic estimation biases, our approach provides a powerful tool for predicting abundance across the species range at a fine scale. The potential for robust abundance predictions from occurrence-based species distribution models shown in this study are numerous, and it could have a significant impact in enhancing species conservation and management decisions.</p>
Abundance decline in the avifauna of the European Union reveals global similarities in biodiversity change: Input datasets & species results
<p>This archive contain the two input datasets of bird population estimates and trend estimates underpinning the journal article: <strong>Abundance decline in the avifauna of the European Union reveals global similarities in biodiversity change. </strong>It also contains the species level results obtained from the Bayesian hierarchical model described in section 2.2.1 of the paper.</p>
Urbanization decreases species richness, and increases abundance in dry climates whereas decreases in wet climates: A global meta-analysis
<p>Soil invertebrates have an essential role in decomposition, nutrient turnover and soil structure formation, all of which are strongly threatened by urbanization. Sealing, compaction by trampling and pollution destroy and degrade city soils and potentially damage soil-living invertebrates. The existing literature on how urbanization affects soil invertebrates is inconsistent, presenting both negative and positive effects. Therefore, here we aimed to synthesize the effects of urbanization on soil invertebrates considering their taxonomic (Acari, Annelida, Carabidae, Collembola, Gastropoda, Isopoda, Myriapoda, Nematoda) and functional (soil living vs. soil-related; mobility) identities, as well as to examine how the overall effect is modulated by climatic conditions (total annual precipitation, annual mean ambient temperature), urban heat island effect (based on ambient temperature differences between urban and rural areas) and city population. In a systematic review using hierarchical and categorical meta-analyses, we extracted 158 effect sizes from 75 studies on abundance and 125 effect sizes from 84 studies on species richness. Invertebrate abundance showed an increase, whereas species richness significantly decreased with increasing urbanization. The reason behind this could be that a few generalist species can adapt well to the urban environment and achieve strongly elevated densities. The species richness of annelids, springtails, and snails decreased with advancing urbanization, most probably because these animals are sensitive to soil compaction and pollution, both of which are common consequences of urbanization. The temperature did not modify the effects of urbanization, but precipitation modified the effects on abundance. Abundance increased with advancing urbanization in drier climates, probably because irrigation increased soil moisture, whereas it decreased in wet climates, as urban areas were drier than their surroundings. Making future cities more climate-neutral could better sustain soil biodiversity.</p>
Bayesian species distribution models integrate presence-only and presence-absence data to predict deer distribution and relative abundance
<p>Using geospatial data of wildlife presence to predict a species distribution across a geographic area is among the most common tools in management and conservation. The collection of high-quality presence-absence data through structured surveys is, however, expensive, and managers usually have access to larger amounts of low-quality presence-only data collected by citizen scientists, opportunistic observations, and culling returns for game species. Integrated Species Distribution Models (ISDMs) have been developed to make the most of the data available by combining the higher-quality, but usually scarcer and more spatially restricted presence-absence data, with the lower quality, unstructured, but usually more extensive presence-only datasets. Joint-likelihood ISDMs can be run in a Bayesian context using INLA (Integrated Nested Laplace Approximation) methods that allow the addition of a spatially structured random effect to account for data spatial autocorrelation. Here, we apply this innovative approach to fit ISDMs to empirical data, using presence-absence and presence-only data for the three prevalent deer species in Ireland: red, fallow and sika deer. We collated all deer data available for the past 15 years and fitted models predicting distribution and relative abundance at a 25 km<sup>2</sup> resolution across the island. Models' predictions were associated to spatial estimates of uncertainty, allowing us to assess the quality of the model and the effect that data scarcity has on the certainty of predictions. Furthermore, we checked the performance of the three species-specific models using two datasets, independent deer hunting returns and deer densities based on faecal pellet counts. Our work clearly demonstrates the applicability of spatially-explicit ISDMs to empirical data in a Bayesian context, providing a blueprint for managers to exploit unexplored and seemingly unusable data that can, when modelled with the proper tools, serve to inform management and conservation policies.</p>
Space resource utilization of dominant species integrates abundance- and functional-based processes for better predictions of plant diversity dynamics
<p>Sustainable ecosystem management relies on our ability to predict changes in plant diversity and to understand the underlying mechanisms. Empirical evidence demonstrates that abundance- and functional-based processes simultaneously explain the loss of plant diversity in response to human activities. Recently, a novel indicator based on percent cover (CoverD) and maximum height (HeightD) of the dominant plant species – Space Resource Utilization (SRUD) – has proven to give robust and better predictions of plant diversity dynamics than community biomass. Whether the superior predictive ability of SRUD is due to its capacity to simultaneously capture abundance- and functional-based processes remains unknown. Here, we tested this hypothesis by quantifying mechanistic links between changes in SRUD and biodiversity in response to nutrients and herbivores. Furthermore, we assessed the relative contribution of dominant, intermediate, and rare species to reduced density of individuals by combining null model analysis with field experiments. We found that SRUD successfully captured changes in ground-level light availability and changes in the number of individuals to predict plant diversity dynamics, and each of CoverD and HeightD partly and independently contributed to both processes. Comparative results from null model analysis and field experiments confirmed that individual losses of dominant, intermediate, and rare species followed non-random processes. Specifically, compared with random loss process, rare species lost proportionally more individuals and thus disproportionately contributed to species loss, while dominant and intermediate species lost less. Our results demonstrate that SRUD captures both abundance- and functional-based processes thus explaining why SRUD provides more accurate predictions of changes in species diversity. Given that rare species can play an important role in shaping community structure, resisting against invasion, impacting higher trophic levels, and providing multiple ecosystem functions, reducing the SRU of dominant species could alleviate the risk of exclusion of rare species by mitigating abundance- and functional-based competition processes.</p>
Plant–hummingbird pollination networks exhibit limited rewiring after experimental removal of a locally abundant plant species
<p>In this study, we simulated the local extinction of a hummingbird-pollinated understory plant, <em>Heliconia</em> <em>tortuosa</em>, from tropical forest fragments using a replicated Before-After-Control-Impact (BACI) experimental design while quantifying plant-hummingbird interactions through two parallel techniques: pollen collected from individual hummingbirds ('pollen networks', created from >300 pollen samples) and observations of hummingbirds visiting focal plants ('camera networks', created from >19,000 observation hours). Each response variable was measured during each experimental period (pre and post) in sites with and without <em>H. tortuosa</em> removal (treatment and control).</p>
Unveiling global species abundance distributions - Callaghan et al. 2023 - Nature Ecology and Evolution
<p>This repository represents some data and code to reproduce the main figures from Callaghan et al. 2023. Unveiling the global species abundance distributions of Eukaryotes. Nature Ecology and Evolution.</p>
How environmental factors affect the abundance and distribution of two congeneric species of Amazonian frogs
<p>In this study, we test the hypothesis that, at a fine scale, environmental variables influence differently sister species that live in sympatry and are phylogenetically closely related. We sampled two Amazonian anuran species, <em>Phyzelaphryne</em> <em>miriamae</em> and <em>Phyzelaphryne</em> sp., in 11 permanent sampling modules distributed across ~600 km in the Purus-Madeira Interfluve between 2013 and 2014. Using mixed generalized linear models, we found that the species have distinct environmental associations, which may facilitate their coexistence in sympatry. <em>Phyzelaphryne</em> <em>miriamae</em> was more frequent in environments with low precipitation and low water tables, suggesting this species is better adapted to live in drier places. In contrast, <em>Phyzelaphryne</em> sp. appeared to be a generalist regarding to habitat and resource use. These patterns are in accordance with the hypothesis that environmental variables influence sister species differently on a fine scale. <em>Phyzelaphryne</em> <em>miriamae</em> is larger than <em>Phyzelaphryne</em> sp., which may make it more resistant to dehydration, allowing it to explore drier environments. In conclusion, our results are in concordance with the hypothesis that the evolution of characteristics resulting from selection may have reduced competition for resources between closely related species, thus facilitating coexistence in sympatry.</p>
Tree species richness around urban red maples reduces pest abundance but does not enhance biological control
<p>Urban trees often host greater insect pest abundance than trees in rural forests. This may be due, in part, to differences in tree diversity and canopy cover between these settings. Urban trees are often planted in isolation or monoculture, which favors pest accumulation. The gloomy scale, <em>Melanaspis tenebricosa</em> Comstock, is a pest of urban red maples (<em>Acer rubrum </em>L.) that is abundant where impervious surfaces dominate the local landscape. Increasing tree diversity and canopy cover around urban red maples may reduce gloomy scale abundance by supporting natural enemy communities. We investigated the effect that surrounding tree species richness and tree canopy cover had on gloomy scale abundance, natural enemy abundance, and biological control in red maple trees in Raleigh, NC, USA. We collected scales and natural enemies from red maples that spanned a gradient of tree species richness, canopy cover, and impervious surface values. We also measured gloomy scale parasitism and predation of sentinel prey in red maple canopies. Greater tree species richness and canopy cover were associated with lower gloomy scale density. Red maples in diverse settings also hosted fewer scales per natural enemy. Parasitoids were less common in maples in diverse settings, but generalist predator abundance was unaffected by tree diversity. Finally, tree species richness and canopy cover did not increase biological control of scales or sentinel prey. Our findings suggest that higher tree diversity and greater canopy cover may reduce gloomy scale density, but this is not entirely explained by the effects of natural enemies and biological control.</p>
Data for "Negative density dependence promotes persistence of a globally rare yet locally abundant plant species (Oenoethera coloradensis)"
<p>This dataset was used to perform the analyses in the manuscript "Negative density dependence promotes persistence of a globally rare yet locally abundant plant species (Oenoethera coloradensis)"</p>
Tree species abundance through time in tropical forest census plots, Panama
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The effect of niche filtering on plant species abundance in temperate grassland communities
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Predicting species abundance by implementing the ecological niche theory
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Data from: Among-species variation in six decades of changing migration timings explained through ecology, life-history and abundance
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Species niches, not traits, determine abundance and occupancy patterns: a multi-site synthesis
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Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference
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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)
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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.