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552 results for “species abundance”
Insects caught in pitfall traps: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Lepidoptera species abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Miscellaneous inscet species abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Orthoptera species abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Formicidae species (ants) abundance: Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
All Insect Savanna Sweepnet Sampling 2004:Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
Old Field All Arthropod Sweepnet Sampling 2004 :Trophic Structure: Insect Species Diversity, Abundance and Body Size
The goal of this study was to examine the populations of insects in prairies and savannas. Most of the prairies had developed after being abandoned from agriculture, but none of the savannas had been cultivated. The history of burning varied between sites. The main sampling for this study was conducted in 1992 by the lead investigators: John Haarstad, Evan Siemann, and David Tilman. Insects were sampled via sweep-net sampling, pitfalls and ant scent plates throughout the growing season in each of 49 grassland fields and savannas. In total, 89,596 individuals of 1,167 species were captured and enumerated. Body size was measured for a subset of grasshoppers collected. In 2004, John Haarstad conducted two similar studies by identifying and enumerating all insects collected in sweepnet samples taken in old fields (prairies) as part of E014 grasshopper studies and from sweepnet samples taken in savannas.
FIGURE 5 in An abundant new genus and species of fan worms (Polychaeta: Sabellidae) from Hawaii
FIGURE 5. Longitudinal, histological sections of Euchonoides moeone n. sp. A, body, regenerating thorax; B, base of radiolar crown and collar, lateral view; C, same, frontal view; D, pre-pygidial depression and pygidium; E–F, belt on third abdominal chaetiger, G, sexual abdominal segments; H, J, details of glandular epithelium of belt of third abdominal chaetiger; I, detail of a mature oocyte and follicle cells. In A–B, D and I, the section plane is shown, where A refers to the anterior region, P to the posterior region, d dorsal zone and v ventral zone. Black arrows in A, E–G, I–J points to glandular belt on third abdominal chaetiger. Abbreviations: A1: abdominal chaetiger 1, A2: abdominal chaetiger 2, A3: abdominal chaetiger 3.
FIGURE 3 in An abundant new genus and species of fan worms (Polychaeta: Sabellidae) from Hawaii
FIGURE 3. SEM of Euchonoides moeone n. sp. A, complete specimen in lateral view, inset showing glandular belt on third abdominal chaetiger; B, radiolar crown; C, anterior peristomial ring and posterior peristomial ring collar in dorsal view; D, posterior peristomial ring collar in ventro-lateral view; E, posterior end with pygidium, ventro-lateral view.
FIGURE 1. Euchonoides moeone n in An abundant new genus and species of fan worms (Polychaeta: Sabellidae) from Hawaii
FIGURE 1. Euchonoides moeone n. sp. A, complete paratype, lateral view; B, complete paratype, ventral view; C, detail of patch of cilia (pc) on posterior peristomial ring collar and glandular ridge (gr) on chaetiger 2; D, dissected radiolar crown with arrows showing elongate dorsal lips and ventral radiolar appendages; E, inferior, thoracic, short, broadly hooded chaetae; F, inferior, thoracic bayonet chaeta; G, thoracic acicular uncini; H, anterior abdominal uncinus; I, posterior abdominal uncini, frontal and lateral view, respectively; J, posterior end showing pre-pygidial segments and pygidium, ventral view; K, posterior end, dorsal view. Abbreviations: ar, abdominal ridge; ch, chaetiger; es, eyespots; fg, faecal groove; gr, glandular ridge; pc, patch of cilia; pyg, pygidium; pre-pyg, pre-pygidial chaetigers. Pinnules in A–B may be confused with radioles, there are only three pairs or radioles.
Data from Jenkinson et al. 2020: Biogeographical variation in the distribution, abundance, and interactions among key species on rocky reefs of the northeast Pacific
<p>See Metadata tab for full description of transect survey data.</p>
Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities
<p>Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multi-species plant communities remains particularly challenging.</p> <p><span><span><span><span><span><span><span><span><span><span><span>Here we present a novel methodology, multi-species Genotyping By Sequencing (msGBS), as a next step to tackle this challenge. First, a multi-species meta-reference database containing thousands of gDNA clusters per species is created from GBS derived High Throughput Sequencing (HTS) reads. Second, GBS derived HTS reads from multi-species root samples are mapped to this meta-reference which, after a filter procedure to increase the taxonomic resolution, allows the parallel quantification of multiple species. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>The msGBS signal of 111 mock-mixture root samples, with up to 8 plant species per sample, was used to calculate the within-species abundance. Optional subsequent calibration yielded the across-species abundance. The within- and across-species abundances highly correlated (R<sup>2 </sup>range 0.72-0.94 and 0.85-0.98, respectively) to the biomass-based species abundance. Compared to a qPCR based method which was previously used to analyze the same set of samples, msGBS provided similar results. Additional data on 11 congener species groups within 105 natural field root samples showed high taxonomic resolution of the method. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><a>msGBS is highly scalable in terms of sensitivity and species numbers within samples, which is a major advantage compared to the qPCR method and advances our tools to reveal hidden belowground interactions.</a></span></span></span></span></span></span></span></span></span></span></span></p> <p>This dataset belongs to the article "<span><span><span><span><span><span><span><span><span><span><span><b>msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities</b>". </span></span></span></span></span></span></span></span></span></span></span>msGBS is a technique that uses Genotyping By Sequencing on mixed plant species root samples which, after a filtering step to increase the taxonomic resolution and calibration, is able to estimate plant species abundances. </p> <p>The article uses data of two different experiment:</p> <ol> <li>the Jena field survay (13 plant species) and</li> <li>the Dutch field survay (120 plant species).</li> </ol>
Data from: Species-habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape
Tropical butterfly conservation strategies often focus on total and/or common species richness to assess the conservation value of a patch or habitat. However, such a strategy overlooks the unique dynamics of rare species. We evaluated the species-habitat relationships of 209 common, intermediate, and rare butterfly species (including morphospecies) across four habitat types (mature, degraded, or fragmented forest, and urban parks) and two patch sizes (<400 ha, ≥400 ha) in Singapore. Common species richness was consistent across habitat types. Intermediate species richness declined by more than 50 percent in urban parks (relative to all forest habitats), and rare species richness was reduced by 50 percent in degraded and fragmented forest and by 90 percent in urban parks (relative to mature forest). Large patches had comparable overall richness to small patches, but they supported more rare species and three times as many habitat-restricted species over a similar area. Importantly, a number of rare species were confined to single small patches. Mixed-effects regression models were constructed to identify habitat and ecological/life history variables associated with butterfly abundance. These models revealed that species with greater habitat specialization, rare larval host plants, few larval host plant genera, and narrow global geographic ranges were more likely to be rare species. Overall, these results demonstrate that the richness of habitat-restricted and rare species do not follow the same spatial distribution patterns as common species. Therefore, while conserving mature forests is key, effective butterfly conservation in a transformed landscape should take into account rare and habitat-restricted species.
Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism
<p>Current global warming trends are expected to have direct effects on species through their sensitivity to temperature, as well as on their biotic interactions, with cascading indirect effects on species, communities, and entire ecosystems. To predict the community-level consequences of global change we need to understand the relative roles of both the direct and indirect effects of warming. We used a laboratory experiment to investigate how warming affects a tropical community of three species of <em>Drosophila</em> hosts interacting with two species of parasitoids over a single generation. Our experimental design allowed us to distinguish between the direct effects of temperature on host species performance, and indirect effects through altered biotic interactions (competition among hosts and parasitism by parasitoid wasps). Although experimental warming significantly decreased parasitism for all host-parasitoid pairs, the effects of parasitism and competition on host communities did not vary across temperatures. Instead, effects on host relative abundances were species-specific, with one host species dominating the community at warmer temperatures, independently of parasitism and competition treatments. Our results show that temperature shaped a <em>Drosophila </em>host community directly through differences in species’ thermal performance, and not via its influences on biotic interactions.</p>
Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics
<p>Amplicon metabarcoding is an established technique to analyse the taxonomic composition of communities of organisms using high-throughput DNA sequencing, but there are doubts about its ability to quantify the relative proportions of the species, as opposed to the species list. Here, we bypass the enrichment step and avoid the PCR-bias, by directly sequencing the extracted DNA using shotgun metagenomics. This approach is common practice in prokaryotes, but not in eukaryotes, because of the low number of sequenced genomes of eukaryotic species. We tested the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced degree. We shotgun-sequenced, at low-coverage DNA, 18 species of insects in 22 single-species and 6 mixed-species libraries and mapped the reads against 110 reference genomes of insects. We used the single-species libraries to calibrate the process of assignation of reads to species and the libraries created from species mixtures to evaluate the ability of the method to quantify the relative species abundance. Our results showed that the shotgun metagenomic method is easily able to set apart closely-related insect species, like four species of <i>Drosophila</i> included in the artificial libraries. However, to avoid the counting of rare misclassified reads in samples, it was necessary to use a rather stringent detection limit of 0.001, so species with a lower relative abundance are ignored. We also identified that approximately half the raw reads were informative for taxonomic purposes. Finally, using the mixed-species libraries, we showed that it was feasible to quantify with confidence the relative abundance of individual species in the mixtures.</p>
Data from: Inferring invasive species abundance using removal data from management actions
Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480–19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (<50) the effective removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and inaccurate removal rates, we suggest auxiliary information that could be collected and included in the model as covariates (e.g., habitat effects, differences between pilots) to improve accuracy of removal rates and hence abundance estimates.
Data from: Evidence for a stochastic geometry of biodiversity: the effects of species abundance, richness and intraspecific clustering
Most ecological theories that aim to explain coexistence in megadiverse communities employ a set of three rules to describe the stochastic geometry of biodiversity: (i) individuals exhibit intraspecific clustering; (ii) species abundances vary according to a log-normal distribution and (iii) the spatial arrangement between species is independent. The first two rules have received strong empirical support, but the third remains largely unexplored. To address this deficiency, we evaluated the independent species arrangement rule in a species-rich shrubland and its potential drivers, that is, the levels of species richness and intraspecific clustering exhibited by a given species at different scales, and the relative abundance of such species in the community. We found that interspecific associations were rare and that independence was positively related to species richness and intraspecific clustering, but negatively related to relative species abundances. Synthesis. Our results agree with the independent species arrangement rule and they provide empirical support for the stochastic geometry of biodiversity. In the context of species-rich plant communities, the likelihood of two species encountering is very small. However, our study demonstrated a novel feature of this context, where both intraspecific clustering (due limitations on dispersal) and relative species abundances play fundamental roles in determining the probability of two species encountering and interacting, especially at very fine spatial scales.
Data from: The importance of factors controlling species abundance and distribution varies in native and non-native species.
How variation in factors controlling species abundance and distribution between native and non-native ranges compares to that within ranges remains poorly understood. We used a globally distributed ruderal, Centaurea solstitialis (Centaurea), to explore the possibility that the importance of those factors exhibits great variation between and within ranges. To test our hypothesis, we established seed addition experiments with soil disturbance (turnover and control) and biocide (fungicides, insecticide, and control) treatments in two regions within native (the Caucasus and south-western Turkey) and non-native (the western United States – US – and central Argentina) distributions. Also, we estimated the rate of vegetation recovery after disturbance (resilience) and related it to Centaurea density in experimental plots. Disturbance strongly increased Centaurea density in all regions. Density was similar between the native Caucasus and non-native Argentina and much greater in those regions than in the native Turkey and non-native US in biocide-free plots. Fungicides had positive effects on density in the US and negative ones in the Caucasus and Argentina, resulting in no differences between those three regions and greater density in the US than Turkey. Insecticide applications promoted Centaurea density in Turkey and Argentina, but inter-regional comparisons of density in treated plots were comparable to those in biocide-free plots. Overall, plants were smaller and less fecund in Turkey than the other regions, except the US. The greatest fungal attack was documented in Turkey, and herbivory was stronger there and in Argentina than in the Caucasus and US. The resilience of the local community explained a large proportion of variation in Centaurea density. These results support our hypothesis, and reveal that the speed at which competition is re-gained after disturbance may influence global variation in Centaurea abundance. Because many ruderals exhibit native and non-native distributions, our results are likely to be generalized to other systems.
Data from: Species traits and abundances predict metrics of plant–pollinator network structure, but not pairwise interactions
Plant–pollinator mutualistic networks represent the ecological context of foraging (for pollinators) and reproduction (for plants and some pollinators). Plant–pollinator visitation networks exhibit highly conserved structural properties across diverse habitats and species assemblages. The most successful hypotheses to explain these network properties are the neutrality and biological constraints hypotheses, which posit that species interaction frequencies can be explained by species relative abundances, and trait mismatches between potential mutualists respectively. However, previous network analyses emphasize the prediction of metrics of qualitative network structure, which may not represent stringent tests of these hypotheses. Using a newly documented temporally explicit alpine plant–pollinator visitation network, we show that metrics of both qualitative and quantitative network structure are easy to predict, even by models that predict the identity or frequency of species interactions poorly. A variety of phenological and morphological constraints as well as neutral interactions successfully predicted all network metrics tested, without accurately predicting species observed interactions. Species phenology alone was the best predictor of observed interaction frequencies. However, all models were poor predictors of species pairwise interaction frequencies, suggesting that other aspects of species biology not generally considered in network studies, such as reproduction for dipterans, play an important role in shaping plant–pollinator visitation network structure at this site. Future progress in explaining the structure and dynamics of mutualistic networks will require new approaches that emphasize accurate prediction of species pairwise interactions rather than network metrics, and better reflect the biology underlying species interactions.
Data from: The interplay among intraspecific leaf trait variation, niche breadth and species abundance along light and soil nutrient gradients
It is assumed that widespread, generalist species have high phenotypic variation, but we know little about how intraspecific trait variation (ITV) relates to species abundance and niche breadth. In the temperate rainforest of southern Chile, we hypothesized that species with wide niche breadth would exhibit 1) high among-plot ITV, 2) a strong relationship between trait values and the environment, and 3) a close fit between traits and local environment trait optima. We measured leaf functional traits (leaf area, LMA, leaf N and P concentrations) of saplings in woody species, and compared the relative abundance of each species with its niche breadth, measured as the range of light, soil N and P availability. We used the slope of the linear regression of species' trait-environment relationships to assess the strength and direction of these relationships, and measured the degree to which species' trait values track the environmental optimum across plots. In some cases, species having wide niche breadth had high ITV in leaf N and also matched traits (LMA and leaf P) to local optima along the light gradient; they also had high ITV in general and matched leaf P to local optima along the soil P gradient. The relationship between species with wide niche breadth and the strength of intraspecific trait-environment relationships was generally weak and varied depending on the niche dimension and trait in question. Species varied considerably in the strength of trait-environment relationships and total magnitude of ITV, and this variation was not generally strongly related to species abundances or niche breadth patterns. In conclusion, trait variation at the community level is not driven by a few abundant, widely distributed species, but depends on the aggregate trait responses of both abundant and rare species. This makes it difficult to scale individual species trait responses up to the community level.
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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)
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.