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141 results for “species density”
Density-dependent within-patch movement behavior of two competing species
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Effects of tree species diversity and conspecific seedling density on insect herbivory and pathogen infection on big-leaf mahogany seedlings
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SGS-LTER Effects of water and nitrogen additions on plant species density and cover in shortgrass ecosystems on the Central Plains Experimental Range, Nunn, Colorado, USA 1997-2011, ARS Study Number 143
This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. The objective of this research is to evaluate the long-term response of shortgrass ecosystems to additional water and nitrogen inputs. An experiment was conducted during the IBP project (1970-1975) in which water and nitrogen were applied (Lauenroth et al. 1978, Dodd and Lauenroth 1979, Milchunas and Lauenroth 1995). While we gained an enormous increment in our knowledge about shortgrass ecosystems from this experiment it raised as many questions as it answered. One of the problems was that the treatments were very high levels of nitrogen (100-150kg/ha N) and water (600 mm/growing season) additions. Additional information and referenced materials can be found: http://hdl.handle.net/10217/85629.
PLSS Density by Species and PFT, Upper Midwest: Level 1
EuroAmerican land use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Gridded (8x8km) estimates of pre-settlement (1800s) forests from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan) using 19th Century Public Land Survey System (PLSS) records provide relative composition, biomass, stem density, and basal area for 26 tree genera. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection. We compare pre-settlement to modern forests using US Forest Service Forest Inventory and Analysis (FIA) data to show the prevalence of lost forests, pre-settlement forests with no current analogue, and novel forests, modern forests with no past analogs. Differences between PLSS and FIA forests are spatially structured as a result of differences in the underlying ecology and land use impacts in the Upper Midwestern United States. Modern biomass is higher than pre-settlement biomass in northern Minnesota, northwestern and south central Wisconsin along the former prairie-forest border through Minnesota that was largely open savanna and the Big Woods of Minnesota. PLSS biomass was higher than today in northern Wisconsin and upper and lower Michigan due to shifts in species composition and, presumably, average stand age. Modern forests are more homogeneous, and ecotonal gradients are more diffuse today than in the past. Novel forest assemblages represent 29% of all FIA cells, while 25% of pre-settlement forests no longer exist in a modern context. Lost forests are centered around the forests of the Tension Zone, particularly in hemlock dominated forests of north-central Wisconsin, and in oak-elm-basswood forests along the forest-prairie boundary in south central
FIGURE 1. Species richness and sampling density. A in Tardigrades of Finland: new records and an annotated checklist
FIGURE 1. Species richness and sampling density. A) Sampling density map. Type localities in Finland shown (A: type locality of Acanthechiniscus distinctus, G: type localities of Grevenius pulcher, I: type locality of Itaquascon enckelli, M: type locality of Milnesium quadrifidum, U: neotype locality of Ursulinius septentrionalis). Additionally, biggest five Finnish cities by population shown; B) Species richness by biogeographical province (For abbreviations see https://laji.fi/theme/emk); C) Species richness by administrative region (1 = Lapland, 2 = North Ostrobothnia, 3 = Kainuu, 4 = Central Ostrobothnia, 5 = Central Finland, 6 = North Savo, 7 = North Karelia, 8 = Ostrobothnia, 9 = South Ostrobothnia, 10 = Satakunta, 11 = Pirkanmaa, 12 = Päijät-Häme, 13 = South Savo, 14 = Southwest Finland, 15 = Kanta-Häme, 16 = Uusimaa, 17 = Kymenlaakso, 18 = South Karelia, 19 = Åland).
Remotely sensed forest understory density and nest predator occurrence interact to predict suitable breeding habitat and the occurrence of a resident boreal bird species
<p>Habitat suitability models (HSM) based on remotely sensed data are useful tools in conservation work. However, they typically use species occurrence data rather than robust demographic variables, and their predictive power is rarely evaluated. These shortcomings can result in misleading guidance for conservation. Here, we develop and evaluate a HSM based on correlates of long term breeding success of an open nest building boreal forest bird, the Siberian jay. In our study site in northern Sweden, nest failure of this permanent resident species is driven mainly by visually hunting corvids that are associated with human settlements. Parents rely on understory nesting cover as protection against these predators. Accordingly, our HSM includes a light detection and ranging (LiDAR) based metric of understory density around the nest and the distance of the nest to the closest settlement to predict breeding success. It reveals that a high understory density 15-80 m around nests is associated with increased breeding success in territories close to settlements (<1.5 km). Farther away from human settlements breeding success is highest at nest sites with a more open understory providing a favourable warmer microclimate. We validated this HSM by comparing the predicted breeding success with landscape-wide census data on Siberian jay occurrence. The correlation between breeding success and occurrence was strong up to 40 km around the study site. However, the HSM appears to overestimate breeding success in regions with a milder climate, and therefore higher corvid numbers. Our findings suggest that maintaining patches of small diameter trees may provide a cost-effective way to restore the breeding habitat for Siberian jays up to 1.5 km from human settlements. This distance is expected to increase in the warmer, southern, and coastal range of the Siberian jay where the presence of other corvids is to a lesser extent restricted to settlements.</p>
Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: effect of null alleles
<p>Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79 and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null alleles frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity, and indicate that null alleles were not the only cause of deviation from HW equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlun effect.</p>
Data from: eDNA surveys to detect species at very low densities: a case study of European carp eradication in Tasmania, Australia
1. Eradications of invasive species are usually expensive and difficult to conduct. Knowing when to declare an eradication successful requires distinguishing between failed detection of the target species due to imperfect sensitivity of the detection method and true species absence. This is difficult because the sensitivities of many detection methods are unknown. 2. Environmental DNA (eDNA) methods can be used to detect species by analysing DNA present in environmental samples. eDNA has been promoted as a particularly sensitive and cost-effective way to detect species at low densities and, importantly, the sensitivity of eDNA surveys can be quantified. Nevertheless, the effort and costs involved in detecting species at extremely low densities, such as required during eradication, have not been previously calculated. 3. We evaluated the sensitivity of eDNA surveys in detecting the invasive European carp, Cyprinus carpio, in two lakes in Tasmania, Australia, one in which carp have been eradicated and a second in which carp are currently being eradicated. We determined the sampling effort and associated cost required to detect the species at very low density in these lakes. 4. While our eDNA survey detected the current low density carp population present in in Lake Sorell, we show that an exponential increase in sampling effort and associated cost will be required to confidently detect the species as the population declines. Similarly, while our eDNA survey corroborated the species absence from Lake Crescent, our detection confidence was low. We quantify the survey effort and financial investment required to confidently establish eradication success in Lake Crescent. Synthesis and applications: 5. Estimating the eDNA survey effort and cost required to detect species at a given density will enable practitioners to make informed decisions on the feasibility of implementing such surveys. Quantifying the sensitivity of eDNA surveys will also inform the confidence practitioners should place in the results of eDNA detection surveys to ensure appropriate management actions are implemented and provide a suitable stopping point at which to confidently declare eradication success.09-Jul-2019
Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Data from: Separating sources of density-dependent and density-independent establishment limitation in invading species
Successful colonization by invasive species depends on both the ability to disperse seeds to a site and an ability to establish once seeds have arrived. While seed and establishment limitation are known to jointly influence colonization, decomposing establishment limitation into density-dependent and density-independent components has remained challenging. Here, we couple theoretical models of recruitment with a multispecies invasion experiment conducted within a natural gradient of soil moisture and productivity to assess how variation in establishment limitation shapes outcomes for invasion. Recruitment was affected by both density-dependent and density-independent sources of establishment limitation in three of four species. Soil moisture stress and productivity both increased density-independent mortality in one species, whereas density-dependent mortality increased in locations with favourable soil moisture. Synthesis. Successful establishment of invading species can be limited by both density-dependent and density-independent mechanisms. In particular, the strength of density-independent limitation may depend on natural gradients in abiotic factors. The varying strengths of establishment limitation suggest that patterns of invasion are likely to be uneven both in space and in time. Understanding how intraspecific competitive constraints and density-independent limitation vary with abiotic gradients can assist with predicting when invasions are likely to occur, information that can be harnessed in the development of better methods for control.
Data from: Scale-dependent shifts in the species composition of flower visitors with changing floral density
Responses of flower-visiting animals to floral density can alter interactions between plants, influencing a variety of biological processes, including plant population dynamics and the evolution of flowering phenology. Many studies have found effects of floral or plant density on pollinator visitation rates at patch scales, but little is known about responses of flower visitors to floral densities at larger scales. Here, I present data from an observational field study in which I measured the effects of floral density on visitation to the annual composite Holocarpha virgata at both patch (4 m(2)) and site (12.6 ha) spatial scales. The species composition of flower visitors changed with floral density, and did so in different ways at the two scales. At the site scale, average floral density within patches of H. virgata or within patches of all summer-flowering species combined had a significant positive effect on per-flowerhead visitation by the long-horned bee Melissodes lupina and no significant effects on visitation by any other taxa. At the patch scale, per-flowerhead visitation by honeybees significantly increased whereas visitation by M. lupina often decreased with increasing floral density. For both species, responses to patch-scale floral density were strongest when site-scale floral density was high. The scale-dependence of flower visitor responses to floral density and the interactions between site- and patch-scale effects of floral density observed in this study underscore the importance of improving our understanding of pollinators' responses to floral density at population scales.
Data from: Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community
To understand how ecosystems are structured and stabilized, and to identify when communities are at risk of damage or collapse, we need to know how the abundances of the taxa in the entire assemblage vary over ecologically meaningful timescales. Here, we present an analysis of species temporal variability within a single large vertebrate community. Using an exceptionally complete 33-year monthly time series following the dynamics of 81 species of fishes, we show that the most abundant species are least variable in terms of temporal biomass, because they are under density-dependent (negative feedback) regulation. At the other extreme, a relatively large number of low abundance transient species exhibit the greatest population variability. The high stability of the consistently common high abundance species—a result of density-dependence—is reflected in the observation that they consistently represent over 98% of total fish biomass. This leads to steady ecosystem nutrient and energy flux irrespective of the changes in species number and abundance among the large number of low abundance transient species. While the density-dependence of the core species ensures stability under the existing environmental regime, the pool of transient species may support long-term stability by replacing core species should environmental conditions change.
Data from: Estimating density for species conservation: comparing camera trap spatial count models to genetic spatial capture-recapture models
Density estimation is integral to the effective conservation and management of wildlife. Camera traps in conjunction with spatial capture-recapture (SCR) models have been used to accurately and precisely estimate densities of "marked" wildlife populations comprising identifiable individuals. The emergence of spatial count (SC) models holds promise for cost-effective density estimation of "unmarked" wildlife populations when individuals are not identifiable. We evaluated model agreement, precision, and survey costs, between i) a fully marked approach using SCR models fit using non-invasive genetic data, and ii) an unmarked approach using SC models fit using camera trap data, for a recovering population of the mesocarnivore fisher (Pekania pennanti). The SCR density estimates ranged from 2.95 to 3.42 (2.18–5.19 95% BCI) fishers 100 km−2. The SC density estimates were influenced by their priors, ranging from 0.95 (0.65–2.95 95% BCI) fishers 100 km−2 for the uninformative model to 3.60 (2.01–7.55 95% BCI) fishers 100 km−2 for the model informed by prior knowledge of a 16 km2 fisher home range. We caution against using strongly informative priors but instead recommend using a range of unweighted prior knowledge. Thin detection data was problematic for both SCR and SC models, potentially producing biased low estimates. The total cost of the genetic survey ($47 610) was two-thirds of the camera trap survey ($77 080), or comparable ($75 746) if genetic sampling effort was increased to include sex and trap-behaviour covariates in SCR models. Density estimation of unmarked populations continues to be a series of trade-offs but as methods improve and integrate, so will our estimates.
Data from: Experimental small-scale flower patches increase species density but not abundance of small urban bees
1. Large flower plantings are often used to combat negative effects of habitat loss on pollinators, but whether these floral additions are effective at smaller scales remains unclear, particularly in urban settings. 2. To test the effectiveness of small-scale floral additions on enhancing urban bee populations, as well as their impact from one year to the next, different quantities of potted sweet alyssum (Lobularia maritima) flowers were placed across sites in Ann Arbor, Michigan for two consecutive years and the resulting Halictid bee visitors were monitored. 3. Overall we found the number of flowers added at the local level was significantly and positively correlated with small Halictid bee abundance and species density in an urban landscape. At smaller flower quantities dynamics were clearly linear, where incremental increases in number of flowers showed significant increases in bee abundance and species density. At larger quantities of floral additions, however, dynamics were nonlinear in that incremental increases in flower quantity had no effect on bee abundance and highly variable effects on bee species density. 4. When comparing the change in small Halictid bee abundance and species density from one year to the next, we found a significant increase in bee species density in the second year of small-scale floral additions, but no significant difference in bee abundance. 5. Synthesis and applications. Our results show that small flower plantings can have positive effects on small bee communities in urban systems even over a short period of time, and therefore confirm that encouraging citizens to plant flowers can be an effective conservation strategy for certain urban pollinator populations. In addition, our finding that smaller flower plantings may have higher impacts on small pollinators than larger plantings suggests resource managers interested in pollinator conservation should consider spreading multiple, smaller floral plantings across the urban landscape, rather than pooling all resources into one large flower patch.29-Nov-2017
Data from: Introducing resprouters to enhance Mediterranean forest resilience: importance of functional traits to select species according to a gradient of pine density
Resprouter species are important for Mediterranean ecosystem resilience, but they are scarce in landscapes dominated by pioneer pines. Sound knowledge of resprouter seedling functional responses and establishment success across different pine habitats would help guide forest restoration efforts. Four broadleaved resprouter species, that is two shrubs – Arbutus unedo and Pistacia terebinthus – and two trees – Fraxinus ornus and Sorbus domestica – were planted under an experimentally created gradient of pine cover from totally open conditions to dense pine cover. Seedling survival and growth were monitored for 5 years. Phenological, physiological and morphological traits were measured to gain insight into the mechanisms of pine–seedling interaction. Interaction outcomes varied according to species identity, pine cover treatment and time. Light-to-moderate pine cover induced greater height growth and little or no effects on diameter and survival of the two trees. Competition was always detected for shrubs, whereas competition and facilitation were noted for trees. Within pine stands, negative interactions increased with tree cover, making dense stands the most limiting. Interactions were only detectable after 2–3 years, but increased in intensity with time. Functional responses to increasing pine cover indicated a seedling strategy of carbon gain optimization in the shade (increased specific leaf area and leaf area, decreased leaf dry matter content), particularly in tree species seedlings. Increasing pine cover induced higher water stress, but lower photochemical stress. The deciduous species had a longer vegetation season under pine canopies, whereas the evergreen shrub Arbutus unedo showed a lower polycyclism rate and flower production. Synthesis and applications. Moderate pine cover facilitates the establishment of deciduous trees at the expense of shrubs. This pattern can be attributed to a higher shade tolerance of the trees than the shrubs combined with a low tolerance of trees to photoinhibition. We therefore recommend using evergreen shrubs for the restoration of open land and high-specific-leaf-area deciduous trees for pine stand diversification. However, in dense forests, thinning is needed to increase light availability prior to seedling introduction.
Modelled 1-km resolution population densities for 49 bird species in the UK between 2007 and 2009
<p>This is a dataset derived from the BTO/JNCC/RSPB Breeding Bird Survey (BBS) used to produce <a href="https://www.bto.org/our-science/projects/breeding-bird-survey/latest-results/maps-population-density-and-trends">modelled maps of population density</a> for 49 bird species at 1-km square resolution across the UK between 2007 and 2009. </p> <p>Acknowledgement: These data may be used subject to the appropriate acknowledgement of the BTO/JNCC/RSPB Breeding Bird Survey. Acknowledgements should be in the form of the most recent BBS Report citation, available <a href="https://www.bto.org/our-work/science/publications/reports/bbs-reports" target="_blank" rel="noopener">online</a>, or as follows: “<em>The BTO/JNCC/RSPB Breeding Bird Survey is a partnership jointly funded by the BTO, RSPB and JNCC, with fieldwork conducted by volunteers.</em>”</p> <p>Please refer to the metadata for a more detailed description, and for information on dataset usage.</p> <p>........................................................................................</p> <p>We would also greatly appreciate if you could fill out <a href="https://forms.gle/DCc58VXpdmqnTmTk8" target="_blank" rel="noopener">this very short form</a> to tell us how you intend to use these data. Thanks in advance!</p>
Density-dependent effects of parasitism on the activity of a benthic engineer species: potential impact on ecosystem functioning
<p>While parasitism is a common lifestyle on Earth, its importance for the functioning of marine ecosystems has been overlooked for a long time. In particular, parasites have significant potential to influence central ecological processes through their impacts on hosts that serve as ecosystem engineers. Using an ex-situ experimental approach, we explored the effects of trematode parasites on the engineering bioturbation activity of a common and abundant bivalve along European Atlantic soft-bottom coastlines, the peppery furrow shell <em>Scrobicularia</em> <em>plana</em>, as well as knock-on effects for nutrient exchanges at the sediment-water interface. Trematodes negatively impacted the host's ability to transport sediment particles and solutes in a density-dependent way with parasite burden explaining 22–31% of the inter-individual variability. This could be explained by parasitism impairing the bivalve physiological state and ability to burrow as we observed a decrease in the condition index and the burrowing depth of the bivalves with an increase in the number of parasites they host. In contrast, the influence of <em>S. plana</em> on benthic biogeochemical fluxes did not vary significantly according to parasitic burden over a short time scale. Here, we focused on the effects of trematode parasites on the sole behaviour of <em>S. plana</em> and thus excluded other macrofaunal organisms. We should next test whether trematodes modulate the structure and functioning of benthic communities dominated by <em>S. plana</em> to better understand and quantify the engineering role of parasites in soft-bottom coastal environments.</p>
FIG. 2 in Density-Dependent Fitness Attributes and Carry-Over Effects in Crawfish Frogs (Rana areolata), a Species of Conservation Concern
FIG. 2. Field data showing effects of juvenile density on juvenile body size (A, C) and time to metamorphosis (E), and breeding adult size (B, D) and survivorship (F). Lines reflect regression calculations. While suggestive, none of these trends is significant except for the adult SVL data shown in B.
Figure 2 in Density, occupancy and detectability of tortoise species (Chelonoidis spp.) in the Atlantic Forest: implications for conservation and management
Figure 2. Relationship between the probability of detection of Chelonoidis denticulatus (A) and Chelonoidis carbonarius (B) with the accumulated rainfall of the day before sampling (previous rainfall) in the Vale Natural Reserve, Brazil.
Figure 1 in Density, occupancy and detectability of tortoise species (Chelonoidis spp.) in the Atlantic Forest: implications for conservation and management
Figure 1. Location of the Vale Natural Reserve, municipality of Linhares, Espírito Santo, south-eastern Brazil, showing the location of the linear transects and the types of vegetation present in the Reserve.
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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.