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799 results for “abundance data”
Data and Code for "Drought Influences Habitat Associations and Abundances of Birds in California's Central Valley"
Open the record for dataset details and reuse information.
Data for Context-dependent biotic interactions control plant abundance across altitudinal environmental gradients, 2014, 2016, Colorado, USA
Many biotic interactions influence community structure, yet most distribution models for plants have focused on plant competition or used only abiotic variables to predict plant abundance. Furthermore, biotic interactions are commonly context-dependent across abiotic gradients. For example, plant-plant interactions can grade from competition to facilitation over temperature gradients. We used a hierarchical Bayesian framework to predict the abundances of 12 plant species across a mountain landscape and test hypotheses on the context-dependency of biotic interactions over abiotic gradients. We combined field-based estimates of six biotic interactions (foliar herbivory and pathogen damage, fungal root colonization, fossorial mammal disturbance, plant cover, and plant diversity) with abiotic data on climate and soil depth, nutrients, and moisture. All biotic interactions were significantly context-dependent along temperature gradients. Results supported the stress gradient hypothesis: As abiotic stress increased, the strength or direction of the relationship between biotic variables and plant abundance generally switched from negative (suggesting suppressed plant abundance) to positive (suggesting facilitation/mutualism). For half of the species, plant cover was the best predictor of abundance, suggesting that the prior focus on plant-plant interactions is well-justified. Explicitly incorporating the context-dependency of biotic interactions generated novel hypotheses about drivers of plant abundance across abiotic gradients and may improve the accuracy of niche models.
Far northeastern Siberia boreal forest data: Coarse woody debris abundance across a larch forest density gradient
This dataset includes coarse woody debris abundance within four larch stands near Cherskii, Siberia collected in 2012-2013. Data have not been published.
Far northeastern Siberia boreal forest data: Fine woody debris abundance across a larch forest density gradient
This dataset includes fine woody debris abundance within four larch stands near Cherskii, Siberia collected in 2012-2013. Data have not been published.
Presence, abundance, and environmental data from 1996 on Celastrus orbiculatus and other exotic plant species in the southern Appalachians, USA
A variety of abiotic, biotic, human and historic variables related to environmental suitability and propagule pressure determine the distribution of invasive plants in a landscape. Understanding the role of these variables for invasive species is challenging because environmental variables are often correlated, many invaders have broad ecological niches, and invasive distributions are often highly dynamic. The researchers examined the role of environmental variables at multiple spatial scales on the distribution of an invasive vine Celastrus orbiculatus (Celastraceae) and other exotic plant species in the southern Appalachians, USA. Data were collected in the Southern Blue Ridge Province of the southern Appalachian Mountains in western North Carolina, USA. This data set includes data on elevation, environmental disturbance, and the presence and abundance of various plant species. The researchers extracted presence and absence data from various sources, including the National Park Service and U.S. Forest Service survey data (NPS/USFS) and Southern Appalachian Volunteer Environmental Monitoring data (SAVEM) (Albright et al. 2009).
Soil microbial activity and abundance data in the rhizosphere and bulk soils of O horizon in the MELNHE study, 2014
The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N and P acquisition and limitation through a series of nutrient manipulations in northern hardwood forests. This data set includes rhizosphere processes and microbial abundance at the Bartlett Experimental Forest. Samples were collected once, in summer 2014, in the forth year of fertilization with N and P. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
MCR LTER: Coral Reef: Pocillopora Abundance, Cover and Recruitment data for Tsounis and Edmunds 2016 Peer J
The dataset contains stony coral cover percent and Pocillopora cover obtained in on the north shore of Moorea in 2010 and 2014/2015 using photoqudrats. A subset of the data were obtained by counting adults and juveniles in situ using quadrats. Recruitment rates were quantified using settlement tiles. These data support the publication Tsounis and Edmunds, The potential for self-seeding by the coral Pocillopora spp. In Moorea, French Polynesia, Peer J, 2016.
Macroinvertebrate trait, abundance and site quality data from the Green Lakes Valley, 2018
This research was conducted to get a sense of the current spatial distribution of benthic macroinvertebrates among various aquatic habitats throughout the Green Lakes Valley. Benthic macroinvertebrates are small organisms that lack a backbone (invertebrate), live on the bottom (benthic), and are visible with the naked eye (macro). To estimate the community structure of benthic macroinvertebrates communities, 53 benthic macroinvertebrate samples were collected over the summer of 2018 from three alpine lakes and two streams in the Green Lakes Valley, CO at multiple points throughout the season. Benthic macroinvertebrates were sampled from the shoreline, inlet (inflow of water), and outlet (outflow of water) of each sampled lake, alongside estimates for habitat quality like surrounding vegetation, temperature (C°), rock volume (L), nitrate (mg/L,) pH, and dissolved oxygen saturation. The methods from this survey are broadly consistent with historic surveys ranging from 1960 to 1987 that have also sought to characterize aquatic invertebrate community composition within the Green Lakes Valley (Bushnell et al. 1987 The Great Basin Naturalist).
Data from: Prey abundance and leopard diet in a plantation and rainforest landscape, Anamalai Hills, Western Ghats
<p>Leopards use a wide range of habitats from natural forests to plantations in human-dominated landscapes. Within interface areas, understanding leopard ecology and diet can help in conservation management and conflict avoidance. In a fragmented rainforest and plantation landscape in southern India, we examined diet of large carnivores (with a focus on leopards) using scat analysis with DNA-based identification of predator species, and estimated relative abundance of prey species in different land uses through transect surveys. Large carnivores predominantly consumed wild prey species (98.1%) and domestic prey species contributed <2% to overall prey biomass. For leopards, four wild prey species (Indian muntjac, Indian spotted chevrotain, sambar and Indian porcupine) contributed 95.1% of prey biomass, with the rest being minor wild prey species (no livestock in identified scats). Wild prey species occurred across the landscape but varied in relative abundance by land-use type, with forest fragments supporting higher abundance of many species relative to tea and coffee plantations. As large carnivores mainly depend on wild prey and rainforest fragments act as refuges for these mammals within the tea and coffee plantations, it is important to continue to retain or restore these forest fragments.</p> <p>This dataset contains abundance data on mammals (large carnivores and their prey species), using direct and indirect sign surveys along line and belt transects, respectively, as well as data on remains of prey species in large carnivore scats. This dataset is part of a study (published paper under Related works) on leopard ecology in a landscape containing commercial plantations of tea and coffee, and rainforest fragments and protected area. These data were collected between 2008 and 2010 in Valparai plateau and Anamalai Tiger Reserve in the Western Ghats, India. The dataset contains following files:</p> <p>1) Transect_details.csv<br> 2) Transect_repeats.csv<br> 3) Mammals_Direct_signs.csv<br> 4) Mammals_Indirect_signs.csv<br> 5) Large_carnivores_Indirect_signs.csv<br> 6) Large_carnivore_Diet.csv</p> <p>More details regarding the above files can be found in ReadMe_Data_ColumnNames.txt.</p> <p><strong>Update, version 2</strong>: Data were updated on 4 May 2020. There was an error in the following file: Large_carnivore_Diet.csv. This file has been corrected and replaced in this update. All other files are correct and therefore not replaced.</p>
Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling
<p>Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport, and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (<em>Trachurus japonicus</em>) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.</p>
Data from: A closer examination of the 'abundant center' hypothesis for reef fishes
<p>Aim: The 'abundant center' hypothesis states that species are more abundant at the center of their range. However, several recent large-scale studies have failed to find evidence for such a pattern. Here we use extensive global data of reef fishes to test the strength of the 'abundant center' pattern, and to examine variation in the patterns across species using life history and ecological traits.</p> <p>Location: Marine habitat at a global extent: from Indo-Pacific to Atlantic reefs.</p> <p>Methods: We used underwater visual estimates of fish abundance, containing 22,963 transects and 1,215 species. For each species we calculated the slope between abundance and distance to the range center, with the range center estimated using four different methods. We tested whether abundance patterns differ between the range core and margins using segmented regression. Meta-analytic methods were used to synthesize results across species, and to test whether species traits can explain variation in the fit to the pattern among species.</p> <p>Results: The method used to define the range center had a large effect on the results. Nevertheless, in all cases we found large variation between species. Results of the segmented regression revealed that changes in abundance across the range core are very small and that steep declines in abundance happen only toward the range margins. Body size and mean abundance were the main traits affecting the fit to the pattern across species.</p> <p>Main conclusions: We find large variation across species in the fit to the abundance center pattern. Nevertheless, we do find support for a general pattern of a range core with high, but variable, abundance and steep decline in abundance toward the range periphery. Thus, species do tend to be rare at the range margins, making then sensitive to extirpation due to both natural and anthropogenic impacts.</p>
Data from: Holocene increases in palm abundances in northwestern Amazonia
Aim: In Amazonia, 227 of ca. 16,000 tree species account for half the individual trees (termed 'hyperdominant' species), and a disproportionate number of these species are palms. Our objectives are to show how and whether palm abundance has changed through the Holocene. Here, we reconstruct a detailed fire and vegetation history from northwestern Amazonia, with a focus on changes in palm abundances, and compare our results with regional data. Location: Amacayacu, Colombia Taxon: Amazonian palms Methods: We performed charcoal and phytolith analysis on soil cores, and obtained ages of past fires using 14C dating. We measured charcoal abundances and the relative abundances of phytoliths (silica-based microfossils) for all samples. We used these data to reconstruct changes in fire and vegetation, and compared these data with the species composition of palms in the modern forest. Results: Seven 14C dates from charcoal in three cores provided fire ages ranging from 1630 to 2450 calibrated years before present. Charcoal was absent from one-third of the cores. Palm phytoliths from genera such as Iriartea, Socratea, and Astrocaryum have increased through time, while genera such as Euterpe, Hyospathe, and Oenocarpus have remained relatively stable and similar to modern levels. Overall, palm abundances were negatively correlated with charcoal measurements. Decorated sphere phytoliths, produced from unknown arboreal taxa were positively correlated with charcoal presence and abundance. Main conclusions: Palms have increased at Amacayacu and other forest plots through time, but the increases are largest in northwestern Amazonia. The presence of fire, however, dampens the increase in palms through time. When compared with reconstructions from other Amazon regions, our results suggest that increases in palm abundances in the late Holocene occurred both in the presence and absence of direct pre-Columbian human influence, and that response was strongest in northwestern Amazonia when human influence was minimal.
Data from: Abundance, survival, and annual rate of change in Cuvier's beaked whales (Ziphius cavirostris) on a Navy sonar range
<p>Bayesian mark-recapture estimates of survival, abundance, and trend are reported for Cuvier's beaked whales (<em>Ziphius cavirostris</em>) using a Navy training range off southern California. The deep-diving beaked whale family is exceptionally vulnerable to mid-frequency active sonar (MFAS), which has been implicated in mass strandings and altered foraging behavior. Extremely low sighting probabilities impede studies of population-level impacts of MFAS on beaked whales. The San Nicolas Basin hosts a Navy training range subject to frequent MFAS use and attracts high densities of <em>Z. cavirostris</em>. An eleven-year (2007–2018) photo-identification program leveraged automated acoustic detection and location capabilities on the range's 1,800-km<sup>2</sup> hydrophone array to enhance capture probability. Estimated population parameters for <em>Z. cavirostris </em>using the range included mean (90% credibility intervals) apparent annual survival of 0.950 (0.899–0.986), the annual number of individuals as 121 (71–219), and the annual rate of change of -0.8% (-5.6 – 4.1%). Simulations show the probability of detecting abundance changes is currently low, but can be greatly improved through continued monitoring and increased effort. Complementary data collection on habitat use and demographic rates in San Nicolas and surrounding basins is also essential to relating the direct effects of MFAS use to changes in vital rates and broader population outcomes.</p>
Data from: Biological controls over the abundances of terrestrial ammonia oxidizers
<blockquote> <p>Aim: Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the primary agents for nitrification, converting ammonia (NH4+) into nitrate (NO3-) and modulating plant nitrogen (N) utilization and terrestrial N retention. However, there is still lack of a unifying framework describing the patterns of global AOA and AOB distribution. In particular, biotic interactions are rarely integrated into any of the conceptual models.<br> Location: World-wide.<br> Time period: 2005-2016.<br> Major taxa studied: Ammonia-oxidizing archaea and ammonia-oxidizing bacteria. <br> Methods: A meta-analysis and synthesis was conducted to obtain a general picture of global AOA and AOB distribution and identify the primary driving factors. A microcosm experiment was then conducted to assess effects of relative carbon to nitrogen availability for heterotrophic microbes on AOA and AOB in two distinct soils. A mesocosm experiment was further carried out to characterize the effects of plant roots and their arbuscular mycorrhizal fungi (AMF) on AOA and AOB abundances using hyphae- or root-ingrowth techniques. <br> Results: Our meta-analysis showed that soil carbon to nitrogen (C/N) ratios explained the most variance in AOA and AOB abundances, although soil pH had a significant effect. Experimental results demonstrated that high cellulose and mineral N inputs increased total microbial biomass and microbial activities, but inhibited AOA and AOB, suggesting microbial inhibition of AOA and AOB. Also, AMF and roots suppressed AOA and AOB, respectively. <br> Main conclusions: Our study provided convincing evidence illustrating that relative carbon to nitrogen availability can dominate the abundances of AOA and AOB. Our experimental results further validated that biotic competitions among plants, heterotrophic microbes and ammonia oxidizers for substrate N predominantly control AOA and AOB abundances. Together, these findings provide new insights into the role of abiotic and biotic factors in modulating terrestrial AOA and AOB abundances and their potential applications for management of nitrification in an increasing reactive N world.</p> </blockquote>
Bird abundance data for the period 2002-2014 from the French Breeding Bird Survey (STOC)
<p>Abundance data on breeding birds from the French Breeding Bird Survey (Suivi Temporel des Oiseaux Communs, STOC), for the period 2002-2014.</p> <p>The dataset comprises 7,115 bird communities. Only 107 common species were included in the study. </p>
Data and Code for: Comparative species abundance modeling of Capitellidae (Annelida) in Tampa Bay, Florida, USA
<p>This publication contains the R-Scripts, RData, data frames, and other supplementary files necessary to reproduce the analyses and figures of Hilliard J, Karlen D, Dix T, Markham S, Schulze A (2020) Comparative species abundance modeling of Capitellidae (Annelida) in Tampa Bay, Florida, USA. Mar Ecol Prog Ser 653:105-119. <a href="https://doi.org/10.3354/meps13484">https://doi.org/10.3354/meps13484</a></p> <p>All files are compressed into a single ZIP folder. The main directory contains a README file that explains the contents of the subdirectories.</p>
Data from: Species abundance fluctuations over 31 years are associated with plant-soil feedback in a species-rich mountain meadow
<p>1. Increasing evidence suggest that plant-soil interactions play an essential role in plant community assembly processes. Empirical investigations show that plant species abundance in the field is often related to plant-soil biota interactions, however, the direction of these relations have yielded inconsistent results.</p> <p>2. We combined unique 31-year long field data on species abundances from a species-rich mountain meadow with single time point plant-soil feedback greenhouse experiments of 24 co-occurring plant species. We tested whether these relations were dynamic in time, whether coupled increases and decreases in abundance between years were related to plant-soil feedback and whether these changes were underlain by years in which manuring was applied.</p> <p>3. The prevailingly negative relationship between plant-soil feedback and plant relative abundance in the field was significantly time-dependent, which may reconcile the contrasting results in literature. Furthermore, significant coupled oscillations appeared between species relative abundance changes and plant-soil feedback, which were likely moderated by years in which manuring was applied. Our results are consistent with the notion that the more abundant species are stabilised by negative plant-soil feedback, and the less abundant species co-vary with the fluctuations of these more competitive species.</p> <p>4. Synthesis: Our results project plant-soil feedback as an important regulatory mechanism in plant communities, operating in conjunction with a species' competitive ability and soil nutrient availability. We suggest that negative feedback is particularly prominent in more abundant plant species that profit from more readily available soil nutrients than less abundant species with positive feedback. Negative plant-soil feedback may thus prevent more abundant plant species from outcompeting less abundant plant species, facilitating stable species co-existence.</p>
Data from: Factors influencing herpetofauna abundance and diversity in a tropical agricultural landscape mosaic
<p>Agricultural intensification and the associated factors, including land transformation, are among the major global threats affecting biodiversity especially herpetofauna. However, little information is available about how different factors shape herpetofauna species assemblages in agricultural landscape at different spatial scales from patch (125 – 250m) to the landscape (500 – 1000m).</p> <p>We assessed the diversity of amphibians and reptiles in areas under low and high degrees of agricultural intensification and explored different factors regulating diversity at different spatial scales using four sampling methods.</p> <p>Diversity and abundance of amphibians varied significantly between the two zones, but not for reptiles. Agricultural intensification Index (AII), calculated based on agrochemical use and area under agriculture at 250m scale, seemed to affect amphibians both at patch as well as at 500m and 1000m landscape scales. The AII influenced reptilian diversity only at patch and 500m scales. Vicinity of natural forest had a stronger influence on reptilian abundance. Semi-natural vegetation impacted herpetofauna diversities at larger spatial scales. The extent of water bodies influenced the reptilian abundance at 250m patch scale and amphibian abundance both at 250m and 1000m scale. Fallow lands affected only reptilian diversity at all spatial scales. Plantation affected amphibian at all scales but reptiles only at the landscape scale. Habitat heterogeneity regulated only amphibian diversity.</p> <p>These results highlight the fact that different patch and landscape-scale factors regulate the diversity of reptiles and amphibians differentially. Such scale specific information will crucially inform future conservation action for the herpetofauna in the agricultural landscape.</p>
Data from: Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements
Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space, and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N-mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations.
Data from: From forest to city: Urbanization modulates relative abundance of anti-predator coloration
Increased urbanization has resulted in community changes including alteration of predator communities. Little is known, however, about how such changes affect morphological anti-predator traits. Given the importance of coloration in predator avoidance, this trait in particular is expected to be susceptible to novel selective environments in urban areas. Here we investigate the coloration pattern of a Neotropical anuran species, the túngara frog (Engystomops pustulosus), along an urbanization gradient. Túngara frogs have two distinct color patterns (unstriped and striped) which we found to occur at different frequencies along an urbanization gradient. Striped individuals increased in frequency with urbanization. To assess the strength of selection imposed by predators on the two color morphs, we deployed clay models of túngara frogs in forest and semi-urban populations. In addition, we examined microhabitat selection by individuals of the different morphs. We found higher predation rates associated with urbanization than forested areas. In particular, frogs from forested habitats had lower number of attacks by avian predators. Contrary to our predictions, however, predation rates were similar for both color morphs independent of urbanization. Also, coloration of the frogs did not affect their microhabitat preference. Overall, túngara frogs are more likely to have a striped coloration pattern in semi-urban areas where predation by birds is higher than in the forest. Our findings suggest that factors other than predation pressure shape the coloration pattern of urban frogs and emphasize the complex nature of effects that anthropogenic changes in habitat and predator communities may have on prey morphology.
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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.