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53 results for “ecological methods”
Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods
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A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions
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A practical approach to measuring the acoustic diversity by community ecology methods
<p>The study of the diversity of animal signals on within- and among-species levels is the key to uncover mechanisms that shape the evolution of communication systems. However, the methods used to quantify acoustic diversity (like repertoire size) lack to grasp several aspects of acoustic diversity. Here, we propose a new framework for the study of animal communication, in which we decompose the acoustic diversity with the methodological toolbox from community ecology.</p> <p>We explore how different diversity estimates reflecting different aspects of acoustic diversity can be applied to characterise the complexity of acoustic signals. We propose that this approach can be used in a wide range of animal taxa to derive further insights about the function and evolution of communication systems besides the traditional methods.</p> <p>To illustrate the use of our approach in a case study, we used the song of collared flycatcher (<em>Ficedula albicollis)</em> as a model system. Based on three frequency and time variables, we calculated three diversity indies (FRic, FEve, and FDiv) to characterise the distribution of song elements (syllables) in the acoustic parameter space. We aimed to uncover the interrelations of diversity indices, reveal the degree of among-individual consistency, and investigate their relationships with certain aspects of individual quality.</p> <p>We found that the chosen diversity indices were largely independent from each other and showed different consistency patterns that were timescale dependent indicating different signalling potential of individual-specific attributes. We also found that FEve strongly related to the age of males. Our case study showed that decomposing the diversity into different components can reveal additional biologically meaningful aspects of birdsong.</p>
Data from: Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity
1. Natural communities commonly contain many different species and functional groups, and multiple types of species interactions act simultaneously, such as competition, predation, commensalism or mutualism. However, experimental and theoretical investigations have generally been limited by focusing on one type of interaction at a time or by a lack of a common methodological and conceptual approach to measure species interactions. 2. We compared four methods to measure and express species interactions. These approaches are, with increasing degree of model complexity, an extinction-based model, a relative yield model and two generalized Lotka-Volterra (LV) models. All four approaches have been individually applied in different fields of community ecology, but rarely integrated. We provide an overview of the definitions, assumptions and data needed for the specific methods and apply them to empirical data by experimentally deriving the interaction matrices among 11 protist and rotifer species, belonging to three functional groups. Furthermore, we compare their advantages and limitations to predict multispecies community dynamics and ecosystem functioning. 3. The relative yield method is, in terms of final biomass production, the best method in predicting the 11-species community dynamics from the pairwise competition experiments. The LV model, which is considering equilibrium among the species, suffers from experimental constraints given the strict equilibrium assumption, and this may be rarely satisfied in ecological communities. 4. We show how simulations of a LV stochastic community model, derived from an empirical interaction matrix, can be used to predict multispecies community dynamics across multiple functional groups. 5. Our work unites available tools to measure species interactions under one framework. This improves our ability to make management-oriented predictions of species coexistence/extinction and to compare ecosystem processes across study systems.
Congruence of local ecological knowledge (LEK)-based methods and line-transect surveys in estimating wildlife abundance in Amazonian forests
<p>1) Effective estimation of wildlife population abundance is an important component of population monitoring, and ultimately essential for the development of conservation actions. Diurnal line transect surveys are one of the most applied methods for abundance estimations. Local ecological knowledge (LEK) is empirically acquired through the observation of ecological processes by local people. LEK-based methods have only been recognized as valid scientific methods for surveying fauna abundance in the last three decades. However, the agreement between both methods has not been extensively analysed.</p> <p>2) We compared concomitant abundance data for 91 wild species (mammals, birds and tortoises) from diurnal line transects (9,221 km of trails) and a LEK-based method (291 structured interviews) at 18 sites in Central and Western Amazonia. We used biological and socioecological factors to assess the agreements and divergences between abundance indices obtained from both methods.</p> <p>3) We found a significant agreement of population abundance indices for diurnal and game species. This relationship was also positive regardless of species sociality (solitary or social), body size and locomotion mode (terrestrial and arboreal); and of sampled forest type (upland and flooded forests). Conversely, we did not find significant abundance covariances for nocturnal and non-game species. Despite the general agreement between methods, line transects were not effective at surveying many species occurring in the area, with 40.2% and 39.8% of all species being rarely and never detected in at least one of the survey sites. On the other hand, these species were widely reported by local informants to occur at intermediate to high abundances.</p> <p>4) Although LEK-based methods have been long neglected by ecologists, our comparative study demonstrated their effectiveness for estimating vertebrate abundance of a wide diversity of taxa and forest environments. This can be used simultaneously with line transects surveys to calibrate abundance estimates and record species that are rarely sighted during surveys on foot, but that are often observed by local people during their daily extractive activities. Thus, the combination of local and scientific knowledge is a potential tool to improve our knowledge of tropical forest species and foster the development of effective strategies to meet biodiversity conservation goals. --</p>
Data from: A novel integrative method for measuring body condition in ecological studies based on physiological dysregulation
1. The body condition of free-ranging animals affects their response to stress, decisions, ability to fulfil vital needs and, ultimately, fitness. However, this key attribute in ecology remains difficult to assess, and there is a clear need for more integrative measures than the common univariate proxies. 2. We propose a systems biology approach that positions individuals along a gradient from a 'normal/optimal' to 'abnormal/suboptimal' physiological state based on Mahalanobis distance computed from physiological biomarkers. We previously demonstrated the validity of this approach for studying ageing in humans; here, we illustrate its broad potential for ecological studies. 3. As an example, we used biomarker data on shorebirds and found that birds with an abnormal condition had a lower maximal thermogenic capacity and higher scores of inflammation, with important implications for their ecology and health. Moreover, Mahalanobis distance captured a signal of condition not detected by the individual biomarkers. 4. Overall, our results on birds and humans show that individuals with abnormal physiologies are indeed in worse condition. Moreover, our approach appears not to be particularly sensitive to which set of biomarkers is used to assess condition. Consequently, it could be applied easily to existing ecological data sets. 5. Our approach provides a general, powerful way to measure condition that helps resolve confusion as to how to deal with complex interactions and interdependence among multiple physiological and condition measures. It can be applied directly to topics such as the effect of environmental quality on body condition, risks of health outcomes, mechanisms of adaptive phenotypic plasticity, and mechanisms behind long-term processes such as senescence.
Data and R Code from "PAT-GEOM: A Software Package for the Analysis of Animal Patterns" (published in Methods in Ecology and Evolution)
<p>Datasets for Figures 2 and 4 in the article "PAT-GEOM: A Software Package for the Analysis of Animal Patterns" (published in Methods in Ecology and Evolution) and the R code used to perform the analysis described in the article.</p>
Data from: Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity
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Congruence of local ecological knowledge (LEK)-based methods and line-transect surveys in estimating wildlife abundance in Amazonian forests
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Data from: Diet tracing in ecology: method comparison and selection
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A practical approach to measuring the acoustic diversity by community ecology methods
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Data from: A novel integrative method for measuring body condition in ecological studies based on physiological dysregulation
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Data from: Methods for normalizing microbiome data: an ecological perspective
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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.