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10 results for “ecological methodology”
Diagramms and Figures for a Bachelor Thesis: "Morphological Diversity of Bryophytes: Methodological Approaches and Ecological Implications"
<p>This depository holds all diagramms and figures that were created with the collected data used in the Bachelor's Thesis using R Version 4.4.0 or Python Version 3.12.4. <br><br></p>
Ecology and methodology of comparing traits and decomposition rates of green leaves versus senesced litter across plant species and types
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Protein quantification in ecological studies: a literature review and empirical comparisons of standard methodologies
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Datasets from the publication "Delineating the geographic context of physical activities: A systematic search and scoping review of the methodological approaches used in social ecological research over two decades"
<p>Data from research article Rinne, T., Kajosaari, A., Söderholm, M., Berg, B., Pesola, A.J., Smith, M., Kyttä, M. (2022). Delineating the geographic context of physical activities: A systematic search and scoping review of the methodological approaches used in social ecological research over two decades, <em>Health and Place</em>.</p> <p>This data includes supplementary materials 1, 2, 3 and 4, PRISMA checklist and a translated research protocol.</p>
Data from: Divergent estimates of herd-wide caribou calf survival: ecological factors and methodological biases
Population monitoring is a critical part of effective wildlife management, but methods are prone to biases that can hinder our ability to accurately track changes in populations through time. Calf survival plays an important role in ungulate population dynamics and can be monitored using telemetry and herd composition surveys. These methods, however, are susceptible to unrepresentative sampling and violations of the assumption of equal detectability, respectively. Here we capitalized on 55 herd-wide estimates of woodland caribou (Rangifer tarandus caribou) calf survival in Newfoundland, Canada using telemetry (n = 1,175 calves) and 252 herd-wide estimates of calf:cow ratios (C:C) using herd composition surveys to investigate these potential biases. These data included 17 herd-wide estimates replicated from both methods concurrently (n = 448 calves and n =17 surveys) which we used to understand which processes and sampling biases contributed to disagreement between estimates of herd-wide calf survival. We used Cox proportional hazards models to determine if estimates of calf mortality risk were biased by the date a calf was collared. We also used linear mixed effects models to determine if estimates of C:C ratios were biased by survey date and herd size. We found that calves collared later in the calving season had a higher mortality risk and that C:C tended to be higher for surveys conducted later in the autumn. When we used these relationships to modify estimates of herd-wide calf survival derived from telemetry and herd composition surveys concurrently, we found that formerly disparate estimates of woodland caribou calf survival now overlapped (within a 95% confidence interval) in a majority of cases. Our case study highlights the potential of under-appreciated biases to impact our understanding of population dynamics and suggests ways that managers can limit the influence of these biases in the two widely applied methods for estimating herd-wide survival.
Data from: Divergent estimates of herd-wide caribou calf survival: ecological factors and methodological biases
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Combining biogeographic approaches to advance invasion ecology and methodology
<p>1) Understanding the causes of plant invasions requires that parallel field studies are conducted in the native and introduced ranges to elucidate how biogeographic shifts alter the individual performance, population success, and community-level impacts of invading plants. Three primary methods deployed in in situ biogeographic studies are directed surveys, where researchers seek out populations of target species, randomized surveys, and field experiments. Despite the importance of these approaches for advancing biogeographic research, their relative merits have not been evaluated.</p> <p>2) We concurrently deployed directed surveys, randomized surveys, and in situ field experiments for studying six grassland plant species in the native and introduced ranges. Metrics included plant size, fecundity, recruitment, abundance, and invader impact, as well as soil properties and root associations with putative fungal mutualists and pathogens.</p> <p>3) Consistent with key invasion hypotheses, Bromus tectorum experienced increased size and fecundity in the introduced range linked to population increases and significant invader impacts, along with altered fungal associations. However, performance differences did not predict population increases and invader impacts across species. Rather, the differential effect of disturbance in facilitating greater recruitment in the introduced range appeared to play a crucial, though previously underexplored, role in driving invader success.</p> <p>4) Directed surveys consistently generated information on plant performance and fungal associations. However, soil sampling suggested that directed surveys may have been biased toward disturbed conditions for half the species. Randomized surveys generated robust data for population comparisons and impact, but generally failed to produce performance metrics for species that were uncommon or flowered outside the peak sampling window. Field experiments controlled for bias and confounding factors and provided rare information on recruitment and disturbance effects, but scant recruitment in the native range and ethical constraints on growing invaders in the introduced range limited information on performance and plant-fungal interactions.</p> <p>5) Synthesis. Each method had strengths and weaknesses. However, when combined they provided complementary information to paint the most complete biogeographic picture to date for several introduced plants. We propose a hybrid approach to optimize biogeographic studies.</p>
Combining biogeographic approaches to advance invasion ecology and methodology
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Data from: From environmental DNA sequences to ecological conclusions: how strong is the influence of methodological choices?
Aim: Environmental DNA (eDNA) is increasingly used for analysing and modelling all-inclusive biodiversity patterns. However, the reliability of eDNA-based diversity estimates is commonly compromised by arbitrary decisions for curating the data from molecular artefacts. Here, we test the sensitivity of common ecological analyses to these curation steps, and identify the crucial ones to draw sound ecological conclusions. Location : Valloire, French Alps. Taxon: Vascular plants and Fungi. Methods: Using soil eDNA metabarcoding data for plants and fungi from twenty plots sampled along a 1000-m elevation gradient, we tested how the conclusions from three types of ecological analyses: (i) the spatial partitioning of diversity, (ii) the diversity-environment relationship, and (iii) the distance-decay relationship, are robust to data curation steps. Since eDNA metabarcoding data also comprise erroneous sequences with low frequencies, diversity estimates were further calculated using abundance-based Hill numbers, which penalize rare sequences through a scaling parameter, namely the order of diversity q (Richness with q=0, Shannon diversity with q~1, Simpson diversity with q=2). Results: We showed that results from different ecological analyses had varying degrees of sensitivity to data curation strategies and that the use of Shannon and Simpson diversities led to more reliable results. We demonstrated that MOTU clustering, removal of PCR errors and of cross-sample contaminations had major impacts on ecological analyses. Main conclusions: In the Era of Big Data, eDNA metabarcoding is going to be one of the major tools to describe, model and predict biodiversity in space and time. However, ignoring crucial data curation steps will impede the robustness of several ecological conclusions. Here, we propose a roadmap of crucial curation steps for different types of ecological analyses.
Data from: From environmental DNA sequences to ecological conclusions: how strong is the influence of methodological choices?
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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.