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59 results for “ecological indicators”
Data from: Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia
<p>1. Curbing habitat loss, reducing fragmentation, and restoring connectivity are frequent concerns of conservation planning. In this respect, the incorporation of spatial constraints, fragmentation, and connectivity indices into optimization procedures is an important challenge for improving decision support.</p> <p>2. Here we present a novel optimization approach developed to accurately represent a broad range of conservation planning questions with spatial constraints and landscape indices. Relying on constraint programming, a technique from artificial intelligence based on automatic reasoning, this approach provides both constraint satisfaction and optimality guarantees.</p> <p>3. We applied this approach in a real case study to support managers of the ``Côte Oubliée -- `Woen Vùù -- Pwa Pereeù'' provincial park project, in the biodiversity hotspot of New Caledonia. Under budget, accessibility, and equitable allocation constraints, we identified restorable areas optimal for reducing forest fragmentation and improving inter-patch structural connectivity, respectively measured with the effective mesh size and the integral index of connectivity.</p> <p>4. Synthesis and applications. Our work contributes to more effective and policy-relevant conservation planning by providing a spatially-explicit and problem-focused optimization approach. By allowing an exact representation of spatial constraints and landscape indices, it can address new questions and ensure whether the solutions will be socio-economically feasible, through optimality and satisfiability guarantees. Our approach is generic and flexible, thus applicable to a wide range of conservation planning problems such as ecological restoration planning, reserve or corridor design.</p>
Data supplementing the article "Assessing ecological status with diatoms DNA metabarcoding : scaling-up on a WFD monitoring network (Mayotte island, France)" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal
<p>These data supplement the article"Assessing ecological status with DNA metabarcoding or microscopy? Comparison using benthic diatoms in tropical rivers" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal.</p> <p>The directory contains the following files:</p> <p><strong>80 PGM sequencing libraries (raw data, fastq files).rar </strong>- contains the 80 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>80 fastq files information.xlsx</strong> - contains the information relative to the 80 samples including: the ID used in Mothur analyses (corresponding to the name of the fastq files), the sample name, the sampling site code, the name of the river, the monitoring network to which rivers belong, the year of sampling and the GPS coordinates of sampling sites.</p> <p><strong>OTU (95 percent of similarity) list of 80 Mayotte samples.xlsx</strong> - contains the final OTU list obtained after applying all the bioinformatics treatments (trimming, clustering,...): OTUs created at 95% of similarity, the number of DNA reads per sample was normalized at 5710 reads (the smallest values obtained in one sample). A DNA representative sequence and the taxonomic assignment determined using Mothur (using classify.otu command) are also provided for each OTU.</p>
Dataset: 'Protected Designations of Origin' (PDO) per NUTS-3 regions plus PDO-scores and social-ecological indicators (v2)
<p>The dataset contains the original research data belonging to the research article "EU-wide mapping of ‘Protected Designations of Origin’ food products (PDOs) reveals correlations with social-ecological landscape values" (Flinzberger et al. 2022: <a href="https://doi.org/10.1007/s13593-022-00778-4">https://doi.org/10.1007/s13593-022-00778-4</a>).</p> <p>Based on the mapping of 638 food products registered within the EU as 'Protected Designation of Origin' (PDO), the first excel file <em>"EU28_all_PDO_products_per_NUTS3.xlsx"</em> shows the distribution of PDO-labeled products across the EU28 NUTS-3 regions. All NUTS-3 regions are listed once for each PDO product they contain (as by 30 June 2020).</p> <p>The second excel file <em>"PDO_scores_and_social_ecological_indicator_data.xlsx"</em> includes the accumulated numbers of PDOs per NUTS-3 region (called PDO score) as registered by 30 June 2020. The PDO score is presented for all food products combined, and for four major food categories separately. Further, the excel file contains all aggregated values of social-ecological indicators (including their sources), used for the correlation analysis between PDO scores and social-ecological characteristics in the above-mentioned article.</p> <p>Code explanations (meta data) can be found on the second sheet of each excel file.</p> <p>- - - </p> <p>second file updated to v2</p>
Crickets as indicators of ecological succession in tropical
<p>Cricket (Ensifera, Grylloidea) are not commonly used as ecological indicators in contrary to other Orthoptera (e.g. grasshoppers and katydids). However, they are sensitive to environmental changes and abundant in tropical regions. To evaluate if crickets are relevant bioindicators of tropical ecosystems, we investigated cricket assemblages along a tropical ecological gradient. We collected crickets during both day and night in southern New Caledonia for three stages of an ecological succession: open shrubland, preforest and forest. Simultaneously, we measured several environmental variables, such as temperature and relative humidity, at each sampling site. Cricket species assemblages showed a clear response to ecological succession. The highest and lowest species richness and abundances of individuals were respectively found in forest and shrubland, with species specialized in each ecological stage revealing the conservation value of each of these stages. Similar results were found when considering only the part of cricket communities with ability to acoustically communicate. This work is part of a larger research program about Neocaledonian crickets and contributes to support the use of acoustic approaches to monitor tropical environments. In conclusion, these findings highlight the potential value of crickets as an environmental indicator in tropical ecosystems. The results also contribute to the discussion of the intrinsic conservational value of shrublands in New Caledonia and similar ecotypes.</p>
Data supplementing the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal
<p>These data supplement the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal.</p> <p>The directory contains the following files:</p> <p><strong>464_samples_fastq_files_(mothur).rar </strong>- contains the 464 fastq files proceed together during the Mothur bioinformatics treatments to produce the OTUs and ISUs tables. As the contig and the demultiplexing steps were performed by the sequencing platform, there is 1 fastq file per sample. From this 464 samples OTU/ISU tables, only information regarding 76 samples were used in this study and are listed in the "<strong>76_samples_list_(mothur).xlsx" </strong>file<strong>.</strong></p> <p><strong>76_samples_list_(mothur).xlsx </strong>- contains the information regarding the 76 samples used to create the OTUs and ISUs tables presented in the paper.</p> <p><strong>76_samples_R1_R2_fastq_files(DADA2).rar - </strong>contains the raw demultiplexed fastq files (R1.fastq and R2.fastq) for each of the 76 samples used in this study to produce the ESVs table using the DADA2 bioinformatics pipeline.</p>
Clear Aligner Cleaning: Brushing, Chlorhexidine, and BlueM Effects on Oral Microbial Ecology and Periodontal Indices
ClinicalTrials.gov study NCT07307716. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Crickets as indicators of ecological succession in tropical
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Data from: Empirical evidence for the ecological significance of interaction network indices within a mutualistic network
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Data from: Bryophyte community composition and diversity are indicators of hydrochemical and ecological gradients in temperate kettle hole mires in Ohio, USA
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Data from: The role of wild bees and cavity-nesting wasps as ecological indicators of the last traditionally managed meadows in Eastern Europe
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Data from: Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia
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Utility of acoustic indices for ecological monitoring in complex sonic environments
<p>Abstract</p> <p>With the continued adoption of passive acoustic monitoring as a tool for rapid and high-resolution ecosystem monitoring, ecologists are increasingly making use of a suite of acoustic indices to summarise the sonic environment. Though these indices are often reported to well represent some aspect of the biology of an ecosystem, the degree to which they are confounded by various extraneous sonic conditions is largely unknown. We conducted an aural inventory across 23 field sites in Okinawa to identify the number of unique animal sounds present in recordings. Using these values of ‘measured richness’, we then examined how the performance of 11 commonly-used acoustic indices varied across a range of sonic conditions (including in the presence and absence of insect stridulations, audible wind or rain, and human-related sounds). Our analysis identified both well- and poor-performing acoustic indices, as well as those that were particularly sensitive to sonic conditions. Only two indices reflected measured richness across the full range of sonic conditions examined. A few indices were relatively insensitive to extraneous sonic conditions, but no index correlated with measured richness when masked by sound from broadband stridulating insects. Our results demonstrate considerable sensitivity of most commonly used acoustic indices to confounding sonic conditions, highlighting the challenges of working with large acoustic datasets collected in the field. We make practical recommendations for acoustic index use based on study design, with the aim of identifying the suite of acoustic indices with greatest utility as indicators for rapid biodiversity monitoring and management of the world’s natural soundscapes.</p> <p>Methods</p> <p>The dataset contains the names of audio files collected across 23 field sites between April 2017 and January 2018 as part of the OKEON-Churamori project on the island of Okinawa, Japan. We conducted an aural inventory, manually counting and recording the number of unique biotic sounds (approximately corresponding to species richness) and noting the presence or absence of three potentially confounding sonic conditions: audible geophony (wind, rain etc.), anthropophony (human-related sounds), and broadband sounds produced by stridulating insect (e.g. cicadas, orthopterans). We then calculated 11 commonly used acoustic indices from the literature and compared their performance (correlation with richness) in the presence vs absence of each sonic condition. Our dataset also contains time and date information for each recording, and the mean site-level richness (i.e. across multiple recordings) for each site and for each unique site-by-season combination. See Table A2 and Methods section in the associated manuscript for details on data processing and the calculation of acoustic indices.</p> <p>Usage notes</p> <p>See readme file for descriptions of data table structure.</p>
Acoustic indices perform better when applied at ecologically meaningful time and frequency scales
Abstract: 1. Acoustic indices are increasingly employed in the analysis of soundscapes to ascertain biodiversity value. However, conflicting results and lack of consensus on best practices for their usage has hindered their application in conservation and land-use management contexts. Here we propose that the sensitivity of acoustic indices to ecological change and fidelity of acoustic indices to ecological communities are severely impacted by signal masking. Signal masking can occur when acoustic responses sensitive to the effect being monitored are masked by less sensitive acoustic groups, or target taxa sonification is masked by non-target noise. We argue that by calculating acoustic indices at ecologically appropriate time and frequency bins, masking effects can be reduced and the efficacy of indices increased. 2. We test this on a large acoustic dataset collected in Eastern Amazonia spanning a disturbance gradient including undisturbed, logged, burned, logged-and-burned, and secondary forests. We calculated values for two acoustic indices: the Acoustic Complexity Index and the Bioacoustic Index, across the entire frequency spectrum (0-22.1 kHz), and four narrower subsets of the frequency spectrum; at dawn, day, dusk and night. 3. We show that signal masking has a large impact on the sensitivity of acoustic indices to forest disturbance classes. Calculating acoustic indices at a range of narrower time-frequency bins substantially increases the classification accuracy of forest classes by random forest models. Furthermore, signal masking led to highly misleading correlations, including spurious inverse correlations, between biodiversity indicator metrics and acoustic index values compared to correlations derived from manual sampling of the audio data. 4. Consequently, we recommend that acoustic indices are calculated either at a range of time and frequency bins, or at a single narrow bin, predetermined by a priori ecological understanding of the soundscape.
Data from: Latitudinal variation in ecological opportunity and intraspecific competition indicates differences in niche variability and diet specialization of Arctic marine predators
Individual specialization (IS), where individuals within populations irrespective of age, sex, and body size are either specialized or generalized in terms of resource use, has implications on ecological niches and food web structure. Niche size and degree of IS of near-top trophic-level marine predators have been little studied in polar regions or with latitude. We quantified the large-scale latitudinal variation of population- and individual-level niche size and IS in ringed seals (Pusa hispida) and beluga whales (Delphinapterus leucas) using stable carbon and nitrogen isotope analysis on 379 paired ringed seal liver and muscle samples and 124 paired beluga skin and muscle samples from eight locations ranging from the low to high Arctic. We characterized both within- and between-individual variation in predator niche size at each location as well as accounting for spatial differences in the isotopic ranges of potential prey. Total isotopic niche width (TINW) for populations of ringed seals and beluga decreased with increasing latitude. Higher TINW values were associated with greater ecological opportunity (i.e., prey diversity) in the prey fish community which mainly consists of Capelin (Mallotus villosus) and Sand lance (Ammodytes sp.) at lower latitudes and Arctic cod (Boreogadus saida) at high latitudes. In beluga, their dietary consistency between tissues also known as the within-individual component (WIC) increased in a near 1:1 ratio with TINW (slope = 0.84), suggesting dietary generalization, whereas the slope (0.18) of WIC relative to TINW in ringed seals indicated a high degree of individual specialization in ringed seal populations with higher TINWs. Our findings highlight the differences in TINW and level of IS for ringed seals and beluga relative to latitude as a likely response to large-scale spatial variation in ecological opportunity, suggesting species-specific variation in dietary plasticity to spatial differences in prey resources and environmental conditions in a rapidly changing ecosystem.
Data from: Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage
Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614–622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.
Data from: At least some meiofaunal species are not everywhere. Indication of geographic, ecological and geological barriers affecting the dispersion of species of Ototyphlonemertes (Nemertea, Hoplonemertea)
Most meiofaunal species are known to have a broad distribution with no apparent barriers to their dispersion. However, different morphological and/or molecular methods supported patterns of diversity and distribution that may be different among taxa while also conflicting within the same group. We accurately assessed the patterns of geographic distribution in actual genetic species of a marine meiofaunal animal model: Ototyphlonemertes. Specimens were collected from several sites around Europe, Northern and Central America, Southern America, Pacific Islands and Asia. We sequenced regions of two mitochondrial and two nuclear genes. Using single-gene, a concatenated data set, multilocus approaches and different DNA taxonomy methods, we disentangled the actual diversity and the spatial structures of haplotypes and tested the possible correlation between genetic diversity and geographic distance. The results show (i) the importance of using several genes to uncover both diversity and highlight phylogeographic relationships among species and that (ii) independent genetic evolutionary entities have a narrower distribution than morphological species. Moreover, (iii) a Mantel test supported a positive correlation between genetic and geographical distance. By sampling from the two sides of Isthmus of Panama, we were additionally able to identify lineage divergence times that are concordant with vicariance mechanisms caused by the geological closure of the seaway across the Isthmus. We therefore propose that in addition to distance, other geological and ecological conditions are also barriers to the dispersion of and gene flow in marine meiofaunal organisms.
Data from: Ants as ecological indicators of rainforest restoration: community convergence and the development of an Ant Forest Indicator Index in the Australian wet tropics
Ecosystem restoration can help reverse biodiversity loss, but whether faunal communities of forests undergoing restoration converge with those of primary forest over time remains contentious. There is a need to develop faunal indicators of restoration success that more comprehensively reflect changes in biodiversity and ecosystem function. Ants are an ecologically dominant faunal group and are widely advocated as ecological indicators. We examine ant species and functional group responses on a chronosequence of rainforest restoration in northern Australia, and develop a novel method for selecting and using indicator species. Four sampling techniques were used to survey ants at 48 sites, from grassland, through various ages (1–24 years) of restoration plantings, to mature forest. From principal components analysis of seven vegetation metrics, we derived a Forest Development Index (FDI) of vegetation change along the chronosequence. A novel Ant Forest Indicator Index (AFII), based on the occurrences of ten key indicator species associated with either grassland or mature forest, was used to assess ant community change with forest restoration. Grasslands and mature forests supported compositionally distinct ant communities at both species and functional levels. The AFII was strongly correlated with forest development (FDI). At forest restoration sites older than 5–10 years that had a relatively closed canopy, ant communities converged on those of mature rainforest, indicating a promising restoration trajectory for fauna as well as plants. Our findings reinforce the utility of ants as ecological indicators and emphasize the importance of restoration methods that achieve rapid closed-canopy conditions. The novel AFII assessed restoration status from diverse and patchily distributed species, closely tracking ant community succession using comprehensive species-level data. It has wide applicability for assessing forest restoration in a way that is relatively independent of sampling methodology and intensity, and without a need for new comparative data from reference sites.
Replication package of the Paper "On the Relationships between the Initial Ecology Indicators of OSS Projects and Their Long-Term Popularity: An Exploratory Study on GitHub"
<p>The dataset is collected from GitHub API and GitHub GHTorrent dataset. A brief description of each folder is provided below:</p> <p><strong>1. "Dataset_and_Code" folder</strong></p> <p>Contains the final dataset and algorithms</p> <p><strong>2. "Test_parameters" folders </strong></p> <p>Includes datasets under different parameters and the corresponding reproduction code, which corresponds to the first experiment of RQ1</p> <p><strong>3. "Compare_baseline"folder</strong></p> <p>Includes the dataset used by our method, the dataset used by the baseline method, and the reproduction code, corresponding to the second experiment of RQ1</p> <p><strong>4. "PLS" folder</strong></p> <p>Includes the dataset used by PLS and the corresponding reproduction code, which corresponds to experiment of RQ2</p> <p><strong>5. " Indicator_Calculation " folder</strong><br>It contains the calculation methods for various metrics in the paper, as well as the corresponding key files. </p> <p><span><strong>6. " Appendix " folder</strong><br></span><span>It includes supplementary materials such as the methodology for metric calculations to address the reviewers' questions.</span> </p> <p><strong>Note</strong></p> <p>We have provided a corresponding README file in each folder to help others reproduce our results</p>
Data from: Oceanographic currents and local ecological knowledge indicate, and genetics does not refute, a contemporary pattern of larval dispersal for the ornate spiny lobster, Panulirus ornatus in the South-East Asian archipelago
Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.
Data from: Parentage analysis of Ansell's mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal
To better understand evolutionary pathways leading to eusociality, interspecific comparisons are needed, which would use a common axis, such as that of reproductive skew, to array species. African mole-rats (Bathyergidae, Rodentia) provide an outstanding model of social evolution because of a wide range of social organizations within a single family; however, their reproductive skew is difficult to estimate, due to their cryptic lifestyle. A maximum skew could theoretically be reached in groups where reproduction is monopolized by a stable breeding pair, but the value could be decreased by breeding-male and breeding-female turnover, shared reproduction and extra-group mating. The frequency of such events should be higher in species or populations inhabiting mesic environments with relaxed ecological constraints on dispersal. To test this prediction, we studied patterns of parentage and relatedness within 16 groups of Ansell's mole-rat (Fukomys anselli) in mesic miombo woodland. Contrary to expectation, there was no shared reproduction (more than one breeder of a particular sex) within the studied groups, and proportion of immigrants and offspring not assigned to current breeding males was low. The within-group parentage and relatedness patterns observed resemble arid populations of 'eusocial' Fukomys damarensis, rather than a mesic population of 'social' Cryptomys hottentotus. As a possible explanation, we propose that the extent ecological conditions affect reproductive skew may be markedly affected by life history and natural history traits of the particular species and genera.
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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.