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403 results for “occurrence data”
Data from: Occurrence-habitat mismatching and niche truncation when modelling distributions affected by anthropogenic range contractions
<p><strong>Aims: </strong>Human-induced pressures such as deforestation cause anthropogenic range contractions (ARCs). Such contractions present dynamic distributions that may engender data misrepresentations within species distribution models. The temporal bias of occurrence data—where occurrences represent distributions before (past bias) or after (recent bias) ARCs—underpins these data misrepresentations. Occurrence-habitat mismatching results when occurrences sampled before contractions are modelled with contemporary anthropogenic variables; niche truncation results when occurrences sampled after contractions are modelled without anthropogenic variables. Our understanding of their independent and interactive effects on model performance remains incomplete but is vital for developing good modelling protocols. Through a virtual ecologist approach, we demonstrate how these data misrepresentations manifest and investigate their effects on model performance.</p> <p><strong>Location:</strong> Virtual Southeast Asia</p> <p><strong>Methods:</strong> Using 100 virtual species, we simulated ARCs with 100-year land-use data and generated temporally biased (past, recent) occurrence datasets. We modelled datasets with and without a contemporary land-use variable (conventional modelling protocols) and with a temporally dynamic land-use variable. We evaluated each model's ability to predict historical and contemporary distributions.</p> <p><strong>Results:</strong> Greater ARC resulted in greater occurrence-habitat mismatching for datasets with past bias and greater niche truncation for datasets with recent bias. Occurrence-habitat mismatching prevented models with the contemporary land-use variable from predicting anthropogenic-related absences, causing overpredictions of contemporary distributions. Although niche truncation caused underpredictions of historical distributions (environmentally suitable habitats), incorporating the contemporary land-use variable resolved these underpredictions, even when mismatching occurred. Models with the temporally dynamic land-use variable consistently outperformed models without.</p> <p><strong>Main conclusions:</strong> We showed how these data misrepresentations can degrade model performance, undermining their use for empirical research and conservation science. Given the ubiquity of anthropogenic range contractions, these data misrepresentations are likely inherent to most datasets. Therefore, we present a three-step strategy for handling data misrepresentations: maximise the temporal range of anthropogenic predictors, exclude mismatched occurrences, and test for residual data misrepresentations.</p>
The occurrence data of Ageratina adenophora in China and Mexico
<p><strong><span>Aim:</span></strong><span> Niche dynamics of invasive alien plants (IAPs) play pivotal roles in biological invasion. </span><em><span>Ageratina adenophora</span></em><span>—one of the most aggressive IAPs in China and some parts of the world—poses severe </span><span>ecological and socioeconomic threats. However, the spatiotemporal niche dynamic</span><span>s of </span><em><span>A. adenophora</span></em><span> in China remain unknown, which we aimed to elucidate in the present study.</span></p> <p><span><strong>Location:</strong> </span><span>China, Mexico</span></p> <p><strong><span>Methods:</span></strong><span> Using a unifying framework</span><span>,</span><span> we reconstructed the climate niche dynamic</span><span>s</span><span> of<em>. adenophora</em> and applied the optimal MaxEnt model to predict its potential geographical distribution in China. Furthermore</span><span>, we</span><span> compared the heterogeneity of <em>A. adenophora</em> niche between Mexico (native) and China (invasive).</span></p> <p><strong><span>Results:</span></strong><span> We observed a low niche overlap between Mexico (native) and China (invasive). Specifically, the niche of <em>A. adenophora</em> in China has distinctly expanded compared with that in Mexico, enhancing</span><span> the </span><span>invasion risk of this IAP in the former country. In fact, </span><span>the climatic niche of <em>A. adenophora</em> in Mexico is a subset of that in China</span><span>. The potential geographical distribution of <em>A. adenophora</em>is concentrated in the tropical and subtropical zones of Southwest China, and its geographical distribution pattern in China is shaped by the combination of precipitation and temperature variables. </span></p> <p><span><strong>Main conclusions:</strong> </span><span>The niche dynamic</span><span>s of </span><span><em>A. adenophora</em> follow the hypothesis of niche shift and conservatism. The present work provides a unifying framework for studies on the niche dynamics of other IAPs worldwide.</span></p>
The occurrence data of wild apple in the Mountains of Central Asia Biodiversity Hotspot
<p><span>To obtain high-quality occurrence records for wild apple across its whole distribution range, we compiled data from field surveys, herbariums and the literature. The field surveys were conducted in all of the countries with wild apple distribution in Central Asia. Precisely, we had several exhaustive investigations of wild apple populations in Xinjiang, China from 2008 to 2021, including distribution range and abundance of wild apple across its whole elevational ranges in six counties. For herbarium data, we combined the records from Global Biodiversity Information Facility </span><span>and Chinese Virtual Herbarium</span><span>. Finally, we obtained 8344 occurrence records for wild apple. </span></p>
Data from: Influence of different data cleaning solutions of point-occurrence records on downstream macroecological diversity models
<p><span>Digital point-occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time-consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. This study examined the extent to which cleaned data from six pipelines using data cleaning tools (e.g., the GBIF web application, different R packages) affect downstream species distribution models. In addition, we assessed how the pipeline data differ from expert data. From 13,889 North American <i>Ephedra</i> observations in GBIF, the pipelines removed 31.7% to 62.7% false-positives, invalid coordinates, and duplicates, leading to data sets that included between 9,484 (GBIF application) and 5,196 records (manual-guided filtering). The expert data consisted of 703 thoroughly handpicked records, comparable to data from field studies. Although differences in the record numbers were relatively large, stacked species distribution models (sSDM) from the pipelines and the expert data were strongly related (mean Pearson's <i>r</i> across the pipelines: 0.9986, versus the expert data: 0.9173). The ever-stronger correlations resulted from occurrence information that became increasingly condensed in the course of the workflow (from individual occurrences to collectivized occurrences in grid cells to predicted probabilities in the sSDMs). In sum, our results suggest that the <i>R</i> package-based pipelines reliably identified invalid coordinates. In contrast, the GBIF-filtered data still contained both spatial and taxonomic errors. However, major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of expert taxonomic knowledge. We conclude that application-filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high-quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.</span></p>
Species occurrence data for Colorado restoration project (derived dataset from GBIF)
<p>GBIF species occurrence data downloaded for 53 species included a restoration project. The data have been cleaned to remove incorrect and imprecise coordinates, as well as records older than 1950. </p>
Data from: Palaeoscolecids from the Ludlow Series of Leintwardine, Herefordshire (UK) – the latest occurrence of palaeoscolecids in the fossil record.
<p>The documentation of cuticular micro-ornament is vital for the taxonomic assignment of palaeoscolecids – vermiform lower Palaeozoic ecdysozoans interpreted as stem-group priapulans or early diverging panarthropods. This is due to the absence of the character-rich proboscis and tail hooks in palaeoscolecid material not from Burgess Shale-type Konservat-Lagerstätten. Here, the cuticular micro-ornamentation of palaeoscolecids from the upper Silurian (Ludlow) fauna of Leintwardine (Herefordshire, England), is described using scanning electron microscopy (SEM) and Reflectance Transformation Imaging (RTI). This material is taxonomically unstable as it was included in an effective wastebasket genus (Protoscolex) long before these imaging techniques were developed. This reveals the Leintwardine material is most closely comparable to a palaeoscolecid from the Darriwilian (Middle Ordovician) of the Builth-Llandrindod inlier, Powys, Wales and is transferred accordingly to Radnorscolex Botting et al. as Radnorscolex latus Bather. The Leintwardine fauna represents the uppermost stratigraphic occurrence of palaeoscolecids, constrained to the Saetograptus leintwardinensis Zone (lower Ludfordian), and the comparatively sparse Silurian palaeoscolecid record is subsequently discussed. It is hypothesised palaeoscolecids may have become extinct during the mid-Ludfordian Lau Event, the onset of which is recorded in the biozone immediately above the Leintwardine fauna (Bohemograptus Zone). Finally, the British palaeoscolecid fauna is summarised, including a new record from the Dapingian (Middle Ordovician) of Carmarthenshire, South Wales. --</p>
Data from: Occurrence, ecology and management of Fascioloides magna in Bavaria, Southern Germany
<p>In 2015, red deer infected with American liver fluke were discovered in the Veldenstein Forest area for the first time. This was the first detection of the fluke in a wild deer population in Bavaria. </p> <p>The aim of the study was to determine the American liver fluke prevalence rates in red deer, roe deer and wild boar in the Veldenstein Forest, as well as factors influencing these rates.</p> <p>Since 2018, the livers of 83% of the red deer culled in the study area have been examined, as well as those of the occasional roe deer and wild boar. The livers are classified by adspection and dissection into four levels of infection. The age of the animals was estimated on the basis of dentition and tooth cementum annuli in the first molar (M1). The livers of 520 red deer, 226 roe deer and 75 wild boar were dissected. All wild boar livers tested negative. 3% of roe deer and 36% of red deer livers were positive. To lower the prevalence, the red deer population was reduced, beginning in 2018. In the following years, it fell significantly. Medium and high levels of infection were initially detected in 61% of adult red deer. Since 2018, the median number of flukes per infected liver has decreased significantly from 17.51 flukes/liver to 10.0 flukes/liver. On driven hunts, significantly more diseased deer were found than during hunting from raised hides.</p> <p>Furthermore, there are close correlations between infectations and the age of the red deer, and infections and the distance from the Pegnitz floodplains. The American liver fluke leads to the extinction of roe deer locally and to a massive infectation and decimation of the red deer population. Without a drastic reduction of the numbers in infected red deer populations, there is a risk of large-scale infection of native deer species across large areas in Bavaria.</p>
Annex B – Occurrence data on TBBPA and TBBPA derivatives in food submitted to EFSA, dietary surveys per country and age group available in the EFSA Comprehensive Database considered in the exposure assessment, and chronic dietary exposure to TBBPA and the contribution of different food groups to the dietary exposure
<p><span>This Annex contains the occurrence data submitted to EFSA, the dietary surveys per country and age group, and the chronic dietary exposure to PBDEs and the contribution of different food groups to the dietary exposure related to the Update of the risk assessment of TBBPA and its derivatives in food.</span></p>
Occurrence data on Pyrrolizidine Alkaloids (PAs) in food
<p>The dataset contains data on the occurrence of Pyrrolizidine Alkaloids (PAs) in food products of plant origin, in particular herbal teas and food supplements from different geographic regions in Europe.</p> <p>A total of 359 samples were collected in years 2014 and 2015 and analysed for the presence of 28 PAs. Samples were collected in supermarkets, retail shops and for a small proportion via internet. The samples comprised 168 teas (including black, green, rooibos, chamomile, peppermint and mixed herbal tea) and 191 food supplements. The analytical method for determination of 1,2-unsaturated PAs is based on liquid chromatography combined with tandem mass spectrometry (LC-MS/MS), which complies with the requirements as described by the Commission regulation No. 401/2006.</p> <p>The updates in version 2 mainly refer to the analytical methods and the limits of quantification reported for the analysis of pyrrolizidine alkaloids in different food samples, and to some plant extracts for which wrong levels of pyrrolizidine alkaloids were reported by a data provider.</p>
Annex B – Occurrence data on brominated phenols and their derivatives in food submitted to EFSA, dietary surveys per country and age group available in the EFSA Comprehensive Database considered in the exposure assessment, and the detailed results of the chronic dietary exposure assessment to 2,4,6-TBP and the contribution of different food groups to the dietary exposure
<p>This Annex contains the occurrence data submitted to EFSA, the dietary surveys per country and age group, and the detailed results of the chronic dietary exposure assessment to 2,4,6-TBP and the contribution of different food groups to the dietary exposure related to the Update of the risk assessment of brominated phenols and their derivatives in food.</p>
Bird species occurrence point data(2015-2019)
<p>The data comes from BirdReport.cn(http://www.birdreport.cn/),including the numbers and geographic location of six bird species (<em>Falco tinnunculus, Ardea alba, Aix galericulata, Dendrocopos canicapillus, Streptopelia chinensis, Turdus mandarinus</em>) in 2015-2019.</p>
Data on the occurrence of anisakids in fishery products from wild caught fish in all countries (Jan 2010 – Sept 2023)
<p><span>This file contains data on anisakids in fishery products from wild-caught fish in all countries, covering studies published between January 2010 and September 2023. The systematic review protocol used to identify and extract the information is available at <a href="https://zenodo.org/records/10270810">https://zenodo.org/records/10270810</a>. For the period 2010-2020, the records for data extraction come from primary research studies of interest that have been identified in published meta-analyses. </span></p>
Data for PM2.5/Ozone co-occurrence paper
<p>This repository contains supporting data for the manuscript titled "Increasing co-occurrence of fine particulate matter and ozone extremes in the western United States" by Kalashnikov et al. (2021). Please contact me with any questions at dmitri.kalashnikov@wsu.edu. -Dmitri</p>
Data for "Resource use divergence facilitates the evolution of secondary syntopy in a continental radiation of songbirds (Meliphagoidea): insights from unbiased co-occurrence analyses"
<p>These two files contain data needed to replicate analyses in the associated article.</p> <p>AUTHOR of data files: Vladimir Remes<br> CONTACT: vlad.remes/at/gmail,com<br> AUTHORS of the article: V. Remes, L. Harmackova<br> DATE CREATED: 8 November 2022<br> ARTICLE: published in Ecography</p> <p> </p> <p>The file named "data_syntopy.xlsx" has two sheets:<br> "data": contains the data<br> "legend": contains explanations of data columns</p> <p>The file was saved in MS Excel for Mac 16.65.</p> <p><br> The file named "tree_Mel.tre" is the phylogenetic tree in the parenthetic format used for the analyses. It has been pruned from the tree published by Marki et al. (2017) Mol Phyl Evol 107, 516–529. It was saved using the write.nexus function from the "ape" package for R software.</p>
Data from: Bedrock geological map predictions for Phanerozoic fossil occurrences
<p>This is the supplementary data repository of the <em>Paleobiology</em> paper titled <em>Bedrock Geological Map Predictions for Phanerozoic Fossil Occurrences</em>. Geographically-explicit, taxonomically resolved fossil occurrences are necessary for reconstructing macroevolutionary patterns and for testing a wide range of hypotheses in the Earth and life sciences. Heterogeneity in the spatial and temporal distribution of fossil occurrences in the Paleobiology Database (PBDB) is attributable to several different factors, including turnover among biological communities, socioeconomic disparities in the intensity of paleontological research, and geological controls on the distribution and fossil yield of sedimentary deposits. Here we use the intersection of global geologic map data from Macrostrat and fossil collections in the PBDB to assess the extent to which the potentially fossil-bearing, surface-expressed sedimentary record has yielded fossil occurrences. We find a significant and moderately strong positive correlation between geologic map area and the number of fossil occurrences. This correlation is consistent regardless of map unit age and binning protocol, except at period level; the Neogene and Quaternary have non-marine map units covering large areas and yielding fewer occurrences than expected. The sedimentary record of North America and Europe yields significantly more fossil occurrences per sedimentary area than similarly-aged deposits in most of the rest of the world. However, geographic differences in area and age of sedimentary deposits lead to regionally different expectations for fossil occurrences. Using the sampling of surface-expressed sedimentary units in North America and Europe as a predictor for what might be recoverable from the surface-expressed sedimentary deposits of other regions, we find that the rest of the globe is approximately 45% as well sampled in the PBDB. Using age and area of bedrock and sampling in North America and Europe as a basis for prediction, we estimate that over 639 thousand occurrences from outside of these regions would need to be added to the PBDB to achieve global geological parity in sampling. In general, new terrestrial fossil occurrences are expected to have the greatest impact on macroevolutionary patterns. </p>
Data for: Predator co-occurrence in alpine and Arctic tundra in relation to fluctuating prey
<p>Large carnivores influence ecosystem dynamics in multiple ways, e.g. by suppressing meso-carnivores and providing carrions for smaller scavengers. Loss of large carnivores is suggested to cause meso-carnivore increase and expansion. Moreover, competition between meso-carnivores may be modified by the presence of larger carnivores. In tundra ecosystems, the smallest meso-carnivore, the Arctic fox, has experienced regional declines, whereas its larger and competitively superior congener, the red fox, has increased, potentially due to changes in the abundance of apex predators. We explored if variation in occurrence of wolverine and golden eagle impacted the occurrence and co-occurrence of Arctic fox and red fox in relation to varying abundances of small rodents within the Scandinavian tundra. We applied multi-species occupancy models to an extensive wildlife camera dataset from 2011-2020 covering 98 sites. Daily detection/non-detection of each species per camera trap site and study period (late winter; March-May) was stacked across years and species occupancy was related to small rodent abundance while accounting for time of year and status of simulated carcass. Arctic fox was more likely to co-occur with red fox when wolverine was present, and less likely to co-occur with red fox when golden eagles were present and wolverine absent. Red foxes increased in occupancy when co-occurring with the larger predators. Arctic fox responded more strongly to small rodent abundance than red fox and co-occurred more often with the other species at carcasses when rodent abundance was low. Our findings suggest that the interspecific interactions within this tundra predator guild appear to be surprisingly intricate, driven by facets of fear of predation, interspecific mediation and facilitation, and food resource dynamics. These dynamics of intraguild interactions may dictate where and when conservation actions targeted towards the Arctic fox should be implemented.</p>
Data from: Population recovery and occurrence of the endemic Rhine sculpin (Cottus rhenanus)
<p>Two datasets belonging to the paper "Population recovery and occurrence of the endemic Rhine sculpin (<em>Cottus rhenanus</em>)" published in Knowledge and Management of Aquatic Ecosystems, are provided here. Since little was known about the occurrence, densities and habitat use of<em> C. rhenanus, </em>this study was conducted. The study area was located in the River Geul and tributaries, in the south of the Netherlands.</p> <p>The first dataset "WFD 2005-2010-2015 fish data.csv" contains data of fish in transects sampled as part of ecological status assessments of water systems according to the EU Water Framework Directive. Average 300-metre transects in upstream direction in one run using handheld backpack electrofishing equipment. The second dataset "Habitat characterization Cottus rhenanus 2014.csv" contains data of the Rhine sculpin (and other encountered fish species) in relation to its habitat. The data were collected in the same way as described above. In addition, we estimated the relative abundance of each sediment type (bed substratum) per transect, which yielded the ordinal categories: 0%, <5%, 5-10%, 11-25%, 26-50%, 51-75%, and 76-100%. Distinguished sediment types were silt (mud/sludge), sand, fine granule (0.1-20 mm), pebble (21-65 mm), cobble (66-200 mm), and boulder (>200 mm). Furthermore, we estimated the percentage area of large structures (e.g., woody debris) and riffles. Finally, we measured stream width (m) and depth (cm). This was done by recording width with a tape measure and depth with a measuring rod at five (beginning, middle, end and two representatives in between) locations in a transect. The mean values were recorded as stream width and depth. The included coordinates refer to the start and end of a transect. The coordinate system used here concerns Amersfoort RD (EPSG: 28992). </p> <p>Abstract</p> <p>The Rhine sculpin (<em>Cottus rhenanus</em>) is a benthic rheophilic fish species that is endemic to tributaries of the rivers Rhine and Meuse in North-western Europe. Little is known about its occurrence and individuals density in relation to habitat characteristics. A core population of <em>C. rhenanus</em> occurs in the River Geul in the Netherlands. Since the late 19<sup>th</sup> century, this river was heavily polluted by communal and industrial wastewater, causing a strong population decline. As the core population of <em>C. rhenanus</em> is recovering, the status, distribution, and habitat use should be studied to facilitate recovery in other locations. <em>Cottus rhenanus</em> density of individuals significantly increased over the period 2005-2015 and it became one of the most abundant fish species in assemblages. Negative relationships were observed between <em>C. rhenanus</em> densities and a high abundance of boulders (> 200 mm), large structures such as woody debris, and water depth. The population increase and recolonization of <em>C. rhenanus</em> coincided with water quality improvement, which suggests that this fish species can be used to assess small streams ecosystem integrity. The recent range expansion of the Ponto-Caspian round goby (<em>Neogobius melanostomus</em>) poses a high risk of negative effects on <em>C. rhenanus</em> populations via food and shelter competition. Further water quality improvement, habitat conservation, and prevention of the spread of invasive gobies could favour <em>C. rhenanus</em> populations within their natural range.</p>
Microhabitat data of bryophyte occurrences in and near Sequoia National Park at varying elevations
<p>On the western slope of California's Sierra Nevada, bryophytes were studied from the foothills (summers dry; winters mild) to the alpine zone (summers short; winters with snow cover). Plots of 25 m<sup>2</sup> were chosen from 380 to 3,578 meters above sea level. Within each of the 253 plots, bryophyte species and their abundance were recorded along with microsite wetness, shadiness, incline, and the type of substrate. Data was used to assess changes in species richness and abundance across elevations and microhabitat characteristics. </p>
Data from: Developing a database of Australian grasshopper occurrences from historic field survey notebooks spanning 54 years (Orthoptera: Acrididae, Morabidae, Pyrgomorphidae, Tetrigidae)
<p>The baseline distribution data for all species of a given group in a region can provide fundamental insights into biogeographic questions about historic patterns of species richness, population trends, and extinction. Grasshoppers are one major group of insects for which a continent-wide perspective on their geographic distribution can be obtained. This is because they were extensively surveyed in Australia for 54 years (1936-1989) as part of Commonwealth expeditions to obtain specimens for the Australian National Insect Collection (ANIC). Field notebooks recorded from those surveys, under the direction of ANIC curator and director K. H. L. Key, form the principal source of historic distribution records for grasshoppers in Australia. We digitized all 223 notebooks (2486 pages) and transcribed all the field trips conducted in Western Australia (WA) and Tasmania (47 notebooks, 590 pages). We then carefully geocoded all sampling sites of the transcribed notebooks, following the odometer readings and descriptions of routes from a suitable reference point using historic topographic maps and Google Earth. In total, we extracted 8975 geographic coordinates for 477 species having a confirmed or putative taxonomic name of (only 170 of these species have been formally described). We found that species richness varied spatially, with highest richness in arid interior and north of WA. Historic grasshopper surveys were non-randomly distributed across both WA and Tasmania with the highest survey intensity around coastal regions. Variation was observed among surveyors in terms of the number of species detected per site, between-site distance, and the season of survey being conducted. Overall, however, the dataset is among the most comprehensive continent-wide surveys of Australian invertebrates and will greatly facilitate future work on their ecology, biogeography, conservation, and responses to environmental change.</p>
Data set to: Mapping a brain parasite: occurrence and spatial distribution in fish encephalon
<p>Data for the manuscript "Mapping a brain parasite: occurrence and spatial distribution in fish encephalon", doi: 10.1016/j.ijppaw.2023.03.004. Description of the distribution of metacercariae from the trematode species <em>Cardiocephaloides longicollis</em> in the brain of fish. </p>
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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)
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DANDI Archive for NWB datasets
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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.