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8,729 results for “Ranges”
An experimental test of the Allee effects range limitation hypothesis
<p>Data and code for a simple N-mixture model in JAGS Merker, S.A and Chandler, R.B. In Press. An experimental test of the Allee effects range limitation hypothesis. Journal of Animal Ecology.</p> <p>JAE-data.gzip contains the data required to run the model including:</p> <ol> <li>scaled and center covariates of detection</li> <li>a 3 dimensional array containing counts of Canada warbler (cardellina canadensis) at 71 point count locations over 4 years</li> <li>A climate PCA derived from PRISM data.</li> </ol> <p>The model itself is described in the .jAG file "Abundance_EN_clim-trt-D.JAG"</p> <p>Merker_Chandler_Appendices is an Rmarkdown file for the appendices of the article</p>
Raman spectroscopic data derived from Calluna vulgaris charcoals, experimentally generated across a range of natural wildfire temperatures
<p>This data has been derived from deconvolved Raman spectra, utilising two first order bands - D (Disordered) and G (Graphitic). Spectra were collected from experimentally pyrolysed charcoals, made from Calluna vulgaris (Ling Heather) separated into three main components; stem, root and flower. For each component at 250, 400, 600 and 800 degrees centigrade respectively, 5 charcoal samples (A, B, C, D, E) were analysed. Following deconvolution, median values for each spectra were produced. These correspond to parameters derived from the Raman data, including D- and G-band width (FWHM), intensity (ID/IG or 'R1') and area (AD/AG) ratios, band separation (G-D or 'RBS'), and band width ratios (D-FWHM/G-FWHM). All parameters have been compiled for each component material, and displayed graphically within this dataset.</p>
Dataset for "Toward closure between predicted and observed particle viscosity over a wide range temperature and relative humidity"
<p>Raw data and processing scripts associated with the paper "Toward closure between predicted and observed particle viscosity over a wide range temperature and relative humidity". Please see README.md for details. </p>
Data from: Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains
Aim <p>Physiological tolerances and biotic interactions along habitat gradients are thought to influence species occurrence. Distributional differences caused by such forces are particularly noticeable on tropical mountains, where high species turnover along elevational gradients occurs over relatively short distances and elevational distributions of particular species can shift among mountains. Such shifts are interpreted as evidence of the importance of spatial variation in interspecific competition and habitat or climatic gradients. To assess the relative importance of competition and compression of habitat and climatic zones in setting range limits, we examined differences in elevational ranges of forest bird species among four Bornean mountains with distinct features.</p> Location <p>Bornean mountains Kinabalu, Mulu, Pueh and Topap Oso.</p> Taxon <p>Rain forest bird communities along elevational gradients.</p> Methods <p>We surveyed the elevational ranges of rain forest birds on four mountains in Borneo to test which environmental variables—habitat zone compression or presence of likely competitors—best predicted differences in elevational ranges of species among mountains. For this purpose, we used two complementary tests: a comparison of elevational range limits between pairs of mountains, and linear mixed models with naïve occupancy as the response variable.</p> Results <p>We found that lowland species occur higher in elevation on two small mountains compared to Mt. Mulu. This result is inconsistent with the expectation that distributions of habitats are elevationally compressed on small mountains, but is consistent with the hypothesis that a reduction in competition (likely diffuse) on short mountains, which largely lack montane specialist species, allows lowland species to occur higher in elevation. The relative influence of competition changes with elevation, and the correlation between lower range limits of montane species and the distribution of their competitors was weaker than in lowland species.</p> Main conclusions <p>These findings provide support for the importance of biotic interactions in setting elevational range limits of tropical bird species, although abiotic gradients explain the majority of distribution patterns. Thus, models predicting range shifts under climate change scenarios must include not only climatic variables, as is currently most common, but also information on potentially resulting changes in species interactions, especially for lowland species.</p>
Grouping strategies in number estimation extend the subitizing range
<p>In the calculation folder: each file contains a matrix called “MATR”. Each row of the matrix “MATR” is a trial. </p> <p>The columns contain the following information:</p> <p>1<sup>st</sup>: Number of trial</p> <p>2<sup>nd: Subject response</sup></p> <p>4<sup>th</sup>: Response time</p> <p>5<sup>th</sup>: first number </p> <p>6<sup>th</sup>: math symbol (1=*; 2= +; 3= –)</p> <p>7<sup>th</sup>: second number </p> <p>8<sup>th</sup>: third number </p> <p> </p> <p>In the calculation folder: each file contains a matrix called “matr”. Each row of the matrix “matr” is a trial. </p> <p>The columns contain the following information:</p> <p>1<sup>st</sup>: subject response in the numerosity task</p> <p>2<sup>nd</sup>: the presented numerosity </p> <p>3<sup>rd</sup>: subject response in the numerosity task</p> <p>4<sup>th</sup>: zero</p> <p>5<sup>th</sup>: stimulus duration</p> <p>6<sup>th</sup>: Response time in the numerosity task</p> <p>7<sup>th</sup>: Grouped (1) or random (2) presentation </p> <p>8<sup>th</sup>: 1</p> <p>9<sup>th</sup>: 1</p> <p>10<sup>th</sup>: Number of items of the upper-left quadrant</p> <p>11<sup>th</sup>: Number of items of the lower-left quadrant</p> <p>12<sup>th</sup>: Number of items of the upper-right quadrant</p> <p>13<sup>th</sup>: Number of items of the lower - right quadrant</p> <p>14<sup>th</sup>: odd shape presented (1=diamond; 2=triangle; 3=circle)</p> <p>15<sup>th</sup>: subject response in the shape task</p> <p>16<sup>th</sup>: 0.2 in the single task response time in the shape task when dual task</p> <p>17<sup>th</sup>: single (0) or dual (1) task</p> <p>18<sup>th</sup>: time stimulus on</p> <p>19<sup>th</sup>: time stimulus off</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Latitudinal core habitat prediction data for the manuscript: "Seascape topography slows predicted range shifts in fish under climate change"
<p>Latitudinal locations of core environmental habitat for yellowtail kingfish (<em>Seriola lalandi</em>), Australian bonito (<em>Sarda australis</em>), Australian spotted mackerel (<em>Scomberomorus munroi</em>), narrow-barred Spanish mackerel (<em>Scomberomorus commerson</em>) and common dolphinfish (<em>Coryphaena hippurus</em>) nearshore of the continental shelf break (i.e. 200-m isobath) within 145 – 160°E, 15 – 45°S and between years 1998 – 2018.</p>
Replication Package: Assessing time-based and range-based strategies for commit assignment to releases
<p><strong>Abstract:</strong></p> <p>Release is a ubiquitous concept in software development, referring to grouping multiple independent changes into a deliverable piece of software. Mining releases can help developers understand the software evolution at coarse grain, identify which features were delivered or bugs were fixed, and pinpoint who contributed on a given release. A typical initial step of release mining consists of identifying which commits compose a given release. We could find two main strategies used in the literature to perform this task: time-based and range-based. Some release mining works recognize that those strategies are subject to misclassifications but do not quantify the impact of such a threat. This paper analyzed 13,419 releases and 1,414,997 commits from 100 relevant open source projects hosted at GitHub to assess both strategies in terms of precision and recall. We observed that, in general, the range-based strategy has superior results than the time-based strategy. Nevertheless, even when the range-based strategy is in place, some releases still show misclassifications. Thus, our paper also discusses some situations in which each strategy degrades, potentially leading to bias on the mining results if not adequately known and avoided.</p> <p><strong>Instructions:</strong></p> <p>Visit <a href="https://github.com/gems-uff/release-mining">https://github.com/gems-uff/release-mining</a> for instructions about how to use this dataset.</p> <p><strong>Files:</strong></p> <ul> <li>The <em>repos.tgz</em> contains our project <em>corpus </em>comprising 1,414,997 releases from 100 relevant open source projects.</li> <li>The <em>repos.sha1</em> contains the sha1 checksum of <em>repos.tgz</em></li> </ul> <p><strong>Disclaimer:</strong></p> <p>This replication package contains the source code of 100 relevant open source projects. Its purpose is to enable the replication of the study conducted in the paper "Assessing time-based and range-based strategies for commit assignment to releases." </p> <p>It is essential to check each project license before using the source code or any attached file for any other purposes besides replicating the study.</p> <p> </p>
DEVILS: a tool for the visualization of large datasets with a high dynamic range
<p>This repository accompanying the article “DEVILS: a tool for the visualization of large datasets with a high dynamic range” contains the following:</p> <ul> <li>Extended Material of the article</li> <li>An example raw dataset corresponding to the images shown in Fig. 3</li> <li>A workflow description that demonstrates the use of the DEVILS workflow with BigStitcher.</li> <li>Two scripts (“CLAHE_Parameters_test.ijm” and a “DEVILS_Parallel_tests.groovy”) used for Figure S2, S3 and S4.</li> </ul>
No severe genetic bottleneck in a rapidly range-expanding bumblebee pollinator
<p>Genetic bottlenecking can limit the success of populations colonising new ranges. However, successful colonisations can occur despite bottlenecking, a phenomenon known as the genetic paradox of invasion. Eusocial Hymenoptera such as bumblebees (<em>Bombus</em> spp.) should be particularly vulnerable to genetic bottlenecking, since homozygosity at the sex-determining locus leads to costly diploid male production. The Tree Bumblebee (<em>B. hypnorum</em>) has rapidly colonised the UK since 2001 and has been highlighted as exemplifying the genetic paradox of invasion. Using microsatellite genotyping, combined with the first genetic estimates of diploid male production in UK B. hypnorum, we tested two alternative genetic hypotheses ('bottleneck' and 'gene flow' hypotheses) for B. hypnorum's colonisation of the UK. We found that the UK population has not undergone a recent severe genetic bottleneck and exhibits levels of genetic diversity falling between those of widespread and range-restricted<em> Bombus</em> species. Diploid males occurred in 15.4% of reared colonies, leading to an estimate of 21.5 alleles at the sex-determining locus. Overall, the findings show that this population is not bottlenecked, instead suggesting that it is experiencing continued gene flow from the continental European source population with only moderate loss of genetic diversity, and does not exemplify the genetic paradox of invasion.</p>
Data from: Species distribution models of the Spotted Wing Drosophila (Drosophila suzukii, Diptera: Drosophilidae) in its native and invasive range reveal an ecological niche shift
<p>The Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>) is native to Southeast Asia. Since its first detection in 2008 in Europe and North America, it has been a pest to the fruit production industry as it feeds and oviposits on ripening fruit. Here we aim to model the potential geographical distribution of <em>D. suzukii</em>. We performed an extensive literature review to map the current records. In total, 517 documented occurrences (96 native and 421 invasive) were identified spanning 52 countries. Next, we constructed three species distribution models (SDMs) based on occurrence records in: 1) the native range (SDMnative), 2) the invasive range in Europe (SDMEurope) and 3) a global model of all records (SDMglobal). The models aimed to investigate, whether this species will be able to occupy additional ecological niches beyond its native range and expand its current geographic distribution both globally and in Europe. The SDMs were generated using Maximum Entropy algorithms (Maxent) based on present occurrence records and bioclimatic variables (WorldClim). Predictions of habitat suitability vary greatly depending on the origins of occurrence records. According to all models, precipitation and low temperatures were key limiting factors for the distribution of <em>D. suzukii</em>, which suggests that this species requires a humid environment with mild winters in order to establish a permanent population in its invasive range. Several regions in the invasive range, not presently occupied by this species, were predicted highly suitable, especially in northern Europe, suggesting that <em>D. suzukii</em> is not occupying its full fundamental niche yet. Synthesis and applications. Based on these models of potential geographic distribution of the Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>), we show a shift in the ecological niche in <em>D. suzukii</em> populations, emphasizing the importance of using presence and local environmental data. Further investigation regarding new occurrences is recommended to secure optimal pest management. Despite a continuing expansion, many countries still lack proper surveillance schemes, and we urge policymakers to initiate appropriate management programs.</p>
Data from: The evolution of environmental tolerance and range size: A comparison of geographically restricted and widespread Mimulus
<p>The geographic ranges of closely related species can vary dramatically, yet we do not fully grasp the mechanisms underlying such variation. The niche breadth hypothesis posits that species that have evolved broad environmental tolerances can achieve larger geographic ranges than species with narrow environmental tolerances. In turn, plasticity and genetic variation in ecologically important traits and adaptation to environmentally variable areas can facilitate the evolution of broad environmental tolerance. We used five pairs of western North American monkeyflowers to experimentally test these ideas by quantifying performance across eight temperature regimes. In four species pairs, species with broader thermal tolerances had larger geographic ranges, supporting the niche breadth hypothesis. As predicted, species with broader thermal tolerances also had more within-population genetic variation in thermal reaction norms and experienced greater thermal variation across their geographic ranges than species with narrow thermal tolerances. Species with narrow thermal tolerance may be particularly vulnerable to changing climatic conditions due to a lack of plasticity and insufficient genetic variation to respond to novel selection pressures. Conversely, species experiencing high variation in temperature across their ranges may be buffered against extinction due to climatic changes because they have evolved tolerance to a broad range of temperatures.</p>
Fig. 8 in A new vertebrate for Europe: the discovery of a range-restricted relict viper in the western Italian Alps
Fig. 8. Currently known extent of occurrence of Vipera walser sp. nov. (in blue) and V. berus (in red) in north western Italy
Fig. 3 in A new vertebrate for Europe: the discovery of a range-restricted relict viper in the western Italian Alps
Fig. 3. Results of the non-metric multidimensional scaling (nMDS, Bray – Curtis with similarity index), for the females (left) and males (right) conducted separately. The following variables were considered: subcaudals, crown scales, apicals, perioculars, parietals and loreals (only on the right side because V. walser show a much higher degree of asymmetry on loreal scales count, compared to V. berus). The analysis was carried out on V. walser and three groups of V. berus having the same number of samples, in order to evaluate intraspecific variability. V. walser are in red. The graphs show V. walser to be well differentiated in respect to the three groups of V. berus, which are mostly overlapping.
Fig. 10 in A new vertebrate for Europe: the discovery of a range-restricted relict viper in the western Italian Alps
Fig. 10. Current and projected (2035; CMIP 5 [IPPC Fifth Assessment]) mean annual rainfall and mean minimum temperatures (° C) for the months May – October within the current range of Vipera walser sp. nov.
Fig. 9 in A new vertebrate for Europe: the discovery of a range-restricted relict viper in the western Italian Alps
Fig. 9. Habitat of Vipera walser sp. nov. Valle Strona at about 1650 m (upper left), Valle Strona at about 1800 m (upper right), Valle Mastallone at 2070 m (bottom left) and Valle della Vecchia at 1830 m (bottom right)
Fig. 7 in A new vertebrate for Europe: the discovery of a range-restricted relict viper in the western Italian Alps
Fig. 7. Variation in head scalation in adult female (upper four photographs) and adult male (lower four photographs) of Vipera walser sp. nov.
Fig. 4 in A new vertebrate for Europe: the discovery of a range-restricted relict viper in the western Italian Alps
Fig. 4. Discriminant analysis, based on the six meristic variables, correctly classifies 94 % of females (left) and 88 % of males. The strongest discriminatory variables are crown scales and parietals. Blue = V. berus; red = V. walser
Fig. 7. Dordrecht Mountain, where a in Neoclita pringlei (Scarabaeidae, Cetoniinae), a new relict genus and species from the Drakensberg Range of South Africa
Fig. 7. Dordrecht Mountain, where a second population of Neoclita pringlei gen. et sp. nov. was Frst recorded in Dec. 2013 (photo: Lynette Clennell, Dordrecht, 31 Dec. 2015).
Fig. 4 in Neoclita pringlei (Scarabaeidae, Cetoniinae), a new relict genus and species from the Drakensberg Range of South Africa
Fig. 4. Neoclita pringlei gen. et sp. nov., ♂, specimen in its natural habitat (photo: Lynette Clennell, Matatiele, 6 Dec. 2018).
Fig. 5 in Neoclita pringlei (Scarabaeidae, Cetoniinae), a new relict genus and species from the Drakensberg Range of South Africa
Fig. 5. Neoclita pringlei gen. et sp. nov., ♀, specimen in its natural habitat (photo: Lynette Clennell, Matatiele, 6 Dec. 2018).
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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.