Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
5,371
datasets available to search
ShareScore release 0.9.0
Dataset results
5,371 results for “Flow”
Simulation data and scripts for CFD-DEM simulation of granular flows in ambient fluid
<ul> <li>Data sets - contains the raw data required to replicate and validate all plots in the main article. Contains folders in containing measurements of basic flow properties, e.g. velocities, shear rates, etc., of monodisperse and bidisperse granular flows in different flow regimes. Each folder contains a ReadMe.txt briefly explaining the content and lay out of each data set.</li> <li>Sample case - a .zip file which includes codes which are needed to simulate a CFD-DEM case of a steady granular flow in water with cyclic boundaries in the stream wise direction. Also enclosed is a ReadMe.txt file detailing the implementation instructions for both Esys particle and OpenFOAM codes. Download links for Esys particle and OpenFOAM are also included.</li> <li>Geo file generator - a .zip file which includes Esys particle codes that can be used to generate a .geo file specifying the initial position of the particles used in the test simulations. A ReadMe.txt file is enclosed with more detailed implementation instructions.</li> </ul>
CellCognize: a neural network pipeline for cell type classification from flow cytometry data
<p>Readme file content</p> <p>The files stored here contain the following material as supplementary and source data for the publication</p> <p>Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data</p> <p>Birge D. Özel Duygan1, Noushin Hadadi1, Ambrin Farizah Bab1, Markus Seyfried2, Jan R. van der Meer1</p> <p>1 Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland<br> 2 Biotechnology Department, Firmenich SA, Geneva, Switzerland</p> <p>%%%%%%%<br> Flow cytometry data<br> %%%%%%</p> <p>FCM_files:</p> <p>.mat files with cleaned data as described in the supplementary methods section</p> <p>Ecoli_lakewater: raw FCM data (in .csv format) of E. coli cultures and E. coli cultures mixed to lakewater</p> <p>MIX_experiment_ACL_AJH_PVR: raw FCM data (in .csv format) of the synthetic three culture experiment with E. coli, A. johnsonii and P. veronii, as described in the main text and SI methods.</p> <p>PHE_OCT_enrichments: raw FCM data (in .csv format) of the phenol and 1-octanol enrichments and the 1-octanol isolates, as described in the main text and SI methods.</p> <p>%%%%%%%<br> Neural network data<br> %%%%%%</p> <p>NN_file_example: three ANN functions, to be used in conjunction with the SI methods section</p> <p>Supplementary_Methods.docx: Detailed description on the construction, usage and scripts for the ANN. To be used in conjunction with the Flow Cytometry data</p> <p>%%%%%%%<br> 16S sequencing data<br> %%%%%%</p> <p>raw fastq- files of the sample reads of the 1-octanol and phenol enrichments described in the paper, at t=0 and t=3d, each in triplicates, forward and reverse.</p> <p>Readme_16S_sequence_files.txt: sample description of the read files</p>
Importance of snowmelt contribution to seasonal runoff and summer low flows in Czechia
<p>The file in this record represents a supplementary data for the journal paper Jenicek, M., Ledvinka, O. (2020). Importance of snowmelt contribution to seasonal runoff and summer low flows in Czechia. Hydrology and Earth System Sciences, https://doi.org/10.5194/hess-2019-611. The file contain simulations of the HBV rainfall-runoff model for 59 mountain catchments in Czechia. The model simulated different water balance components, such as runoff, snow water equivalent, evapotranspiration and groundwater storage for the study period 1980-2014.</p>
Experiments on granular flow behavior and deposit characteristics: implications for rock avalanche kinematics
<p>Seven excel files which includes the data supporting Figure 5, Figure 6, Figure 7, Figure 8, Figure 10, Figure 12 and Figure 14 is uploaded saparately.</p> <p>Data Set S1. Data supporting the relationship between flow height and time in Figure 5.</p> <p>Data Set S2. Data supporting normalized velocity profiles and normalized shear rate profiles in Figures 6(a)-6(d).</p> <p>Data Set S3(a). Data supporting the relationships between mean grain size and global shear rate in Figure 7(a).</p> <p>Data Set S3(b). Data supporting the relationships between mean grain size and Savage number in Figure 7(a).</p> <p>Data Set S4(a). Data supporting the relationships between depth averaged velocity and time in Figure 8(a).</p> <p>Data Set S4(b). Data supporting the relationships between depth averaged velocity and time in Figure 8(b).</p> <p>Data Set S4(c). Data supporting the relationships between mean grain size and equivalent friction coefficient in Figure 8(c).</p> <p>Data Set S5(a). Data supporting Figures 10(a) and 10(b).</p> <p>Data Set S5(b). Data supporting the relationships between relative flow height and λ in Figure 10(c).</p> <p>Data Set S5(c). Data supporting the relationships between relative flow height and λ in Figure 10(d).</p> <p>Data Set S6(a). Data supporting the velocity profiles in Figure 12(a).</p> <p>Data Set S6(b). Data supporting the relationships between global shear rate and equivalent friction coefficient in Figure 12(b).</p> <p>Data Set S7. Data supporting the relationships between normalized flow height and Savage number in Figure 14.</p>
Supplementary videos for "The mechanical origin of snow avalanche dynamics and flow regime transitions"
<p>We are releasing the videos as the supplementary information for our submitted manuscript to The Cryosphere. </p> <p>Movie 1. Velocity of the flows in the four typical flow regimes in Fig. 2(a). Frame rate is 24 FPS.</p> <p>Movie 2. Volumetric plastic strain of the flows in the four typical flow regimes in Fig. 2(a). Frame rate is 24 FPS.</p> <p>Movie 3. Velocity of the flow in transition from cold dense to warm shear regimes in Fig. 2(b). Frame rate is 24 FPS.</p> <p>Movie 4. Volumetric plastic strain of the flow in transition from cold dense to warm shear regimes in Fig. 2(b). Frame rate is 24 FPS.</p>
Reduction of blob-filament radial propagation by parallel variation of flows: analysis of a gyrokinetic simulation
<p>The accompanying files contain digital data for figures in the article "Reduction of blob-filament radial propagation by parallel variation of flows: analysis of a gyrokinetic simulation" by J. R. Myra, S. Ku, D.A. Russell, J. Cheng, I. Keramidas Charidakos, S. E. Parker, R.M. Churchill, and C.S. Chang, submitted to the journal Physics of Plasmas.</p> <p> </p> <p><strong>Abstract</strong></p> <p>Data from the XGC1 gyrokinetic simulation is analyzed to understand the three-dimensional spatial structure and the radial propagation of blob-filaments generated by quasi-steady turbulence in the tokamak edge pedestal and scrape-off layer plasma. Spontaneous toroidal flows vary in the poloidal direction and shear the filaments within a flux surface resulting in a structure that varies in the parallel direction. This parallel structure allows the curvature and grad-B induced polarization charge density to be shorted out via parallel electron motion. As a result, it is found that the blob-filament radial velocity is significantly reduced from estimates which neglect parallel electron kinetics, broadly consistent with experimental observations. Conditions for when this charge shorting effect tends to dominate blob dynamics are derived and compared with the simulation.</p>
Data from: When does gene flow facilitate evolutionary rescue?
Experimental and theoretical studies have highlighted the impact of gene flow on the probability of evolutionary rescue in structured habitats. Mathematical modelling and simulations of evolutionary rescue in spatially or otherwise structured populations showed that intermediate migration rates can often maximize the probability of rescue in gradually or abruptly deteriorating habitats. These theoretical results corroborate the positive effect of gene flow on evolutionary rescue that has been identified in experimental yeast populations. The observations that gene flow can facilitate adaptation are in seeming conflict with traditional population genetics results that show that gene flow usually hampers (local) adaptation. Identifying conditions for when gene flow facilitates survival chances of populations rather than reducing them remains a key unresolved theoretical question. We here present a simple analytically tractable model for evolutionary rescue in a two-deme model with gene flow. Our main result is a simple condition for when migration facilitates evolutionary rescue, as opposed as no migration. We further investigate the roles of asymmetries in gene flow and / or carrying capacities, and the effects of density regulation and local growth rates on evolutionary rescue.
Data from: Quaternary land bridges have not been universal conduits of gene flow
<p>Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population-genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of hundreds of individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in non-dispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes, and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.</p>
Data from: Out of sight, out of mind: Widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal
Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting as a cause of intra- or inter-genomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both incomplete lineage sorting and introgression as a case for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both incomplete lineage sorting and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by incomplete lineage sorting, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that results from the plastid genome do not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought.
Data from: Persistent firing and adaptation in optic-flow-sensitive descending neurons
<p>A general principle of sensory systems is that they adapt to prolonged stimulation by reducing their response over time. Indeed, in many visual systems, including higher-order motion sensitive neurons in the fly optic lobes and the mammalian visual cortex, a reduction in neural activity following prolonged stimulation occurs. In contrast to this phenomenon, the response of the motor system controlling flight maneuvers persists following the offset of visual motion. It has been suggested that this gap is caused by a lingering calcium signal in the output synapses of optic lobe neurons. However, whether this directly affects the responses of the post-synaptic descending neurons, leading to the observed behavioral output, is not known. We use extracellular electrophysiology to record from optic flow sensitive descending neurons in response to prolonged wide-field stimulation. We find that, as opposed to most sensory and visual neurons, and in particular to the motion vision sensitive neurons in the brains of flies and mammals, the descending neurons show little adaption during stimulus motion. In addition, we find that the optic flow sensitive descending neurons display persistent firing, or an after-effect, following the cessation of visual stimulation, consistent with the lingering calcium signal hypothesis. However, if the difference in after-effect is compensated for, subsequent presentation of stimuli in a test-adapt-test paradigm reveals adaptation to visual motion. Our results thus show a combination of adaptation and persistent firing, in the neurons that project to the thoracic ganglia, and thereby control behavioral output.</p>
SAPFLUXNET: A global database of sap flow measurements
<p><strong>General description</strong></p> <p>SAPFLUXNET contains a global database of sap flow and environmental data, together with metadata at different levels.<br> SAPFLUXNET is a harmonised database, compiled from contributions from researchers worldwide. </p> <p>The SAPFLUXNET version 0.1.5 database harbours 202 globally distributed datasets, from 121 geographical locations. SAPFLUXNET contains sap flow data for 2714 individual plants (1584 angiosperms and 1130 gymnosperms), belonging to 174 species (141 angiosperms and 33 gymnosperms), 95 different genera and 45 different families. More information on the database coverage can be found here: <a href="http://sapfluxnet.creaf.cat/shiny/sfn_progress_dashboard/">http://sapfluxnet.creaf.cat/shiny/sfn_progress_dashboard/</a>. </p> <p><br> The SAPFLUXNET project has been developed by researchers at CREAF and other institutions (<a href="http://sapfluxnet.creaf.cat/team/">http://sapfluxnet.creaf.cat/#team</a>), coordinated by Rafael Poyatos (CREAF, <a href="http://www.creaf.cat/staff/rafael-poyatos-lopez">http://www.creaf.cat/staff/rafael-poyatos-lopez</a>), and funded by two Spanish Young Researcher's Grants (SAPFLUXNET, CGL2014-55883-JIN; DATAFORUSE, RTI2018-095297-J-I00 ) and an Alexander von Humboldt Research Fellowship for Experienced Researchers).</p> <p><strong>Changelog </strong></p> <p>Compared to version 0.1.4, this version includes some changes in the metadata, but all time series data (sap flow, environmental) remain the same. </p> <ul> <li>For all datasets, climate metadata (temperature and precipitation, ‘si_mat’ and ‘si_map’) have been extracted from CHELSA (https://chelsa-climate.org/), replacing the previous climate data obtained with Wordclim. This change has modified the biome classification of the datasets in ‘si_biome’.</li> <li>In ‘species’ metadata, the percentage of basal area with sap flow measurements for each species (‘sp_basal_area_perc’) is now assigned a value of 0 if species are in the understorey. This affects two datasets: AUS_MAR_UBD and AUS_MAR_UBW, where, previously, the sum of species basal area percentages could add up to more than 100%.</li> <li>In ‘species’ metadata, the percentage of basal area with sap flow measurements for each species (‘sp_basal_area_perc’) has been corrected for datasets USA_SIL_OAK_POS, USA_SIL_OAK_1PR, USA_SIL_OAK_2PR.</li> <li>In ‘site’ metadata, the vegetation type (‘si_igbp’) has been changed to SAV for datasets CHN_ARG_GWD and CHN_ARG_GWS.</li> </ul> <p><strong>Variables and units</strong></p> <p>SAPFLUXNET contains whole-plant sap flow and environmental variables at sub-daily temporal resolution. Both sap flow and environmental time series have accompanying flags in a data frame, one for sap flow and another for environmental<br> variables. These flags store quality issues detected during the quality control process and can be used to add further quality flags. </p> <p>Metadata contain relevant variables informing about site conditions, stand characteristics, tree and species attributes, sap flow methodology and details on environmental measurements. The description and units of all data and metadata variables can be found here: <a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/metadata-and-data-units.html">Metadata and data units</a>.</p> <p>To learn more about variables, units and data flags please use the functionalities implemented in the sapfluxnetr package (<a href="https://github.com/sapfluxnet/sapfluxnetr">https://github.com/sapfluxnet/sapfluxnetr</a>). In particular, have a look at the package vignettes using R:</p> <pre><code># remotes::install_github( # 'sapfluxnet/sapfluxnetr', # build_opts = c("--no-resave-data", "--no-manual", "--build-vignettes") # ) library(sapfluxnetr) # to list all vignettes vignette(package='sapfluxnetr') # variables and units vignette('metadata-and-data-units', package='sapfluxnetr') # data flags vignette('data-flags', package='sapfluxnetr')</code></pre> <p><strong>Data formats</strong></p> <p>SAPFLUXNET data can be found in two formats: 1) RData files belonging to the custom-built 'sfn_data' class and 2) Text files in .csv format. We recommend using the sfn_data objects together with the sapfluxnetr package, although we also provide the text files for convenience. For each dataset, text files are structured in the same way as the slots of sfn_data objects; if working with text files, we recommend that you check the data structure of 'sfn_data' objects in the <a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/sfn-data-classes.html">corresponding vignette</a>.</p> <p><strong>Working with sfn_data files</strong></p> <p>To work with SAPFLUXNET data, first they have to be downloaded from Zenodo, maintaining the folder structure. A first level in the folder hierarchy corresponds to file format, either RData files or csv's. A second level corresponds to how sap flow is expressed: per plant, per sapwood area or per leaf area. Please note that interconversions among the magnitudes have been performed whenever possible. Below this level, data have been organised per dataset. In the case of RData files, each dataset is contained in a sfn_data object, which stores all data and metadata in different slots (see the vignette 'sfn-data-classes'). In the case of csv files, each dataset has 9 individual files, corresponding to metadata (5), sap flow and environmental data (2) and their corresponding data flags (2).</p> <p>After downloading the entire database, the sapfluxnetr package can be used to:<br> - Work with data from a single site: data access, plotting and time aggregation.<br> - Select the subset datasets to work with.<br> - Work with data from multiple sites: data access, plotting and time aggregation.</p> <p>Please check the following package vignettes to learn more about how to work with sfn_data files:</p> <p><a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/sapfluxnetr-quick-guide.html">Quick guide</a></p> <p><a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/metadata-and-data-units.html">Metadata and data units</a></p> <p><a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/sfn-data-classes.html">sfn_data classes</a></p> <p><a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/custom-aggregation.html">Custom aggregation</a></p> <p><a href="http://sapfluxnet.creaf.cat/sapfluxnetr/articles/memory-and-parallelization.html">Memory and parallelization</a></p> <p><strong>Working with text files</strong></p> <p>We recommend to work with sfn_data objects using R and the sapfluxnetr package and we do not currently provide code to work with text files. </p> <p><strong>Data issues and reporting</strong></p> <p>Please report any issue you may find in the database by sending us an email: sapfluxnet@creaf.uab.cat.</p> <p>Temporary data fixes, detected but not yet included in released versions will be published in SAPFLUXNET main web page ('Known data errors').</p> <p><strong>Data access, use and citation</strong></p> <p>This version of the SAPFLUXNET database is open access and corresponds to the data paper submitted to Earth System Science Data in August 2020.</p> <p>When using SAPFLUXNET data in an academic work, please cite the data paper, when available, or alternatively, the Zenodo dataset (see the ‘Cite as’ section on the right panels of this web page).</p>
Data from: Gene flow at the leading range edge - the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)
Aim: Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long-term isolation on genetic diversity and population genetic structure within populations of this species. Location: Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon: Fagaceae Methods: Using historical sources, we obtained area- and distance-based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen-mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen-mediated gene flow. Results: Long-term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north-eastern distribution of beech. Main conclusions: Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long-term cumulative effects of isolation on this wind-pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated.
Codes and datasets associated with the paper "On the dissipation rate of temperature fluctuations in stably stratified flows"
<p>Here, you will find some of the codes and datasets utilized in the article: "On the dissipation rate of temperature fluctuations in stably stratified flows". (<a href="https://arxiv.org/abs/2001.06369">https://arxiv.org/abs/2001.06369</a>)</p> <p>The direct numerical simulations were performed using the HERCULES code (<a href="https://github.com/friedenhe/HERCULES">https://github.com/friedenhe/HERCULES</a>). For all the simulations, the bulk Reynolds number is kept at 20,000. The bulk Richardson number is varied from 0.1 to 0.5. The zip files Re20000RiXX.zip contains the various turbulence statistics. </p> <p>Re20000Ri10: Ri_b = 0.1</p> <p>Re20000Ri20: Ri_b = 0.2</p> <p>Re20000Ri30: Ri_b = 0.3</p> <p>Re20000Ri40: Ri_b = 0.4</p> <p>Re20000Ri50: Ri_b = 0.5</p> <p>Every dat file (within the zip archives) is in ascii format and has 10 rows and 286 columns. Each row corresponds to normalized time (ranging from 1 to 10). Each column represents vertical model levels. </p>
Data from: Ocean warming and acidification alter the behavioural response to flow of the sea urchin Paracentrotus lividus
Ocean warming (OW) and acidification (OA) are intensively investigated as they pose major threats to marine organism. However, little effort is dedicated to another collateral climate change stressor, the increased frequency and intensity of storm events, here referred to as intensified hydrodynamics. A 2-month experiment was performed to identify how OW and OA (temperature: 21°C; pHT: 7.7, 7.4; control: 17°C-pHT7.9) affect the resistance to hydrodynamics in the sea urchin Paracentrotus lividus using an integrative approach that includes physiology, biomechanics and behaviour. Biomechanics was studied under both no-flow condition at the tube foot (TF) scale and flow condition at the individual scale. For the former, TF disk adhesive properties (attachment strength, tenacity) and TF stem mechanical properties (breaking force, extensibility, tensile strength, stiffness, toughness) were evaluated. For the latter, resistance to flow was addressed as the flow velocity at which individuals detached. Under near- and far-future OW and OA, individuals fully balanced their acid-base status, but skeletal growth was halved. TF adhesive properties were not affected by treatments. Compared to the control, mechanical properties were in general improved under pHT7.7 while in the extreme treatment (21°C-pHT7.4) breaking force was diminished. Three behavioural strategies were implemented by sea urchins and acted together to cope with flow: improving TF attachment, streamlining and escaping. Behavioural responses varied according to treatment and flow velocity. For instance, individuals at 21°C-pHT7.4 increased the density of attached TF at slow flows or, controlled TF detachment at fast flow to compensate for weakened TF mechanical properties. They also showed an absence of streamlining favouring an escaping behaviour as they ventured in a riskier faster movement at slow flows. At faster flows, the effects of OW and OA were detrimental causing earlier dislodgment. These plastic behaviours reflect a potential scope for acclimation in the field, where this species already experiences diel temperature and pH fluctuations.
Designing and Comparing Optimized Pseudo-Continuous Arterial Spin Labeling Protocols for Measurement of Cerebral Blood Flow
<p>This repository contains the the simulation data, preprocessed in vivo data, and analysis code used in the NeuroImage article titled 'Designing and Comparing Optimized Pseudo-Continuous Arterial Spin Labeling Protocols for Measurement of Cerebral Blood Flow' (<a href="https://doi.org/10.1016/j.neuroimage.2020.117246">https://doi.org/10.1016/j.neuroimage.2020.117246</a>). Please cite this article if you use this code or data in your work.</p>
Data from: Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype
<p><span><span>Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident </span><span><span>European </span></span><span>brook lamprey (</span><i><span><span>Lampetra planeri</span></span></i><span>) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) a </span><span><span>positive effect of</span></span><span> admixture with the closely related anadromous</span><span><span> river lamprey</span></span><span> (</span><i><span><span>L. fluviatilis</span></span></i><i><span><span>)</span></span></i><span> ecotype on </span><i><span><span>L. planeri</span></span></i><span> genetic diversity. We genotyped 2472 individuals, including 225 </span><i><span><span>L. fluviatilis</span></span></i><span>, sampled </span><span><span>from</span></span><span> 81 sites upstream and downstream barriers to migration, in 29 </span><span><span>western </span></span><span>European rivers. Linear modelling revealed a strong positive relationship between </span><span><span>genetic diversity and</span></span><span> the distance </span><span><span>from </span></span><span><span>the</span></span><span><span> river</span></span><span> source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal </span><span><span>mediated by</span></span><span> water flow. Downstream </span><i><span><span>L. planeri </span></span></i><span>populations in sympatry with </span><i><span><span>L. fluviatilis </span></span></i><span>displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic </span><span><span>make-</span></span><span>up of upstream </span><i><span><span>L. planeri </span></span></i><span>populations</span><i><span> </span></i><span>whereas admixture between ecotypes maintains higher levels of genetic diversity in </span><i><span><span>L. planeri </span></span></i><span>populations</span><i><span> </span></i><span>sympatric</span><i><span> </span></i><span>with </span><i><span><span>L. fluviatilis</span></span></i><span>. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks. </span></span></p>
Datasets for Mixed support for gene flow as a constraint to local adaptation and contributor to the limited geographic range of an endemic salamander
<p>Understanding mechanisms that underlie species range limits is at the core of evolutionary ecology. Asymmetric gene flow between larger core populations and smaller edge populations can swamp local adaptation at the range edge and inhibit further range expansion. However, empirical tests of this theory are exceedingly rare. We tested the hypothesis that asymmetric gene flow can constrain local adaptation and thereby species' range limits in an endemic US salamander (<i>Ambystoma barbouri</i>) by determining if gene flow is asymmetric between the core and peripheries of the species' geographic distribution and testing whether local adaptation is swamped at range edges with a reciprocal transplant experiment. Using putatively neutral loci from populations across three core-to-edge transects that covered nearly the entire species' geographic range, we found evidence for asymmetric, core-to-edge gene flow along western and northern transects, but not along a southern transect. Subsequently, the reciprocal transplant experiment suggested that northern and western edge populations are locally adapted despite experiencing asymmetric gene flow yet have lower fitness in their respective home regions than center populations do. Conversely, southern populations exhibit low deme quality, experiencing high mortality regardless of where they were reared, likely due to harsher edge habitat conditions. Consequently, we provide rare species-wide evidence that local adaptation can occur despite asymmetric gene flow, though migration from the core may prohibit range expansion by reducing fitness in edge populations. Further, our multi-transect study shows that multiple, non-mutually exclusive mechanisms can lead to range limits within a single species.</p>
Marilao River Flow Direction
<p>Marilao River Flow Direction</p>
Dataset for paper "Flow Resistance for a Varying Density of Obstacles on Smooth and Rough Beds"
<p>This dataset contains the experimental data that supports the paper:</p> <p>Guillén-Ludeña, S., Lopez, D., Mignot, E., & Riviere, N. (2019). Flow Resistance for a Varying Density of Obstacles on Smooth and Rough Beds. <em>Journal of Hydraulic Engineering</em>, <em>146</em>(2), 04019059.</p> <p>The file Readme.txt contains al explanations regarding the data organization.</p>
A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations
<p>Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that form two large-small pairs. We sequenced thousands of ultraconserved elements (UCEs) of the Fiji bush-warbler<i> Horornis ruficapilla</i>, a passerine distributed on these four Fijian islands, and performed a demographic analysis to test hypotheses of the effects of island size and distance on rates of gene flow. Our demographic analysis inferred low levels of gene flow from each large island to its small counterpart and little or none in the opposite direction. The difference in the distance between these two island pairs manifested itself in lower levels of gene flow between more distant islands. Both findings are generally concordant with classic island biogeography. The amount of reduction in gene flow based on distance was consistent with predictions from island biogeographic equations, while the reduction from small to large islands was possibly greater than expected. These findings offer a hypothesis and framework to guide future study of inter-island gene flow in archipelagos as the study of island biogeography progresses into the genomic era.</p>
ScienceDex guides
Understand access before you commit
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.