Find research datasets worth reusing

opencc-zeroAug 2020View details →

Data from: Foraging behaviour and habitat-use drives niche segregation in sibling seabird species

<p>To mediate competition, similar sympatric species are assumed to utilise different resources, or the same but geographically separated resources. The two giant petrels (<em>Macronectes</em> spp.) are intriguing in that they are morphologically similar seabirds with overlapping diets and distributions. To better understand the mechanisms allowing their co-existence, we investigated intra- and interspecific niche segregation at Marion Island (Southern Indian Ocean), one of the few localities where they breed in sympatry. We used GPS tracks from 94 individuals and remote-sensed environmental data to quantify habitat-use, combined with blood carbon and nitrogen stable isotope ratios from 90 individuals to characterise their foraging habitat and trophic ecology. Females of both species made distant at sea foraging trips and fed at a similar trophic level. However, they used distinct pelagic habitats. In contrast, males of both species mainly foraged on or near land, resulting in significant sexual segregation, but high interspecific habitat and diet overlap. However, some males showed flexible behavioural strategies, also making distant, pelagic foraging trips. Using contemporaneous tracking, environmental and stable isotope data we provide a clear example of how sympatric sibling species can be segregated along different foraging behaviour dimensions.</p>

opencc-by-4.0Dec 2020View details →

DEM simulations of size-segregation during bedload transport

<p>This depository contains the data of all DEM simulations used in the publication Chassagne, R., Maurin, R., Chauchat, J., Gray, J., & Frey, P. (2020). Discrete and continuum modelling of grain size segregation during bedload transport. <em>Journal of Fluid Mechanics,</em> <em>895</em>, A30. doi:10.1017/jfm.2020.274, as well as post processing scripts to use the data.</p> <p>The simulations are located in two folders, fine/ (simulations for which the amount of fine particles is varied) and sizeRatio (simulations for which the size ratio between large and small particles is varied). The data of each simulations are contained in separate subfolders named after the simulation. For example, Fine2R1.5/ corresponds to a simulation with 2 layers of small particles and a size ratio of 1.5. For each simulation, the time data are saved in data.hdf5 and averaged data in average.hdf5. A GeomParam.txt file is also in each folder. It contains information of the simulation that the  post processing programm will read. The python script used to initiate the YADE-DEM simulation  is also given for information (it contains all parameters of the simulation).</p> <p>The post-processing program has been coded in python2.7 with an oriented-object procedure.  The h5py package is necessary to read the .hdf5 files. The scripts do not work in python3, but can be  very easily adapted if necessary (you only have to modify the "print" functions).  The scripts are available in ScriptsPP/ and are organized as follow. A mother class in SegregationPP and two child classes SegFull (to load the full time data set) and SegMean (to load only average data). A script examplePP.py is proposed and shows how to manipulate theses classes and the data.</p>

opencc-zeroAug 2014View details →

VCF file of Variants in a wide onion cross segregating for bolting

<p>VCF (variant call format) file of variants from bulked segregant RNA PoolSeq (BSR-seq) of F2 progeny pools of a wide onion cross segregating for bolting (precocious flowering). The reference assembly is GBGJ00000000.1 http://www.ncbi.nlm.nih.gov/nuccore/656904698</p> <p>The pools were taken from materials sampled for validation of the <em>AcBlt1</em> locus as described in http://www.ncbi.nlm.nih.gov/pubmed/24247236</p> <p>Pools were from bolting or non-bolting plants homozygous at the most closely linked marker to <em>AcBlt1  </em>either for the bolt-associated genotype (AA) or the non-bolt genotype (BB). </p>

opencc-by-4.0Mar 2024View details →

Human Psychophysics Dataset on Figure Ground Segregation in Texture Stimuli

<div> <div>The dataset is derived from a psychophysics experiment where 8 participants discriminated the orientation of a rectangular figure within a texture stimulus comprised of Gabor annuli. The figure region differed from the background in its contrast distribution, controlled by two independent variables: Contrast Heterogeneity and Grid Coarseness. Contrast Heterogeneity refers to the range of contrasts exhibited by Gabor annuli. In this experiment, there were five values for Contrast Heterogeneity in the figure: 0.01, 0.2575, 0.505, 0.7525, and 1. The contrast distribution of the background was always maximally heterogeneous with Contrast Heterogeneity equal to 1.  Grid Coarseness, on the other hand, refers to the scaling factor that controls the spacing between the Gabor annuli. It determines the density of the grid pattern in the background <em>and</em> the figure region. In this experiment, there were five values for Grid Coarseness: 1, 1.125, 1.250, 1.375, and 1.5. The experiment consisted of 9 sessions, each containing multiple blocks of trials. Each block of trials contained 25 unique stimulus conditions, defined by the combination of Contrast Heterogeneity and Grid Coarseness.</div> <div> <p><strong>Stimuli, Tasks, and Procedure </strong></p> </div> <div> <p>Each texture stimulus consisted of a full-screen irregular grid of non-overlapping Gabor annuli placed on a grey background. The Gabor annuli had a diameter of 0.7°, a spatial frequency of 5.7 cycles/degree, and a mean luminance of 60.76 Cd/m2. Embedded within this texture was a rectangular figure region located in the lower right quadrant of the screen, which differed from the rest of the texture in the contrast distribution of its annuli. For sessions 1-8, the figure center was placed at an eccentricity of (7 ± 1)° but slightly varied in terms of polar angle such that it was completely inside the lower right quadrant. For session 9 (transfer session), the figure was placed in the upper left quadrant. </p> </div> <div> <p>Participants were required to indicate whether the rectangular figure was oriented horizontally or vertically by pressing the right and left arrow keys, respectively. The experiment employed a two-alternative forced-choice design, in which participants had to make a decision about the orientation of the figure in each trial. Responses were given with the middle and index fingers of the right hand. In each trial, the stimulus was presented for 1000 ms or less if the participant lost fixation or provided a response. Participants were required to maintain fixation throughout the presentation of the stimulus. </p> </div> <div> <p>After each trial, participants received feedback on their response. If the response was correct, a green fixation point was presented for 500 ms. If the response was incorrect, a red fixation point was presented for 500 ms. </p> </div> <div> <p>The experiment was conducted in a dimly lit room. A chin and head-rest was used to support the participant's head and to keep eye-screen distance constant at 57 cm. Stimuli were displayed on a 19'' Samsung SyncMaster 940BF LCD monitor. Stimulus representation and response recording were performed using Psychtoolbox-3 for Matlab 64-Bit (Version 3.0.14 - Build date: Apr 6th, 2018) running on a Windows operating system. Fixation was monitored with a desktop-mounted Eyelink 1000 eye-tracker (SR Research Ltd.) with a sampling frequency of 500 Hz or 1000 Hz and a spatial resolution of <0.01° RMS. Eye-movement data were down-sampled to 250 Hz. </p> </div> <div> <p><strong>Procedure for Handling Aborted Trials </strong></p> </div> <div> <p>If a participant's gaze fell outside the fixation window during the fixation period preceding the stimulus, or during stimulus presentation, the trial was aborted. Aborted trials were repeated at a randomly chosen time during the experiment. </p> </div> <div> <p><strong>Parametrization of the Experimental Setup </strong></p> </div> <div> <p>The eye-screen distance was set to 57 cm. The stimulus presentation time was set to 1000 ms. The inter-trial interval was set to 900 ms. Each session consisted of 30 blocks, with 25 trials per block. </p> </div> <div> <p><strong>Transfer Session </strong></p> </div> <div> <p>The transfer session (session 9) was unique in that the rectangular figure was presented in the upper left quadrant of the screen, rather than the lower right quadrant as in sessions 1-8. This was done to test the transfer of learning to a new location. Participants were made aware of the figure displacement but were not told in which quadrant to expect it. </p> </div> <div> <p><strong>Variables </strong></p> </div> <div> <p>The dataset includes identifiers for each participant (SubjectID), session (SessionID), and block of trials (BlockID). For each trial, the dataset includes the condition (Condition), the contrast heterogeneity (ContrastHeterogeneity), the grid coarseness (GridCoarseness), the participant's response (IndicatedOrientation), the actual orientation of the rectangular region (ActualOrientation), and whether the participant's response was correct (Correct). The dataset also includes demographic information comprising their unique identifier (SubjectID), age (Age), and sex (Sex). </p> <p><strong>Ethics</strong></p> <p>After receiving full information about all procedures and about the right to withdraw participation at any time, they provided written informed consent according to the Helsinki Declaration. All procedures were approved by the local Ethical Committee of the Faculty of Psychology and Neuroscience (ERCPN). Participants received<br>monetary reward.</p> </div> </div>

opencc-zeroJan 2022View details →

Frequency-dependent hybridization contributes to habitat segregation in monkeyflowers

<p>Spatial segregation of closely related species is usually attributed to differences in stress tolerance and competitive ability. For both animals and plants, reproductive interactions between close relatives can impose a fitness cost that is more detrimental to the rarer species. Frequency-dependent mating interactions may thus prevent the establishment of immigrants within heterospecific populations, maintaining spatial segregation of species. Despite strong spatial segregation in natural populations, two sympatric California monkeyflowers (<i>Mimulus nudatus</i> and <i>M. guttatus</i>) survive and reproduce in the other's habitat when transplanted reciprocally. We hypothesized that a frequency-dependent mating disadvantage maintains spatial segregation of these monkeyflowers during natural immigration. To evaluate this hypothesis, we performed two field experiments. First, we experimentally added immigrants in varying numbers to sites dominated by heterospecifics. Second, we reciprocally transplanted arrays of varying resident and immigrant frequency. Immigrant seed viability decreased with conspecific rarity for <i>M. guttatus</i>, but not <i>M. nudatus</i>. We observed immigrant minority disadvantage for both species, but driven by different factors– frequency-dependent hybridization for <i>M. guttatus</i>, and competition for resources and/or pollinators for <i>M. nudatus</i>. Overall, our results suggest a major role for reproductive interference in spatial segregation that should be evaluated along with stress tolerance and competitive ability.</p>

opencc-zeroMay 2022View details →

Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load

<p>Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive- the driver and the target- linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal, multilocus, male meiotic drive system, Segregation Distorter (SD) in the fruit fly, Drosophila melanogaster. In African populations, the predominant SD chromosome variant, SD-Mal, is characterized by two overlapping, paracentric inversions on chromosome arm 2R and nearly perfect (~100%) transmission. We study the SD-Mal system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying Sd, the main driving allele, and one or more factors within the double inversion. While most SD-Mal chromosomes are homozygous lethal, SD-Mal haplotypes can recombine with other, complementing haplotypes via crossing over, and with wildtype chromosomes via gene conversion. SD-Mal chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, SD-Mal haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of SD haplotypes in different populations around the world, and have implications for supergene evolution broadly.</p>

openmit-licenseJun 2022View details →

The segregation of recycled basaltic material within mantle plumes explains the detection of the X-Discontinuity beneath hotspots: 2D geodynamic simulations: Data

<pre>This repository accompanies the paper ``` The segregation of recycled basaltic material within mantle plumes explains the detection of the X-Discontinuity beneath hotspots: 2D geodynamic simulations by Martina Monaco, Juliane Dannberg, Rene Gassmoeller, Stephen Pugh ``` The global models presented in the manuscript were run using the following dependencies: ``` ----------------------------------------------------------------------------- -- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion. -- . version 2.3.0-pre (master, 74e48be) -- . using deal.II 9.3.0 -- . with 32 bit indices and vectorization level 2 (256 bits) -- . using Trilinos 12.10.1 -- . using p4est 2.2.0 ----------------------------------------------------------------------------- ``` This repository contains: - The 'all_model_series' folder with the files used to analyze the depth averages. Each series (100, Aoki, Hefesto) has its own subfolder; - The 'plugins' folder, with the required plugin to run the models. To compile the plugin, navigate into this directory and follow the steps: 1. `cmake -D Aspect_DIR=PATH_TO_ASPECT` (replace `PATH_TO_ASPECT` with the directory where you compiled ASPECT). 2. `make` - The 'run_series' bash script, with the command to run multiple models at once. The user should modify: ° The input file name: INPUT_FILE=heterogeneity-several-blobs-INSERT-SERIES.prm ° The directory where ASPECT is located: srun --mpi=pmix_v2 $HOME/aspect/aspect-build/aspect --" echo -e $COMMAND | sbatch --job-name gs_${viscosity}_spacing_${blob_spacing} -p hpg2-compute -N 1 -n 32 -t 3-23:59:00 -o output_gs_${viscosity}_spacing_${blob_spacing}.%j -e error_gs_${viscosity}_spacing_${blob_spacing}.%j --constraint 'haswell|skylake' --mem-per-cpu '3gb' --distribution block; - The three parameter files (.prm), one per series; - Two .py files containing the scripts necessary to plot all the figures in the paper</pre>

opencc-zeroAug 2022View details →

Biodiversity cradles and museums segregating within hotspots of endemism

<p>The immense concentrations of vertebrate species in tropical mountains remain a prominent but unexplained pattern in biogeography. A long-standing hypothesis suggests that montane biodiversity hotspots result from endemic species aggregating within ecologically stable localities. Here, the persistence of ancient lineages coincides with frequent speciation events, making such areas both 'cradles' (where new species arise) and 'museums' (where old species survive). Although this hypothesis refers to processes operating at the scale of valleys, it remains supported primarily by patterns generated from coarse-scale distribution data. Using high-resolution occurrence and phylogenetic data on Andean hummingbirds, we find that old and young endemic species are not spatially aggregated. The young endemic species tend to have non-overlapping distributions scattered along the Andean treeline, a long and narrow habitat where populations easily become fragmented. By contrast, the old endemic species have more aggregated distributions, but mainly within pockets of cloud forests at lower elevations than the young endemic species. These findings contradict the premise that biogeographical cradles and museums should overlap in valley systems where pockets of stable climate persist through periods of climate change. Instead, Andean biodiversity hotspots may derive from large-scale fluctuating climate complexity in conjunction with local-scale variability in available area and habitat connectivity.</p>

Fig. 5 in Spatial Segregation of Diploid and Polyploids Spined Loaches (Сobitis elongatoides-taenia-tanaitica) in the River Systems of Western and Central Ukraine

Fig. 5. Changes in the frequency of polyploids in samples of spined loaches from the Teteriv River, depending on the distance from the mouth. The approximation is performed with a polynomial function.

Fig. 4 in Spatial Segregation of Diploid and Polyploids Spined Loaches (Сobitis elongatoides-taenia-tanaitica) in the River Systems of Western and Central Ukraine

Fig. 4. Frequencies of polyploids and its standard errors in different parts of the first and second-order tributaries of the Dnipro River system: Lower — lower third of the channel, Middle — middle part of the channel, Upper — upper third of the channel. The approximation is performed with a polynomial function.

Fig. 3 in Spatial Segregation of Diploid and Polyploids Spined Loaches (Сobitis elongatoides-taenia-tanaitica) in the River Systems of Western and Central Ukraine

Fig. 3. Frequency of polyploids in spined loach settlements and its standard errors of rivers with different channel lengths, as well as in accessory systems of the rivers (ASR) of the Western and Central Ukraine. The approximation is performed with a polynomial function.

Fig. 2 in Spatial Segregation of Diploid and Polyploids Spined Loaches (Сobitis elongatoides-taenia-tanaitica) in the River Systems of Western and Central Ukraine

Fig. 2. Frequencies of polyploids in spined loach settlements and its standard errors depending on the type of water system of the Western and Central Ukraine. M — main channel, Tr-1, Tr-2, Tr-3 — first, second, and the third-order tributaries, L — lakes. The approximation is performed with a polynomial function.

Fig. 1 in Spatial Segregation of Diploid and Polyploids Spined Loaches (Сobitis elongatoides-taenia-tanaitica) in the River Systems of Western and Central Ukraine

Fig. 1. Distribution of polyploid frequencies in spined loach settlements of the water systems of the Western and Central Ukraine. The approximation is performed with a polynomial function.

opencc-by-4.0Apr 2024View details →

An experimental dataset to explore the size ratio impact on an intruder segregating in bedload transport

<p>This repository gathers :</p> <ul> <li>The treated data used in the article "Exploring the size ratio impact on an intruder segregating in bedload transport" from Dedieu B., Rousseau H., Frey P. and Chauchat J. in Physical Review of Fluids (DOI: <a href="https://doi.org/10.1103/PhysRevFluids.9.104302" target="_blank" rel="noopener">10.1103/PhysRevFluids.9.104302</a>),</li> <li>Some re-computed data from the experiments of <a href="https://doi.org/10.1103/PhysRevFluids.7.064305" target="_blank" rel="noopener">Rousseau H. et al.(2022)</a> in csv format,</li> <li>A python3 package <em>codes</em> used to load the data.</li> </ul> <p>Explanations on how to use the codes and how the data are organized can be found in the <em>README.md</em>.</p> <p>Feel free to contact the authors if you need more information or wish to access the raw image data.</p>

opencc-by-4.0Mar 2018View details →

RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology

<p>This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology</p>