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.
32
datasets available to search
ShareScore release 0.9.0
Dataset results
32 results for “population formation”
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone. in Mortality Profiles Of Castor And Trogontherium (Mammalia: Rodentia, Castoridae), With Notes On The Site Formation Of The Mid-Pleistocene Hominin Locality Bilzingsleben Ii (Thuringia, Central Germany)
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone.
Speciation rates are unrelated to the formation of population structure in Malagasy Gemsnakes
<p><span>Speciation rates vary substantially over the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary processes exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have shown both correlation and no correlation. No study has examined the relationship between speciation rates and population structure in a young group endemic to an island. We examine this correlation in 109 Gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar originating in the early Miocene, thus controlling for extinction associated with time and area. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of Gemsnakes. Rates of speciation show low variation, and population structure varying widely across species indicates that speciation rates and population structure disconnection are largely due to persistence of lineages not susceptible to extinction. Extinction can be due to many factors all of which can prevent long-term persistence of species. We discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.</span></p>
Speciation rates are unrelated to the formation of population structure in Malagasy Gemsnakes
Open the record for dataset details and reuse information.
Formation pathway of Population III coalescing binary black holes through stable mass transfer
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2017MNRAS.468.5020I">Inayoshi et al. (2017)</a>. MESA version 8845.</p> <p>Publication DOI: <a href="https://doi.org/10.1093/mnras/stx757">10.1093/mnras/stx757</a></p>
Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
<div> <div> <div> <p>Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain- dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.</p> </div> </div> </div>
Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
Open the record for dataset details and reuse information.
Data from: The social formation of fitness: Lifetime consequences of prenatal nutrition and postnatal care in a wild mammal population
Open the record for dataset details and reuse information.
Fig. 4. Bivariate graphs for the Smilodon populator specimen MNHN-P 957. A in An extremely large saber-tooth cat skull from Uruguay (late Pleistocene -early Holocene, Dolores Formation): body size and paleobiological implications
Fig. 4. Bivariate graphs for the Smilodon populator specimen MNHN-P 957. A, PM3 transverse diameter (PM3ML) versus PM3 anteroposterior diameter (PM3AP); B, PM4 transverse diameter (PM4ML) versus PM4 anteroposterior diameter (PM4AP). Data from different sources (see Material and methods).
Figure 3. Bivariate graphs for the Smilodon populator specimen MNHN-P 957. A in An extremely large saber-tooth cat skull from Uruguay (late Pleistocene -early Holocene, Dolores Formation): body size and paleobiological implications
Figure 3. Bivariate graphs for the Smilodon populator specimen MNHN-P 957. A, zygomatic width (ZW) versus condylobasal length (CBL); B, canine transverse diam- eter (CML) versus canine anteroposterior diameter (CAP). Data from different sources (see Material and methods).
RAW data: Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell Lines - single cell RNAseq - Fastq format and UMI counts
<p>This data set of the single cell sequencing experiment of the urothelial cell line HBLAK belongs to the publication: "Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell Lines" Cancers 2020, 12(4), 1023; https://doi.org/10.3390/cancers12041023.</p> <p> </p>
Data from: Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea
Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.
Data from: The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks
Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host-plant associated ecotype formation in Timema cristinae stick insects. Using mate-pair re-sequencing of 20 new whole genomes we find that modest-sized structural variants such as inversions, deletions, and duplications are widespread across the genome, being retained as standing variation within and among populations. Using 160 previously published, standard-orientation whole genome sequences we find little to no evidence that the DNA sequences within inversions exhibit accentuated differentiation between ecotypes. In contrast, a formerly described large region of reduced recombination that harbors genes controlling color-pattern exhibits evidence for accentuated differentiation between ecotypes, which is consistent with differences in the frequency of color-pattern morphs between host-associated ecotypes. Our results suggest that some types of structural variants (e.g., large inversions) are more likely to underlie adaptive divergence than others, and that structural variants are not required for subtle yet genome-wide genetic differentiation with gene flow.
Dataset in csv format containing labor force data in a synthetic population
Open the record for dataset details and reuse information.
Mechanistic insights into silver-gold nanoalloy formation by two-dimensional population balance modeling
<p>This is the raw data for the manuscript:</p><p>Mechanistic insights into silver-gold nanoalloy formation by two-dimensional population balance modeling<br><br>Abstract:<br><br>The large-scale synthesis of nanoparticles (NPs) with defined properties requires detailed understanding of the underlying formation mechanisms and kinetics. The formation mechanisms of bimetallic NPs are still not sufficiently understood due to the complex reaction chemistry, which makes the control of the supersaturation within the reactor, as the thermodynamic driving force, challenging. Particle size, chemical composition, and the distribution of the elements within the particles change dynamically during particle formation. In this work, we propose a mechanism for the formation of bimetallic silver-gold alloy NPs via a green liquid-phase co-reduction synthesis and develop a two-dimensional population balance model to quantitatively describe the evolution of particle size, composition, and optical properties. We shed light on the complex multi-stage formation mechanism of a highly relevant bimetallic NP system and lay the foundation for tailoring the process conditions to achieve desired optical particle properties and to develop predictive property-process relationships.</p><p> </p><p>All data are sorted according to their appearance in the figures of the main manuscript.</p>
Dataset (MATLAB format) from Yang et al (2022) Thalamus-driven functional populations in frontal cortex support decision-making. Nat. Neurosci.
<p><strong>Summary</strong></p> <p>These experiments measure neuronal responses from the left hemisphere of premotor cortex (anterior lateral motor cortex, ALM) of adult mice performing pole location discrimination with a short-term memory. In a subset of the recordings, we inactivate activity of one of the brain regions providing inputs to ALM (ipsilateral S1/S2, contralateral ALM, and ipsilateral Thal<sub>ALM</sub>) in some trials.</p> <p>This dataset contains data from 9626 single units, 73 mice, 347 sessions. The dataset is described as “the primary dataset” in the paper below. The experiments (including experiment methods) are described in the paper.</p> <p><em>Yang W, Tipparaju SL, Chen G, Li N, (2022). Thalamus-driven functional populations in frontal cortex activity supports decision-making. Nat Neurosci, in press.</em></p> <p> </p> <p>The second dataset used in the paper can be downloaded also from Zenodo at</p> <pre><a href="https://doi.org/10.5281/zenodo.6713616">https://doi.org/10.5281/zenodo.6713616</a></pre> <p> </p> <p><strong>How to cite the data</strong></p> <p>If you publish any work using the data, please cite the Chen et. al., (2021) publication above and also cite the dataset in the following recommended format:</p> <p>Li N (2022); Data and simulations related to: Thalamus-driven functional populations in frontal cortex activity supports decision-making. Yang et al (2022) Nat Neurosci.</p> <p><a href="http://dx.doi.org/10.5281/zenodo.6846161">http://dx.doi.org/10.5281/zenodo.6846161</a></p> <p> </p> <p><strong>How to get started</strong></p> <p>Once downloaded</p> <p>1) unzip “<strong>func</strong>”</p> <p>2) unzip "<strong>scripts</strong>"</p> <p>3) Run any scripts "<strong>demo_*.m</strong>" within "<strong>scripts</strong>"</p> <p> </p> <p>A collection of analyses scripts that reproduce figures in " Yang et al (2022)" is included in the folder "<strong>\scripts\</strong>"</p> <p><strong>demo_compute_activity_modes_independentTrials.m</strong> – plot t-SNE embedding and all the response profile clusters; plots PSTHs from an example cluster; plots neurons connected to S1/S2, cALM, ThalALM on the t-SNE.</p> <p><strong>demo_compute_tSNE_embedding.m</strong> – t-SNE embedding of neuronal response profiles (based on PSTH shape)</p> <p><strong>demo_compute_activity_modes.m</strong> – compute activity modes from neuronal population responses.</p> <p><strong>demo_compute_selectivity_vector_stability.m</strong> – analysis of selectivity vectors</p> <p> </p> <p> </p>
Population synthesis data of massive binaries: NS/BH-core mergers and double compact objects formation and mergers
<p><span>Binary population synthesis data generated using the rapid population synthesis code COMPAS.</span></p> <p><span>Contains:</span></p> <p><span>1. Full COMPAS output in (.csv format) for running massive binaries varying the common envelope efficiency parameter and the metallicity.</span></p> <p><span>2. Identifying seeds of systems that result in neutron star (NS)/black hole (BH)-core mergers, binary NSs, binary BHs and NS-BH binaries. </span></p>
Data from: Genetic connectivity and diversity in inselberg populations of Acacia woodmaniorum, a rare endemic of the Yilgarn Craton banded iron formations
Historically rare plant species with disjunct population distributions and small population sizes might be expected to show significant genetic structure and low levels of genetic diversity due to the effects of inbreeding and genetic drift. Across the globe terrestrial inselbergs are habitat for rich, often rare and endemic flora and are valuable systems for investigating evolutionary processes that shape patterns of genetic structure and levels of genetic diversity at the landscape scale. We assessed genetic structure and levels of genetic diversity across the range of the historically rare inselberg endemic Acacia woodmaniorum. Phylogeographic and genetic structure indicates that connectivity is not sufficient to produce a panmictic population across the limited geographic range of the species. However, historical levels of gene flow are sufficient to maintain a high degree of adaptive connectivity across the landscape. Genetic diversity indicates gene flow is sufficient to largely counteract any negative genetic effects of inbreeding and random genetic drift in even the most disjunct or smallest populations. Phylogeographic and genetic structure, a signal of isolation by distance, and a lack of evidence of recent genetic bottlenecks suggest long term stability of contemporary population distributions and population sizes. There is some evidence that genetic connectivity among disjunct outcrops may be facilitated by the occasional long distance dispersal of Acacia polyads carried by insect pollinators moved by prevailing winds.
Figure 1 in Using short-term surveys and mark-recapture to estimate diversity and population size of orchid bees in forest formations of the Brazilian savanna
Figure 1. Marking method used in the study of euglossine populations. (a) During all populational estimatives. Each geometric shape corresponds to the day when the PTT was collected. Square = 1st day; circle = 2nd day; pentagon = 3rd day; triangle = 4th day; diamond = 5th day. (b) During the samplings occurred simultaneously in seasonal semi-deciduous (ssf) and gallery forest (ssf). Square = 1st day; circle = 2nd day; pentagon = 3rd day; square combined with spot on the wing = 4th day; circle combined with spot on the wing = 5th day.
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
<p class="MsoNormal"><span>We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from an F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies</span><span>. To </span><span>demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of three true albino bison and 45 wild-type pelage color bison. Through the examination of genomic </span>variants fixed in the albino cohort and absent in the controls<span>, we identified a nonsynonymous</span> single nucleotide polymorphism (SNP) <span>mutation on chromosome 29 </span>in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provide a highly robust and informative resource for <span>genomics </span>investigations for this iconic North American species.</p>
CoVid-19 - Infection and Antibody Formation in the Viennese Population
ClinicalTrials.gov study NCT04346264. IPD Sharing: NO. Countries: 1. Publications: 1.
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.