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373 results for “natural selection”
Supplemental data from: Nature or nurture: A genetic basis for the behavioral selection of depth in siscowet and lean lake charr (Salvelinus namaycush) ecomorphs
<p>These files contain the raw depth and temperature sensor data from siscowet and lean lake charr (<em>Salvelinus namaycush</em>) ecomorphs tagged with pop-up satellite archival tags (PSATs). These fish were produced from wild gametes taken from Lake Superior and reared in a common garden study for nine years and then tagged with PSATs and released in southern Lake Superior. The dataset is supplemental to:</p> <p>Goetz, F., Sitar, S., Seider, M., and Jasonowicz, A. 2022. Nature or nurture: A genetic basis for the behavioral selection of depth in siscowet and lean lake charr (<em>Salvelinus namaycush</em>) ecomorphs. Canadian Journal of Fisheries and Aquatic Sciences. (in press).</p> <p><strong>Data description for metadata.csv:</strong></p> <p>This file contains the metadata associated with each tag deployment. This includes biological data as well as key mission paramters.</p> <table> <thead> <tr> <td>Column</td> <td>Type</td> <td>Description</td> </tr> </thead> <tbody> <tr> <td>mission_id</td> <td>integer</td> <td>mission identifier</td> </tr> <tr> <td>tag_sn</td> <td>integer</td> <td>tag serial number</td> </tr> <tr> <td>ecotype</td> <td>string</td> <td>lake trout ecotype</td> </tr> <tr> <td>release_date</td> <td>string</td> <td>date of tag release</td> </tr> <tr> <td>length_mm</td> <td>float</td> <td>total length in mm</td> </tr> <tr> <td>weight_g</td> <td>float</td> <td>weight in g</td> </tr> <tr> <td>lipid</td> <td>float</td> <td>lipid level meadured by Distell fatmeter set in research mode</td> </tr> <tr> <td>release_site</td> <td>string</td> <td>release site (deep or shallow site)</td> </tr> <tr> <td>sampling_rate</td> <td>string</td> <td>sampling interval of tag (format=HH:MM:SS)</td> </tr> <tr> <td>mission_end_utc</td> <td>datetime</td> <td>programmed tag pop off date and time in UTC time (format=YYYY-MM-DD HH:MM:SS)</td> </tr> <tr> <td>notes</td> <td>string</td> <td>notes and comments</td> </tr> </tbody> </table> <p> </p> <p><strong>Data description for the raw sensor data files:</strong></p> <p>The raw sensor data is found in the files that are prefixed with "raw-sensor-data". The data for each tag is in contained in a seperate file and the files are named as follows "raw-sensor-data-{<em><strong>mission_identifier</strong></em>}-{<em><strong>tag_serial_number</strong></em>}.csv".</p> <table> <thead> <tr> <td>Column</td> <td>Type</td> <td>Description</td> </tr> </thead> <tbody> <tr> <td>mission_id</td> <td>integer</td> <td>mission identifier</td> </tr> <tr> <td>tag_sn</td> <td>integer</td> <td>tag serial number</td> </tr> <tr> <td>timestamp_utc</td> <td>datetime</td> <td>timestamp of sensor reading (format=YYYY-MM-DD HH:MM:SS)</td> </tr> <tr> <td>depth_m</td> <td>string</td> <td>depth in meters</td> </tr> <tr> <td>temperature_c</td> <td>string</td> <td>temperature in degrees celcius</td> </tr> </tbody> </table>
Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common "most genes conserved–few genes adaptive" genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.
Data from: Natural selection on antihelminth antibodies in a wild mammal population
<p>An effective immune response is expected to confer fitness benefits through improved resistance to parasites but also energetic costs which negatively impact fitness-related traits such as reproduction. These fitness costs and benefits of an immune response are likely to depend on host age, sex, and levels of parasite exposure. Few studies have examined the full extent to which patterns of natural selection on immune phenotypes vary across demographic groups and environments in the wild. Here, we assessed natural selection on plasma levels of three functionally distinct isotypes (IgA, IgE and IgG) of antibodies against a prevalent nematode parasite measured in a wild Soay sheep population over 25 years. We found little support for environment-dependent selection or reproductive costs. However, antibody levels were negatively associated with parasite egg counts and positively associated with subsequent survival, albeit in a highly age- and isotype-dependent manner. Raised levels of anti-parasite IgA best predicted reduced egg counts but this did not predict survival in lambs, whilst in adult females increased anti-parasite IgG predicted reduced egg counts and improved survival. Our results highlight the potential importance of age-dependent selection on immune phenotypes in nature, and that patterns of selection can vary even amongst functionally-related immune markers.</p>
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome
<p><br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.</p> <p>1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts</p> <p>5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups </p> <p>6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.</p> <p>7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2.</p> <p>8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.</p> <p>9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. </p> <p>10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.</p> <p>11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples. </p>
Data for: Sexual dichromatism may not be a good index of sexual or natural selection in the blue cardinalids (Aves: Passeriformes).
<p>More than a century ago, Darwin and Wallace started a still ongoing debate over which are the predominant forces driving sexual dichromatism (i.e., differences in body coloration between males and females): is it sexual selection on males to become more attractive, or is it natural selection on females to become more cryptic? While these are not mutually exclusive, the degree of sexual dichromatism has been extensively used as a proxy of the intensity of one type of selection (sexual) on one of the sexes (males). Here, we evaluated the relationship between sexual dichromatism and two body-color features that can be under natural and/or sexual selection in each sex: conspicuousness against the background and colorfulness (which we defined as the variety of colors and mechanisms to produce them within an individual's plumage). We focused on the 'blue clade' of the Cardinalidae bird family and considered the properties of their own visual system and those of potential raptor predators. We found that all blue cardinalids are sexually dichromatic, but levels of dichromatism vary within the clade. Males are on average more colorful than females, but neither male nor female colorfulness correlates with sexual dichromatism. Males are not more conspicuous than females against a vegetated background but are significantly more conspicuous against a nesting background than females. Yet, we found no correlation between conspicuousness and degree of sexual dichromatism. Our results suggest that, while both natural and sexual selection can drive color differences between the sexes, levels of sexual dichromatism do not necessarily reflect intensity of selection forces in this clade. Our results highlight the importance of testing assumptions regarding the relationship between sexual dichromatism and color evolution in each sex, considering the properties of different visual systems, relevant to the ecology of the study model.</p>
Genetic diversity and efficacy of natural selection in spiders with pre-copulatory sexual cannibalism
<p>Factors that increase reproductive variance among individuals act to reduce effective population size (Ne), which accelerates loss of genetic diversity and decreases efficacy of purifying selection. These factors include sexual cannibalism, offspring investment, and mating system. Pre-copulatory sexual cannibalism where the female consumes the male prior to mating exacerbates this effect. We performed comparative transcriptomics in two spider species, the cannibalistic Trechaleoides biocellata and the non-cannibalistic T. keyserlingi, to generate genomic evidence to support these predictions. First, we estimated heterozygosity and found that genetic diversity is relatively lower in the cannibalistic species. Second, we calculated dN/dS ratios as a measure of purifying selection, higher dN/dS ratio indicated relaxed purifying selection in the cannibalistic species. These results are consistent with the hypothesis that sexual cannibalism impacts operational sex ratio and demographic processes, which interact with evolutionary forces to shape the genetic structure of populations. However, other factors such as the mating system and life-history traits contribute to shape Ne. Comparative analyses across multiple contrasting species-pairs would be required to disentangle these effects. Our study highlights that extreme behaviours such as pre-copulatory cannibalism may have profound eco-evolutionary effects. </p>
Processed RNA expression count data from Groen et al.: The strength and pattern of natural selection on rice gene expression
<p>We assessed transcriptome variation in populations of 216 accessions of rice, <em>Oryza sativa</em>, which represented all major varietal groups including indica and japonica. During the 2016 Philippines dry season the accessions were planted in triplicate (with two accessions planted in triplicate three times as replicated checks) in identical alpha-lattice layouts of 660 plots in two fields: a continuously wet paddy, and a field where plants were exposed to intermittent drought in the vegetative and reproductive stages. We measured transcript levels in leaf blades of 50-day-old plants at 33 days after seedling transplant, and 17 days after withholding water in the dry field, using a liquid automation-based 3’ mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library. Raw sequencing data are available at the SRA in BioProject accession number PRJNA588478. A key to the raw sequencing data in this BioProject can be found in the metadata of the processed RNA expression count data here.</p>
Selected Simple Natural Antimicrobial Terpenoids as Additives to Control Biodegradation of Polyhydroxy Butyrate
<p><strong>Abstract</strong></p> <div>In this experimental research, different types of essential oils (EOs) were blended with polyhydroxybutyrate (PHB) to study the influence of these additives on PHB degradation. The blends were developed by incorporating three terpenoids at two concentrations (1 and 3%). The mineralization rate obtained from CO<sub>2</sub> released from each sample was the factor that defined biodegradation. Furthermore, scanning electron microscope (SEM), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA) were used in this research. The biodegradation percentages of PHB blended with 3% of eucalyptol, limonene, and thymol after 226 days were reached 66.4%, 73.3%, and 76.9%, respectively, while the rate for pure PHB was 100% after 198 days, and SEM images proved these results. Mechanical analysis of the samples showed that eucalyptol had the highest resistance level, even before the burial test. The other additives showed excellent mechanical properties although they had less mechanical strength than pure PHB after extrusion. The samples’ mechanical properties improved due to their crystallinity and decreased glass transition temperature (Tg). DSC results showed that blending terpenoids caused a reduction in Tg, which is evident in the DMA results, and a negligible reduction in melting point (Tm).</div> <p> </p> <p><strong>Open access data</strong></p> <p>The datasets for this publication can be accessed using the DOI: 10.5281/zenodo.13829790 or via the zip folder below.</p>
Data and Software associated with the paper "``A New Likelihood-based Test for Natural Selection''"
<p>Data and Software associated with the paper ``A New Likelihood-based Test for Natural Selection''</p>
Figure S1 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure S1. Conserved sites of ribosomal protein 40S subunit labeling on crystal structure. The ribbons colored in red represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic s. lat. sites of Eukaryota, and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The magenta ribbons represent the sites related to DBA, and the sites presented by sticks and balls are also synapomorphic sites. Because there are too many synapomorphic sites according to clades lower than Eukaryota in the RP, only the synapomorphic sites related to DBA are colored in this figure (shown in orange).
Figure S2 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure S2. Conserved sites of ribosomal protein 60S subunit labeling on crystal structure. The ribbons colored in red represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic s. lat. sites of Eukaryota and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The magenta ribbons represent the sites related to DBA, and the sites shown by sticks and balls are also synapomorphic sites. Because there are too many synapomorphic sites according to clades lower than Eukaryota in the RP, only the synapomorphic sites related to DBA are colored in this figure (shown in orange).
Figure 1 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure 1. Summarized distribution of group-specific sites in the cladogram of eukaryotic diversification. The numerals shown above the line correspond to RPL, and the numerals shown below correspond to RPS. The Ecdysozoa-Neoptera and Chordata-Mammalia lineages are highlighted with blue and yellow, respectively. The amino acids with equivalent biochemical properties were not taken into account.
Figure 2 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure 2. Conserved sites in the tertiary structures of RPL11 (A) and RPS19 (B). The red ribbons represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic sites s. lat. of Eukaryota, and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The ribbons with sticks and balls represent sites related to DBA. The synapomorphic sites related to DBA are shown in orange. The magenta ones represent the sites for which it is difficult to deduce the synapomorphy but appear to be related to DBA.
The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases
<p>Files used to create binary annotations for LDSC in the following repository: https://github.com/RHReynolds/als-neanderthal-analysis.</p> <p>See the following link for details: https://github.com/RHReynolds/als-neanderthal-analysis/tree/main/raw_data/01_annotations</p>
Quantification of the value of selected Nature's Contributions to People provided by Low Trophic Species aquaculture
<p>This dataset was generated by the work on quantification of Nature’s Contributions to People (NCPs) provided by Low Trophic Species (LTS) aquaculture. The quantification and analysis of selected NCPs was performed based on selected indicators using data from the case studies within the AquaVitae project and literature reviews.</p>
Data from: Natural selection after severe winter favors larger and duller bluebirds
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The role of human hunters and natural predators in shaping the selection of behavioral types in male wild turkeys
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Data from: Natural selection on antihelminth antibodies in a wild mammal population
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Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence
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Data from: Mating competition among females: testing the distinction between natural and sexual selection in an insect
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.
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