Find research datasets worth reusing

opencc-by-4.0Nov 2022View details →

Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays"

Datasets supporting the manuscript: Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays". BMC Ecology and Evolution 23, 31 (2023). https://doi.org/10.1186/s12862-023-02130-0 Nuclear data: "Mobula-alfredi_nuclear_reference_RAD_contigs.fasta" is a fasta of 359,751 contigs that serve as the reference for nuclear alignment of genotypes to RAD loci. Contigs begin and end with GATC cut site. Mobula-alfredi_nuclear_all_2048snps_38genotypes.vcf is a VCF file with all 2048 nuclear SNPs in final filtered SNP dataset. 38 genotypes are included from Maui Nui and Hawaii Island. This 2048 SNPs includes both 2038 neutral and 10 outlier SNPs.  Mobula-alfredi_nuclear_neutral_2038snps_38genotypes.vcf is a VCF file with 2038 neutral nuclear SNPs genotyped in 38 individuals from Maui Nui and Hawaii Island.  Mobula-alfredi_nuclear_outliers_10snps_38genotypes.vcf is a VCF file with 10 outlier SNPs genotyped in 38 individuals from Maui Nui and Hawaii Island.  Structure (.str) files are also provided in addition to VCFs. In all files Population prefixes M=Maui Nui and K=Hawaii Island.  Mitochondrial data: Mobula-alfredi_mitogenome_34haplotypes_9sites_min4x.vcf is a VCF file with 9 variant sites across the mitogenome haplotyped in 34 individuals from Maui Nui and Hawaii Island.  Mobula-alfredi_mitogenome_34haplotypes_allsites_min4x.fasta is a FASTA file with whole mitogenomes aligned to OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409]. Sites with less than 4x coverage were masked with Ns.  Mobula-alfredi_mitogenome_reference_OP562409.fasta is a FASTA file containing the Mobula alfredi reference mitogenome OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409].

opencc-by-4.0Feb 2018View details →

Data for: Patterns of shared signatures of recent positive selection across human populations

Genome-wide summary stats for modified iHS scan in 1KG as reported in: <a href="https://pubmed.ncbi.nlm.nih.gov/29459708/">Patterns of shared signatures of recent positive selection across human populations.</a> Johnson KE, Voight BF.Nat Ecol Evol. 2018 Apr;2(4):713-720. doi: 10.1038/s41559-018-0478-6. Epub 2018 Feb 19. PMID: 29459708 Code available at: https://github.com/bvoightlab/iHS_calc

opencc-by-4.0Oct 2022View details →

Data For: Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data

Simulation output and Genome-wide scan for nIBD variants in UK10K data as reported in: Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data Johnson KE, Adams CJ, Voight BF. Methods Ecol Evol 2022 Nov;13(11): 2429–2442. Code available at: https://github.com/kelsj/EVICORD

opencc-by-4.0Apr 2022View details →

Supporting Data Ferguson, Camenzind, et al., "Measurement-induced induced population switching", Phys. Rev. Research 5, 023028 (2023)

This repository contains data for the publication "Measurement-induced population switching", Phys. Rev. Research 5, 023028 (2023) by Ferguson, Camenzind, et al. Abstract Quantum information processing is a key technology in the ongoing second quantum revolution, with a wide variety of hardware platforms competing toward its realization. An indispensable component of such hardware is a measurement device, i.e., a quantum detector that is used to determine the outcome of a computation. The act of measurement in quantum mechanics, however, is naturally invasive as the measurement apparatus becomes entangled with the system that it observes. This always leads to a disturbance in the observed system, a phenomenon called quantum measurement backaction, which should solely lead to the collapse of the quantum wave function and the physical realization of the measurement postulate of quantum mechanics. Here we demonstrate that backaction can fundamentally change the quantum system through the detection process. For quantum information processing, this means that the readout alters the system in such a way that a faulty measurement outcome is obtained. Specifically, we report a backaction-induced population switching, where the bare presence of weak, nonprojective measurements by an adjacent charge sensor inverts the electronic charge configuration of a semiconductor double quantum dot system. The transition region grows with measurement strength and is suppressed by temperature, in excellent agreement with our coherent quantum backaction model. Our result exposes backaction channels that appear at the interplay between the detector and the system environments, and opens new avenues for controlling and mitigating backaction effects in future quantum technologies.

opencc-by-4.0May 2023View details →

Data from: Trends in butterfly populations in UK gardens – new evidence from citizen science monitoring

This data package describes the annual abundance indices and trend estimates for 22 butterfly species in UK gardens for the period 2007-2020. These data form the basis of the results presented in: Plummer, K.E., Dadam, D., Brereton, T., Dennis, E.B., Massimino, D., Risely, K. et al. (2023) Trends in butterfly populations in UK gardens—New evidence from citizen science monitoring. Insect Conservation and Diversity, 1– 13. Available from: <a href="https://doi.org/10.1111/icad.12645">https://doi.org/10.1111/icad.12645</a> Please refer to the paper for an explanation of the underlying BTO Garden BirdWatch (GBW) data and modelling protocols used to produce the datasets included here. We would also greatly appreciate if you could fill out <a href="https://forms.gle/DCc58VXpdmqnTmTk8" target="_blank" rel="noopener">this very short form</a> to tell us how you intend to use these data. Thanks in advance!

opencc-by-4.0May 2022View details →

Datasets, reproducible codes, and results for evaluating differential expression analysis methods on population-level RNA-seq data

This upload contains the necessary R codes and data to reproduce the FDR and Power results described in our correspondence "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" to Li Y, Ge X, Peng F, Li W, Li JJ, Exaggerated false positives by popular differential expression methods when analyzing human population samples, Genome Biology 23, 79, 2022, DOI: 10.1186/s13059-022-02648-4.

opencc-by-4.0Jan 2023View details →

Open-population models for estimating roadkill rates - Data and R Code

Roadkill carcass capture-recapture data, capture histories for four and eight-occasion designs, and R code (with JAGS code) for roadkill rates estimation.

opencc-by-4.0Oct 2023View details →

Data for Linkage mapping of root shape traits associated with market class in two biparental carrot populations

This repository contains essential data to support the findings presented in the forthcoming publication titled "Linkage Mapping of Root Shape Traits Associated with Market Class in Two Biparental Carrot Populations." It includes VCF files for two distinct carrot biparental populations, as well as R code for filtering, constructing linkage maps, and conducting QTL analysis. Furthermore, the repository hosts phenotypic data gathered from these two biparental populations during the years 2020 and 2021. Two carrot genetic maps, one for each population, have been made available alongside their respective phenotypic data. The provided R code contains absolute working directory paths that may not function as intended on your system. The primary purpose of sharing this code is to offer readers insight into the techniques employed in this study. You may need to adapt the directory paths to suit your specific setup.  To assist readers in understanding the logical sequence of steps involved in our linkage mapping project, the R code scripts have been sequentially numbered from 0 to 10. For more info contact: vegaalfaro@wisc.edu.

dryad44/100

Data from: Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

Open the record for dataset details and reuse information.

publicSep 2021View details →

openCC (other)May 2021View details →

Mammalian herbivores restrict the altitudinal range limits of three alpine grass species (transplant and herbivore exclusion experiment and demographic data from natural populations), West Elk Mountains, Colorado, USA 2015-2018

Though rarely experimentally tested, biotic interactions have long been hypothesized to limit low-elevation range boundaries of species. We tested the effects of herbivory on three alpine-restricted plant species by transplanting plants below (novel), at the edge (limit), or in the center (core) of their current elevational range and factorially fencing-out above- and belowground mammals in the West Elk Mountains, Colorado, USA from 2015-2018. Herbivore damage was greater in range limit and novel habitats than in range cores. Exclosures increased plant biomass and reproduction more in novel habitats than in range cores, suggesting demographic costs of novel interactions with herbivores. We then used demographic models to project population growth rates, which increased 5-20% more under herbivore exclosure at range limit and novel sites than in core habitats. Our results identify mammalian herbivores as key drivers of the low-elevation range limits of alpine plants and indicate that upward encroachment of herbivores could trigger local extinctions by depressing plant population growth.

Plant aboveground biomass data: Long-Term Nitrogen Deposition: Population, Community, and Ecosystem Consequences

The purpose of this experiment is to measure how adding nitrogen over a long time will affect the number of species, the type of species present, the amount of annual growth, and the change from year to year in the growth of each species in a plant community which is also relieved of grazing by large and small mammals. The experiment is being conducted within fields (A, B, C, and D) which were initially low in soil nutrients. There are 8 different levels of nitrogen addition with other nutrients added to ensure that nitrogen remains the limiting nutrient, and a control which receives no nutrients. There are 6 replicates of the 9 treatments in fields A, B, and C and 5 replicates in field D. The treatments were randomly assigned to the plots. In fields A, B, and C the plots are in 6 by 9 grids and are 4 by 4 meters in size with 1 meter aisles between plots. In field D the plots are 1.5 by 4 meters and are placed in a 3 by 17 grid. The plots are enclosed by a fence to keep out mammalian herbivores. Gophers are trapped and removed as they appear. Nitrogenfertilizer (NH4NO3) is applied twice per year, once in early May and once in late June. This experiment was begun in 1982 by David Tilman.

Root biomass data: Long-Term Nitrogen Deposition: Population, Community, and Ecosystem Consequences

Root biomass data: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes

Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.

Plant aboveground biomass data: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes

opencc-by-4.0Apr 2020View details →

zenodo40/100

Data for an unusually dense population of Sphodros rufipes (Latreille 1829) (Mygalomorphae, Atypidae) at the edge of its range on Tuckernuck Island, Massachusetts

Data submitted in fulfillment of a 2008 Nantucket Biodiversity Initiative grant. Paper Abstract: We counted and measured Sphodros rufipes (Latreille 1829) pursewebs in two survey plots on Tuckernuck Island, Massachusetts.  Tuckernuck is 50 Km south of Cape Cod, Massachusetts, and is entirely owned by private landowners or conservation organizations; biological research activities are supported and encouraged by residents on a limited basis.  Our objectives were to quantify web density and determine the main components of the S. rufipes diet.  We counted 479 webs in the two plots and report web densities between 0.058 and 0.18 webs/m2; denser than previously reported populations. Contrary to most previously published literature on S. rufipes, we noted the predominance of the grass-like sedge, Carex pensylvanica, rather than trees, as a web support.  However, we also offer the first report of S. rufipes using a conifer (Pinus rigida) as a web support.  Coleopterans and isopods made up 79 percent of the prey parts collected from 56 pursewebs.  We suggest that the Tuckernuck population offers an opportunity to collect important long-term demographic data. Datasets: sphodrosWebLocations.csv - data from two specific areas sphodrosSpiderMeasurements.csv - measurements of live spiders borrowed from their webs sphodrosRandomWebLocations.csv - data for webs found by happenstance sphodrosDiet.csv - diet data from body parts collected from Sphodros webs sphodrosDataDictionary.csv

opencc-zeroJul 2020View details →

Data from: Genetic and environmental canalization are not correlated among altitudinally varying populations of Drosophila melanogaster

Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. There has been interest regarding the conditions enabling the evolution of canalization. Under some models, the circumstances under which genetic canalization evolves is limited, despite apparent empirical evidence for it. It has been argued that genetic canalization evolves as a correlated response to environmental canalization (congruence model). Yet, empirical evidence has not consistently supported predictions of a correlation between genetic and environmental canalization. In a recent study, a population of Drosophila adapted to high altitude showed evidence of genetic decanalization relative to those from low altitudes. Using strains derived from these populations, we tested if they varied for multiple aspects of environmental canalization We observed the expected differences in wing size, shape, cell (trichome) density and mutational defects between high- and low-altitude populations. However, we observed little evidence for a relationship between measures of environmental canalization with population or with defect frequency. Our results do not support the predicted association between genetic and environmental canalization.

opencc-zeroJun 2020View details →

Data from: Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K= 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92% – 98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise FSTanalysis showed genetic differentiation (P < 0.05)between the village, commercial and wild populations. A per marker per population pairwise FSTanalysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

opencc-zeroJul 2020View details →

Data from: Multiple spawning run behavior and population consequences in migratory striped bass Morone saxatilis

Multiple spawning runs cause different contingents within the same population to experience varying demographic fates that can stabilize populations through the portfolio effect. Multiple spawning runs are reported here for the first time for striped bass, an economically important coastal species, which is well known for plastic estuarine and shelf migration behaviors. Adult Hudson River Estuary striped bass (n=66) were tagged and tracked with acoustic transmitters from two known spawning reaches separated by 90 km. Biotelemetry recaptures for two years demonstrated that each reach was associated with separate spawning runs. Time series of spawning run trajectories were examined via nonparametric dynamic time warping and revealed two dominant time series centroids, each associated with the two spawning reaches. In 2017, the lower reach run occurred earlier than the higher reach run, but difference in timing was not observed in 2018. The majority (84%) of returning adults in 2018 showed the same run behaviors exhibited in 2017. The two spawning run may have been cued differently by temperatures, where warming lagged 1-week at the higher reach in comparison to the lower reach. The two spawning runs exhibited similar Atlantic shelf migration patterns with strong summer fidelity to Massachusetts Bay and winter migrations to the southern US Mid-Atlantic Bight. Still, in 2017, differing times of departure from spawning reaches into nearby shelf waters likely caused the early spawning run to experience substantially higher mortality than the later run. Anecdotal evidence suggests that higher fishing effort is exerted on the early-spawning run as it first enters shelf fisheries. Thus, as in salmon, multiple spawning runs by striped bass can lead to differential demographic outcomes, contributing to overall population dynamics.