Find research datasets worth reusing

opencc-by-4.0Sep 2022View details →

A robust estimate of continental-scale terrestrial carbon sinks using GOSAT XCO2 retrievals

The dataset contains monthly terrestrial ecosystem carbon fluxes (NEE) for 51 terrestrial regions from 2011-2014. We used simulations from 12 terrestrial biosphere models (TBMs) as the prior carbon fluxes, therefore the posterior carbon fluxes correspond to the 12 TBMs.

Cations make a difference: Soil nutrient patches and fine-scale root abundance of individual species in a mountain grassland

1. Root densities in the field vary at the centimetre scale, but we have no information on whether this variation is linked to variation in nutrient concentrations and availability. Roots of many species are able to proliferate in nutrient-rich patches in controlled conditions in culture, but because data on nutrient concentrations and, in particular, on their temporal stability in the field are scarce, we do not know to what extent root distribution in the soil bears traces of such a response. 2. Here, we linked centimetre-scale measurements of soil nutrient concentrations over a period of 6 weeks with estimation of root biomass and its species composition at the same points to determine whether there is any association between the two. In addition to phosphorus, nitrate and ammonium, we determined the concentrations of metal cations (magnesium, calcium and potassium). We used qPCR to determine the quantities of individual species in the root biomass samples. 3. We found that calcium and magnesium (and to a lesser degree phosphorus and potassium) showed fine-scale patchiness that was stable over the duration of the study (6 weeks) and was consistent over all these elements. Nutrient patches were associated with high root biomass and the occurrence of roots of several species. Such patches are formed primarily by elements with known low mobility in soil (cations, phosphorus). In contrast, nitrogen ions showed overwhelmingly high temporal variation with no relationship between root density and nitrogen concentration. 4. Soil nutrient concentrations thus constitute a multidimensional signal. Some elements strongly vary in time, while some are much more stable and thus form stable patches that permit root response over periods of weeks or months. Among them, calcium and magnesium play an important role in forming soil heterogeneity at a scale comparable to the scale at which fine root densities also vary. As these cations affect a number of plant functions, their association with higher root densities confirms their role in growth dynamics of terrestrial ecosystems.

Data from: Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea

Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest oceanic trenches. Their reduced skeletons and limited number of phylogenetically-informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with 12 novel transcriptomes. Using a highly-curated dataset of 1,100 orthologs, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favor one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.

openbsd-3-clauseJan 2023View details →

Artifact For A Large Scale Analysis of Semantic Versioning in NPM

This is the artifact for: A Large Scale Analysis of Semantic Versioning in NPM. The artifact contains: <ul> <li>A full scrape of all metadata from NPM (package / version information, dependencies, etc.) as of October 31, 2022.</li> <li>A copy of our code, which includes the software for scraping metadata and package tarball (code) data, as well as all analysis scripts that are needed to replicate the figures from the paper.</li> </ul>

Supplementary material 2 from: D'Cruze N, Assou D, Coulthard E, Norrey J, Megson D, Macdonald DW, Harrington LA, Ronfot D, Segniagbeto GH, Auliya M (2020) Snake oil and pangolin scales: insights into wild animal use at "Marché des Fétiches" traditional medicine market, Togo. Nature Conservation 39: 45-71. https://doi.org/10.3897/natureconservation.39.47879

Table S1. List of inferred species and their respective scientific names (assigned to each common name provided by questionnaire respondents) based on the documented presence of wild populations in Togo

opencc-by-4.0Jan 2023View details →

Improved National-Scale Flood Prediction for Gauged and Ungauged Basins using a Spatio-temporal Hierarchical Model

Composite data with NWM 2.0 streamflow, basin PET, drainage area and stoage. SAR data used in this study are downloaded from <a href="https://scihub.copernicus.eu/">https://scihub.copernicus.eu/</a>

opencc-by-4.0Jan 2023View details →

Figure data for ``Fatigue crack growth under large scale yielding condition: a tool based on explicit crack growth''

Figure data used for the paper "Fatigue crack growth under large scale yielding condition: a tool based on explicit crack growth" (doi 10.46298/jtcam.9296). The numerical values are provided as raw text in the tikz/pgfplots format. They can be compiled using latex/pdflatex engines. The name of each data file corresponds to the figure numbering in the paper.

opencc-by-4.0Jan 2023View details →

cellsig: a Bayesian sparse random-effect model and large-scale human bulk transcriptional catalogue support cell-type marker selection

Human Bulk Cell-type Catalogue (HBCC): This database harmonises 1,435 samples of 67 cell types from 58 datasets which can be utilised in the cellsig method for estimating cell-type transcriptional profiles.

Data from: Observed and dark diversity dynamics over millennial time scales: Fast-life history traits linked to expansion lags of plants in northern Europe

Global change drivers (e.g. climate and land use) affect the species and functional traits observed in a local site but also its dark diversity—the set of species and traits locally suitable but absent. Dark diversity links regional and local scales and, over time, reveals taxa under expansion lags by depicting the potential biodiversity that remains suitable but is absent locally. Since global change effects on biodiversity are both spatially and temporally scale dependent, examining long-term temporal dynamics in observed and dark diversity would be relevant to assessing and foreseeing biodiversity change. Here, we used sedimentary pollen data to examine how both taxonomic and functional observed and dark diversity changed over the past 14500 years in northern Europe. We found that taxonomic and functional observed and dark diversity increased over time, especially after the Late Glacial and during the Late Holocene. However, dark diversity dynamics revealed expansion lags related to species' functional characteristics (dispersal limitation and stress intolerance) and an extensive functional redundancy when compared to taxa in observed diversity. We highlight that assessing observed and dark diversity dynamics is a promising tool to examine biodiversity change across spatial scales, its possible causes, and functional consequences.

Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions

Data sets for the manuscript with the title "Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions". For further information read README   Code for the MSM construction in the jupyter notebook file. Trajectories of opening and closing in the Trajectories.zip

Data explanation for Manuscript "'An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition (BNI) activity'"

Data explanation for Manuscript "'An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition (BNI) activity'"

opencc-zeroFeb 2023View details →

Date for: The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms due to interesting biological traits such as sequential hermaphroditism, social control of size, symbiosis with anemones, and varying pigmentation patterns. In addition to genus-specific traits, the anemonefish Amphiprion clarkii possesses species-specific characteristics such as interspecies co-habitation, high intraspecies color variation, no anemone specificity, and a broad distribution, that have the potential to further our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. However, despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Here, using PacBio long-read, Illumina short-read and Hi-C chromatin capture technology we generated a high-quality chromosome-scale genome for the anemonefish A. clarkii. The initial assembly consisted of 1840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and then annotated with 25,050 protein-coding gene models. With the chromosome-scale assembly encompassing 98.7% of conserved actinopterygian genes and the annotation containing 97.0%, the quality and completeness of this A. clarkii genome is the highest amongst all published anemonefish genomes. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

opencc-zeroFeb 2023View details →

Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.

Data to reproduce the results presented in Lake et al. 2023. Science of The Total Environment, https://doi.org/10.1016/j.scitotenv.2023.162332 ("Use of a submersible spectrophotometer probe to fingerprint spatial suspended sediment sources at catchment scale")

This repository contains the absorbance data measured on the water samples collected in all sampling sites, for the three campaigns, as described in Lake et al., 2023.  Data consists of: - Absorbance data compensated for measured concentration and compensated for absorbance measured on filtered water  - Absorbance data compensated for measured concentration Shown files are the input files for the MixSIAR modelling exercise as described in Lake et al., 2023.

Dataset of the publication: Large-scale Characterization of Java Streams

This repository contains all the data supporting the findings of the research article: Large-scale Characterization of Java Streams, including the list of all analyzed projects and their metadata. The repository contains two files as follows: 1. database.tar: This archive contains all the data that supports the findings reported in the manuscript entitled “Large-scale Characterization of Java Streams” which is under revision. The data is provided as a database created via PostgreSQL and can be restored to an installation of PostgreSQL (version 12 or later) by following the next procedure: A. Using pgAdmin (https://www.pgadmin.org/): - Enter to the "Restore Dialog" (https://www.pgadmin.org/docs/pgadmin4/development/restore_dialog.html). - Select as "Format" the "Custom or tar" option. - When selecting the "Filename", browse to the folder where this archive was decompressed and select the file "database.tar". 2. ListOfProjects.csv: This comma-separated value file contains the list of all analyzed projects and their metadata.

opencc-zeroMar 2023View details →

Micro-scale spatial preference and temporal cyclicity linked to foraging in harbour porpoises

Habitat heterogeneity is a crucial driver for species distribution across scales. Harbour porpoise Phocoena phocoena basin-wide distribution is linked to prey availability, and small-scale (kilometres to tens of kilometres) differences in distribution are prevalent. However, information on porpoise distribution and foraging-behaviour variations on a micro-scale (hundred meters to kilometres) is limited. To monitor harbour porpoise distribution and foraging activity on a micro-scale we deployed passive acoustic dataloggers, logging porpoise acoustic activity at six sites in a small, high porpoise-density area in southern Sweden. Data were collected for almost a year, giving detailed time series on porpoise activity. The time series were analysed using dynamic time warping to compare activity patterns between sites. Large differences were found between sites separated by only a few hundred meters, indicating micro-scale spatial preference. Spectral analysis for temporal cyclicity in activity revealed a dominant peak for 24-hour cycles with higher activity during the night for all sites. All sites also had a second peak for 29.5 days, linked to the lunar cycle with higher activity during the full moon. Activity was overall highest during autumn and winter (September–December). Spatial and temporal patterns were linked to foraging, showing a positive correlation between porpoise presence and the percent of time present with detected foraging. The study demonstrates that harbour porpoise spatial distribution on a micro-scale should be considered in e.g. behavioural, management, and conservation studies and actions. In addition, we show that time series statistical methodology, such as dynamic time warping and spectral analysis, are informative and appropriate for analysis of acoustic temporal data.

opencc-zeroMar 2023View details →

Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle without understanding of genomic architecture for phenotypic traits. This study provides a high-resolution portrait of genomic variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic variation within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Allele frequency variation in GREB1L/ROCK1 was highly correlated with mean migration timing for early- and late-run populations within each of the lineages (r2 between 0.58–0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

opencc-by-4.0May 2023View details →

Absence of large-scale ice masses in central Northeast Siberia during the Late Pleistocene Dataset

Dataset for the publication: ""Absence of large-scale ice masses in central Northeast Siberia during the Late Pleistocene"

opencc-zeroMar 2023View details →

Repository for: Genetic footprints of a rapid and large-scale range expansion: The case of cyclic common vole in Spain

Te repository contains the neccesary genetic data (microsatellite allele frequencies and GenBank accesion numbers for cytb haplotypes) to be able to replicate the analyses performed in the manuscript.