Find research datasets worth reusing

opencc-zeroDec 2018View details →

Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

opencc-zeroDec 2017View details →

Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.

opencc-zeroDec 2016View details →

Data from: Genetic sampling for estimating density of common species

Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session NGS sampling of hares. We compared spatial capture–recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost-effective sampling protocols.

opencc-zeroApr 2015View details →

Samples and data accessibility in research biobanks

This dataset contains answers at a questionnaire relative to modes of sample and data accessibility in research Biobanks

opencc-by-4.0Jan 2017View details →

Umbrella sampling data of AuNP interacting with a PC bilayer

Files in Gromacs (v4.6) format used to generate the PMF profile shown in Fig. 3 in [1]. The nanoparticle is pulled to the EC leaflet in the 'genstart' simulations. The initial structures for the umbrella sampling windows are extracted from this trajectory. The files obtained from umbrella sampling windows are named 'pullX.*', where X is the distance between the centers of mass of the AuNP and the EC leaflet phosphori. Trajectories (.xtc) are saved every 100ps. Additionally, the initial and final structures (.gro), the run input files (.tpr), energy files (.edr), log files (.log), checkpoint files (.cpt), simulation parameter files (.mdp), and the files generated by the pull code (pull forces and pull distances, .xvg) are given for each umbrella window. Additionally, an index file (index.ndx) and a topology file (topol.top) common for all systems is provided. TOP.tar contains the molecule definitions (.itp). 'pullf-files.dat' and 'tpr-files.dat' are used by g_wham to extract the profile shown in Fig. 3 (except for the choice of the zero level) by 'g_wham -it tpr-files.dat -if pullf-files.dat -b 40000 -nBootstrap 100' [1] Heikkilä et al., Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations, J. Phys. Chem. C, 2014, 118 (20), pp 11131–11141, DOI: 10.1021/jp5024026

opencc-by-4.0Jul 2017View details →

Atomistic Fingerprint of Hyaluronan-CD44 Binding: Umbrella Sampling Data, Crystallographic Mode

Simulation files (Gromacs 4.6.7 format) for the "Free Energy" simulations of crystallographic mode in Ref. [1]. Files include: -trajectories (.xtc) that are saved every 100ps -initial structures (.gro), -run input files (.tpr) -simulation parameter files (.mdp) -system topology file (.top) -topology files included in the system topology file (.itp) 'pullx' ('and pullx2' files, which contain data from the last 80ns) are used to constuct the free energy profile. Command for building the free energy profile is included in 'wham.sh' [1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)

opencc-by-4.0Jul 2017View details →

Atomistic Fingerprint of Hyaluronan-CD44 Binding: Umbrella Sampling Data, Parallel Mode

Simulation files (Gromacs 4.6.7 format) for the "Free Energy" simulations of parallel mode in Ref. [1]. Files include: -trajectories (.xtc) that are saved every 100ps -initial structures (.gro), -run input files (.tpr) -simulation parameter files (.mdp) -system topology file (.top) -topology files included in the system topology file (.itp) 'pullx' ('and pullx2' files, which contain data from the last 80ns) are used to constuct the free energy profile. Command for building the free energy profile is included in 'wham.sh' [1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)

Datasets associated with the manuscript "Differential detection workflows for multi-sample single-cell RNA-seq data"

In this Zenodo repository, we share the data that is required to reproduce all the analyses from our publication "Differential detection workflows for multi-sample single-cell RNA-seq data". This repository includes all* input data, intermediate results and final outputs that are represented in our manuscript. For a more elaborate description of the data, we refer to the companion GitHub. https://github.com/statOmics/DD_benchmarks for the benchmarks and https://github.com/statOmics/DD_cases for the case studies, respectively.

opencc-zeroNov 2023View details →

Raw sequencing data and ngsfilters for snow track eDNA samples

Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present the first successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR) and, for brown bear, a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear samples (5/7) than for wolf (7/10) and lynx (4/9), but locus genotyping success was greater for brown bear (0.88). Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success are needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA–based individual and population-level studies.

opencc-zeroNov 2023View details →

DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2

As an island endemic with a decreasing population, the Critically Endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the ND2 sequences; a single haplotype was identified within the Cyt b sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potential augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species.

opencc-by-4.0Nov 2023View details →

Supplementary Data for Manuscript 'Observing impacts on luminescence depth profile evolutions from surface altered quartzite using OSL laser scanning and controlled light exposed rock sampling techniques'

The attached file contains supplementary documents offered in the Quaternary Geochronology manuscript 'Observing impacts on luminescence depth profile evolutions from surface altered quartzite using OSL laser scanning and controlled light exposed rock sampling techniques' for the LED2023 special issue.

opencc-zeroDec 2023View details →

Data for: The meta-analysis of the effects of spatial sampling bias correction on presence only species distribution models

This dataset contains information extracted from 70 studies identified through a systematic review of the peer-reviewed literature (Web of Science and SCOPUS databases both searched on the 13/02/2023) to evaluate the effect of spatial sampling bias correction methods in presence-only species distribution models.

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - the United Kingdom (Northern Ireland)

This dataset contains monitoring data on zoonoses and zoonotic agents under the Directive 2003/99/EC. This Directive requires Member Sates (MSs) to collect, evaluate and report data on zoonoses and zoonotic agents. MSs can also report monitoring data and information on some other pathogenic microbiological agents in foodstuffs. Relevant EU legislation: Commission Regulation (EC) No 2073/2005,Commission Regulation (EC) No 1441/2007, Commission Regulation (EU) No 1086/2011, Commission Regulation (EU) No 209/2013, Commission Regulation(EU) No 217/2014.

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Croatia

This dataset contains monitoring data on zoonoses and zoonotic agents under the Directive 2003/99/EC. This Directive requires Member Sates (MSs) to collect, evaluate and report data on zoonoses and zoonotic agents. MSs can also report monitoring data and information on some other pathogenic microbiological agents in foodstuffs. Relevant EU legislation: Commission Regulation (EC) No 2073/2005,Commission Regulation (EC) No 1441/2007, Commission Regulation (EU) No 1086/2011, Commission Regulation (EU) No 209/2013, Commission Regulation(EU) No 217/2014.

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Ireland

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Sweden

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Norway

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Luxembourg

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Finland

Greenland 2022 GHOST Project: Sampling Greenland Geothermal Springs - Expedition Report Data

Data from the GHOST GRL22 Leg 1 Expedition report