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.
19
datasets available to search
ShareScore release 0.7.1
Dataset results
19 results for “ddRADseq”
SQLite3 databases of candidate marker loci from ddRADseq in Quercus suber, Quercus ilex and their hybrids
<p>The dataset contatins four SQLite3 databases of candidate marker loci from ddRADseq in <em>Quercus suber</em>, <em>Quercus ilex </em>and their hybrids, corresponding to the data collected for the four filtering/imputation scenarios considered in the manuscript "ddRAD sequencing-based identification of species genomic boundaries and permeability in <em>Quercus ilex</em> and <em>Q. suber</em> hybrids" submitted to Frontiers in Plant Sciences. This work was funded by the project AGL2015-67495-C2-2-R (Spanish Ministry of Economy and Competitiveness).</p>
SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species
<p><span><span><span>We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples from four contact zones between <i>Podarcis carbonelli</i> and four other <em>Podarcis</em> species</span></span>. We obtained a panel of SNPs for each for each contact zone and reference populations and a dataset of diagnostic SNPs between reference populations for each contact zone but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. The final datasets (complete and diagnostic) were obtained after removing loci with depth coverage <8, missing data >20% and removing individuals with more than 35% of missing data. Across complete and diagnostic datasets, mean coverage by individuals ranged from 28 to 47 and by loci from 28 to 44<span><span>. The analysis of replicate samples (about 6% of samples were replicated, i.e. were amplified and sequenced in independent libraries and SNP calling was performed independently) showed high levels (>99%) of multilocus genotype replicability.</span></span></span></p>
Datasets of the paper: Phylogenetic Insights into Central European Chorthippus and Pseudochorthippus (Orthoptera: Acrididae) Species Using ddRADseq Data
<p>Alignments, trees & tree files, Structure plots & structure input files, and a table with relevant metadata of the paper "Phylogenetic Insights into Central European <i>Chorthippus </i>and <i>Pseudochorthippus </i>(Orthoptera: Acrididae) Species Using ddRADseq Data"</p>
Gymnogeophagus labiatus and G. lacustris - ddRADseq - Library 1 - Figueiredo et al.
<p>This dataset contains SNP data for 44 Gymnogeophagus lacustris and 16 G. labiatus individuals.</p> <p>Genomic DNA was obtained using the CTAB method adapted from Doyle, Doyle (1987). DNA quality was quantified with the QubitTM 3 fluorometer, and only samples with concentrations ≥ 30ng/μl. Two RADSeq libraries were constructed following the double digestion protocol of Peterson <em>et al.</em> (2012) with restriction enzymes <em>SphI</em> and *MluCl. Libraries were sequenced on an Illumina HiSeq 2500, targeting single-end 100 bp reads. Sequencing generated approximately 140 million total reads per library that passed initial quality control at the sequencing facility.</p> <p>Raw reads were demultiplexed and processed in STACKS (Catchen et al., 2013). The final run of the POPULATIONS module was executed excluding loci with exceeding values for missing data (maximum 25% missing data per unlinked locus and 10% per individual). The --write-single-snp flag was used to take only one SNP per loci to avoid retaining loci in obvious linkage disequilibrium (LD).</p>
Data from: Species tree estimation using ddRADseq data from historical specimens confirms the monophyly of highly disjunct species of Chloropyron (Orobanchaceae)
Sequence data exist for only about 1/5 of plant species; therefore we are at risk of losing many branches of the tree of life even before they are placed into a molecular evolutionary context. This necessitates methods for phylogeny estimation of understudied, rare, and threatened taxa, which often forces researchers to utilize historical collections. The restriction site-associated DNA sequencing (RADseq) family of reduced representation sequence generation has provided a flexible and efficient method for the rapid generation of hundreds to tens of thousands of loci, and has recently seen adoption for phylogeny estimation. However, these methods have been primarily utilized with freshly collected or well preserved tissue. Here we sample all taxa of a genus of rare flowering plants, Chloropyron (Orobanchaceae), from herbarium sheets dating up to 25 yr and use double digest restriction site-associated DNA sequencing (ddRADseq) to resolve intraspecific relationships. We find all species in Chloropyron to be monophyletic, with the inland taxon C. maritimum ssp. canescens sister to the rest of the coastal C. maritimum (ssp. maritimum + ssp. palustre), and the two distinct subspecies of C. molle to be each other's closest relative with strong support. In addition, we demonstrate the utility of reduced representation libraries to address phylogenomic problems in a group of rare species and address pitfalls of accurately inferring relationships when the amount of missing data is large, as is often the case when using historical specimens and rare taxa.
Collection and ddRadSeq sequencing data for Sitophilus zeamais from Oaxaca and Chiapas, Mexico
<p>The maize weevil, <em>Sitophilus zeamais</em>, is a ubiquitous pest of maize and other cereal crops worldwide and remains a threat to food security in subsistence communities. Few population genetic studies have been conducted on the maize weevil, but those that exist have shown that there is very little genetic differentiation between geographically dispersed populations and that it is likely the species has experienced a recent range expansion within the last few hundred years. While the previous studies found little genetic structure, they relied primarily on mitochondrial and nuclear microsatellite markers for their analyses. It is possible that more fine-scaled population genetic structure exists due to local adaptation, the biological limits of natural species dispersal, and the isolated nature of subsistence farming communities. In contrast to previous studies, here, we utilized genome-wide single nucleotide polymorphism data to evaluate the genetic population structure of the maize weevil from the southern and coastal Mexican states of Oaxaca and Chiapas. We employed strict SNP filtering to manage large next generation sequencing lane effects and this study is the first to find fine-scale genetic population structure in the maize weevil. Here, we show that although there continues to be gene flow between populations of maize weevil, that fine-scale genetic structure exists. It is possible that this structure is shaped by local adaptation of the insects, the movement and trade of maize by humans in the region, geographic barriers to gene flow, or a combination of these factors.</p>
Podarcis bocagei vs P. carbonelli hybrid zone SNP datasets from ddRADseq
<p>We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples across a transect including a hybrid zone between <em>Podarcis carbonelli</em> and <em>Podarcis carbonelli</em>. <span>We used <em>P. bocagei</em> and <em>P. carbonelli</em> samples from the locations at the extremes of the transect as references. We obtained a SNP dataset including all SNPs after removing loci with depth coverage <8, missing data >20%, removing loci containing more than five SNPs, and with more than 70% heterozygosity (complete dataset; 6905 SNPs, 329 individuals). Additionally, we obtained</span> from the complete dataset two other datasets, prior to apply a missing data filter. One dataset contained loci with allele frequencies higher than 0.8 in the reference population containing only parental individuals of one species and lower than 0.2 in the reference population of the other species ("80/20" dataset; 2300 SNPs, 329 individuals); the other dataset comprised diagnostic SNPs between reference populations (diagnostic dataset; 1241 SNPs, 236 individuals) but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. Individuals with missing data >35% were removed from all datasets (the number of individuals reported for each dataset is after applying this filter, but note that the 80/20 and the diagnostic datasets were obtained before applying this filter to the complete dataset). Across datasets, average depth of coverage by individuals was 28 (median = 26.8, min = 12.5, max = 85.8) and by loci was 29 (median = 28.8; min = 15.6; max = 48.6). The analysis of replicate samples (four samples were replicated twice, i.e. were amplified and sequenced in independent libraries and SNP calling was performed independently) showed high levels (99.87%) of multilocus genotype replicability.</p>
Data from: Species tree estimation using ddRADseq data from historical specimens confirms the monophyly of highly disjunct species of Chloropyron (Orobanchaceae)
Open the record for dataset details and reuse information.
Genlight table of ddRADseq-DArTseq Baikal sculpins adaptive radiation
Open the record for dataset details and reuse information.
SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species
Open the record for dataset details and reuse information.
Conservation genomic ddRadseq data for Hymenocallis henryae, a federally petitioned spiderlily endemic to the Florida panhadle; SNP data of 279 individuals from 19 populations
Open the record for dataset details and reuse information.
Podarcis bocagei vs P. carbonelli hybrid zone SNP datasets from ddRADseq
Open the record for dataset details and reuse information.
Collection and ddRadSeq sequencing data for Sitophilus zeamais from Oaxaca and Chiapas, Mexico
Open the record for dataset details and reuse information.
ddRadSeq sequences for Sitophilus zeamais
<p>ddRadSeq Illumina Sequencing data for maize weevil, <em>Sitophilus zeamais</em></p>
Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), using multilocus Sanger sequence and genomic ddRADseq data
<p>The Rough Greensnake, <i>Opheodrys aestivus,</i> is a moderately-sized, semi-arboreal snake broadly distributed throughout eastern North America. While numerous taxa with similar distributions have been shown to be comprised of multiple species, <i>O. aestivus</i> has yet to be examined in a detailed phylogeographic context. Here, we use Sanger-sequence data of one mitochondrial and three nuclear loci for samples from throughout the distribution of <i>O. aestivus</i> to elucidate phylogeographic patterns in this species. We combine this with ddRADseq data for a subset of samples to test patterns on a more genomically comprehensive scale. In both datasets, we find strong support for three deeply divergent clades within <i>O. aestivus</i>: peninsular Florida, central Texas, and a main clade comprising the rest of the distribution, with the Florida clade the earliest diverging lineage of the three. Estimates of divergence time suggest that the central Texas and main clades diverged approximately 1.34 million years ago (Mya), while the peninsular Florida clade diverged from other lineages approximately 2.94 Mya, and these lineages diverged from the sister taxon, <i>O. vernalis</i>, approximately 6.43 Mya.<i> </i>These results also suggest that the historically recognized Florida subspecies, <i>O. a. carinatus</i>, could be elevated to species status. While the divergence of peninsular Florida or central Texas populations is not unique among squamates, nor is low levels of divergence from the Atlantic coast to eastern Texas, this combination of patterns is unusual, and yields important insight into the biogeography of North American biota. Further, our approach helps illustrate how dense geographic sampling with limited genomic sequencing can be used as a guide for the selection of samples to test phylogeographic patterns comprehensively.</p>
Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), using multilocus Sanger sequence and genomic ddRADseq data
Open the record for dataset details and reuse information.
A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera
Open the record for dataset details and reuse information.
Data from: One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data
Open the record for dataset details and reuse information.
Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms
Open the record for dataset details and reuse information.
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.