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.
101
datasets available to search
ShareScore release 0.7.1
Dataset results
101 results for “RadSeq”
Complex basis of hybrid female sterility and Haldane's rule in Heliconius butterflies: Z-linkage and epistasis - RADseq and RNAseq reads, sterility phenotypes and pedigree
<p>RADseq and RNAseq reads (.fastq files), and sterility phenotypes and pedigree (.xlsx) using for QTL mapping of Heliconius pardalinus sterility crosses in Rosser, N., Edelman, N.B., Queste, L.M., Nelson, M., Seixas, F., Dasmahapatra, K.K. and Mallet, J., 2021. Complex basis of hybrid female sterility and Haldane’s rule in Heliconius butterflies: Z-linkage and epistasis, accepted for publication in Molecular Ecology. Queries to Neil Rosser (neil.rosser@york.ac.uk). </p> <p> </p>
Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2
<p>Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis—including parameter optimization—as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.</p>
Training data for 'Reference based RADSeq ' tutorial (Galaxy Training Material)
<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes RAD-seq data from a study published by Hohelnlohe et al., 2010 (DOI:10.1371/journal.pgen.1000862) to identify and type single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations and thus estimate genetic diversity and differentiation among populations. </p>
epiGBS and RADseq data analysis
<p>This release contains the bismark coverage files and stacks pipeline output for analysis of methylation and DNA variation between 4 populations of oysters in Louisiana. This update adds the annotation reference files and a samples described file.</p>
Supplementary materials: RADseq phylogenetics in two frog clades
<p>Restriction-site associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.</p>
Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF
<p>The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species' demographic history should be considered. Furthermore, we provided compelling evidence of selection through the examination of allele frequency changes over time, by taking into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low and decreasing levels of genetic diversity. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.</p>
Supplementary materials: RADseq phylogenetics in two frog clades
Open the record for dataset details and reuse information.
Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2
Open the record for dataset details and reuse information.
Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF
Open the record for dataset details and reuse information.
Data from: Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a "rex-thamnophila" clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a "superba" clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson's D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.
Assembled RADseq Data: "Historical introgression among the American live oaks and the comparative nature of tests for introgression"
<p>Assembled sequence data for Eaton et al. (2015) "Historical introgression among the American live oaks and the comparative nature of tests for introgression". The unassembled sequence data are available on NCBI SRA. </p> <p>Data sets were assembled using pyrad v.2.13 as described in notebook 1 from the study.</p>
Data from: Genomic footprint of cladogenesis revealed through RADseq and Sanger sequencing demonstrates congruent patterns in the velvet worm Peripatopsis sedgwicki species complex (Onychophora: Peripatopsidae)
<p>In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, <em>COI</em>) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, <em>Peripatopsis sedgwicki</em> species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1259 - 11,468 SNPs, in order to assess the species diversity and phylogeographic of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the <em>COI </em>datasets retrieved four distinct, statistically well-supported clades within the species complex. Five species delimitation methods applied to the <em>COI </em>data (ASAP, bPTP, bGMYC, STACEY, and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main <em>P. sedgwicki </em>species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the <em>COI</em> data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq and <em>COI </em>data suggests that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns. </p>
Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea
<p><b>Connectivity of marine populations is shaped by complex interactions of biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications to the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly-dispersive mud crab, <em>Scylla olivacea</em> (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (<em>F</em><sub>ST </sub> = 0.0057, p < 0.001) and a subset of 1,643 putatively neutral SNP markers (<em>F</em><sub>ST</sub></b><b> = 0.0042, p < 0.001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (R<sup>2</sup><sub>adj</sub> = 0.133; p = 0.035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (<em>N</em>e < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (</b><b><em>F</em><sub>ST</sub></b><b> = 0.2390, p < 0.001), significantly correlated with sea surface temperature variabilities during peak spawning months for <em>S. olivacea</em> (R<sup>2</sup><sub>adj</sub> = 0.692-0.763; p < 0.050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of <em>S. olivacea</em> across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly-dispersive marine species, and provides information useful for spatial management of the fishery resource.</b></p>
Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq
<p><em><span>Rattus norvegicus</span></em><span> and </span><em><span>Rattus tanezumi</span></em><span> are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored.</span><span> Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that </span><span><em>R</em>. <em>norvegicus</em></span><span> is widely distributed in China, </span><span>R. <em>tanezumi</em></span><span> is mainly distributed in southern China with currently invading northward; northeast China was the natal region of </span><span><em>R</em>. <em>norvegicus</em></span><span>, while the spread of </span><span><em>R</em>. <em>tanezumi</em></span><span> in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b‐RAD analyses. In the neighbor‐joining tree, individuals of </span><span><em>R</em>. <em>tanezumi</em></span><span> grouped into geographic‐specific branches, and populations from the southeast coast were ancestral groups, which confirmed the colonization route from the southeast coast to central and western China. However, individuals of </span><span><em>R</em>. <em>norvegicus</em></span><span> were generally grouped into two clusters instead of geographic‐specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that the spread history of </span><span><em>R</em>. <em>norvegicus</em></span><span> in China was complex; in addition to on‐land colonization, shipping transportation also played a great role. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the </span><span>R<em>.</em> <em>norvegicus</em></span><span> declined rapidly while the population of </span><span><em>R</em>. <em>tanezumi</em></span><span> continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation of phylogeography of two species in China.</span></p>
Training data for 'Genetic map RADSeq ' tutorial (Galaxy Training Material)
<p>The data provided here are part of a study published by Amores<em> et al.</em> (2011) (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176089/">doi 10.1534/genetics.111.127324</a>), exploiting massively parallel DNA sequencing to develop meiotic maps by genotyping F<sub>1</sub> offspring of a single female and a single male spotted gar (<em>Lepisosteus oculatus</em>).</p>
Raw genomic RadSeq data from: Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data
<p>Raw genomic RadSeq data from individuals used in 'Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data' study.</p>
Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
<p><span>Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera <em>Discoglossus</em>, <em>Rana</em>, <em>Lissotriton</em> and <em>Triturus</em> using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.</span></p>
Data from: RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia
Open the record for dataset details and reuse information.
Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea
Open the record for dataset details and reuse information.
Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq
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.