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.
123
datasets available to search
ShareScore release 0.9.0
Dataset results
123 results for “Genomic islands”
Data from: Genomic evidence for convergent evolution of a key trait underlying divergence in island birds
Open the record for dataset details and reuse information.
Data from: Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands
Open the record for dataset details and reuse information.
Population genomics of big mice from the Faroe islands: Hybridization, colonization, and a new challenge to identifying genomic targets of selection
Open the record for dataset details and reuse information.
Genomic associations with poxvirus across divergent island populations in Berthelot’s pipit
Open the record for dataset details and reuse information.
Data from: Genomes of Galápagos mockingbirds reveal the impact of island size and past demography on inbreeding and genetic load in contemporary populations
Open the record for dataset details and reuse information.
Data from: Recent range expansion and genomic admixture in a kleptoparasitic spider, Argyrodes lanyuensis: A case of adaptive introgression on isolated small island of the Taiwan-Philippine transition zone?
Open the record for dataset details and reuse information.
Sebastes genomic islands of divergence
Open the record for dataset details and reuse information.
Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics
Open the record for dataset details and reuse information.
Genomic diversity and differentiation between island and mainland populations of White‐tailed Eagles (Haliaeetus albicilla)
Open the record for dataset details and reuse information.
Data from: Genomic variation, population history and within-archipelago adaptation between island bird populations
Open the record for dataset details and reuse information.
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
Open the record for dataset details and reuse information.
Data from: Species diversification in the sky islands of southwestern China revealed by genomic, introgression and demographic analyses of Asian shrew moles
Open the record for dataset details and reuse information.
Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation
Open the record for dataset details and reuse information.
Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands
Harnessing the power of genomic scans, we test the debated 'species pump' hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches, we infer a stepping-stone colonization model and high levels of genetic differentiation across the Virgin Islands, which have been periodically inter-connected until 8 ka. Estimates of divergence times from models based on the site frequency spectrum coincide with a period of repeated connection and fragmentation of the islands at 75–130 ka. These results are consistent with a role of island connectivity cycles in promoting genomic divergence and indicate that the genetic distinctiveness of island populations has persisted despite subsequent and extended interisland connections identified from bathymetric data. We discuss these findings in the broader context of Caribbean biogeography, and more specifically why high levels of genomic divergence across the Virgin Islands associated with repeated connectivity cycles do not actually translate into species diversification.
Data from: Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska
Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and colonization histories spanning a range of 2,000 km. We found strong signatures of parallel selection across drainages at the island SNPs and MHC, suggesting that the same loci undergo divergent selection during adaptive radiation. However, patterns of differentiation at most island SNPs and the MHC were not associated with ecotypes, suggesting that these loci are responding differently to a mosaic of selective pressures. Our study provides some of the first evidence that conserved genomic islands may be involved in adaptive divergence of salmon populations. Additionally, our data provide further support for the hypothesis that sockeye salmon inhabiting rivers unconnected to lakes harbor similar genetic diversity across large distances, are likely the ancestral form of the species, and have repeatedly recolonized lake systems as they have become available after glacial recession. Finally, our results highlight the value and importance of validating outlier loci by screening additional populations and regions, a practice that will hopefully become more common in the future.
Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate 'genomic island of speciation'
Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a 'genomic island of divergence' spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.
Data from: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.
Data from: "Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands" in Genomic Resources Notes accepted 1 October 2013 – 30 November 2013
Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands are presented along with annotation and characterization of intragenomic single nucleotide polymorphism (SNPs) and indel variation.
FIGURE 1 in A new species of Amphimedon (Porifera, Demospongiae, Haplosclerida, Niphatidae) from the CapricornBunker Group of Islands, Great Barrier Reef, Australia: target species for the ' sponge genome project'
FIGURE 1. Amphimedon queenslandica sp.nov. A, Holotype QMG315611 in aquarium (scale 1 cm) (photo Nelson Lauzon). B, Peripheral skeletal reticulation (scale 1 mm). C, Closer view of the subectosomal skeleton (scale 1 mm). D, Paratype QMG322874 in aquarium (scale 1 cm) (photo Simon Walker). E, Thicker fibres with embedded spicules forming a denser surface skeleton, supported beneath by the more cavernous subectosomal reticulation (scale 500 μm). F, Network of smaller secondary (uni and paucispicular) tracts overlaying the thicker primary (multi and paucispicular) fibres (scale 500 μm). G, Uni and paucispicular secondary skeletal tracts interconnecting the larger primary fibres (scale 100 μm). H, Isodictyal reticulation of smaller secondary (uni and paucispicular) tracts (scale 50 μm). I, Oxeas embedded in spongin binding the nodes of smaller secondary tracts (scale 50 μm). J, Oxea megascleres (scale 50 μm).
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.