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.
141
datasets available to search
ShareScore release 0.9.0
Dataset results
141 results for “invasion genomics”
Data from: A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World
Open the record for dataset details and reuse information.
Data from: Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer
Open the record for dataset details and reuse information.
Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic
Open the record for dataset details and reuse information.
Data from: Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands
Open the record for dataset details and reuse information.
Data from: Contrasting patterns of genome-wide polymorphism in the native and invasive range of the marine mollusk Crepidula fornicata
Selection processes are believed to be an important evolutionary driver behind the successful establishment of non-indigenous species, however evidence is still scarce. Genome-scans have often identified loci with atypical patterns of genetic differentiation (i.e. outliers) indicative of selection processes. Using microsatellite- and AFLP-based genome-scans, we looked for evidence of post-introduction selection in the mollusk Crepidula fornicata, native from the northwestern Atlantic and introduced in the northeastern Atlantic and northeastern Pacific during the 19th and 20th centuries. We examined 683 individuals from 7 native and 15 introduced populations spanning the latitudinal introduction and native ranges of the species. Our results showed the high genetic diversity in all populations with little genetic structure between the two ranges, a pattern typical of marine invaders. Analyzing 344 loci, no outliers were detected between introduced and native populations or within introduced populations. The genomic sampling may have been insufficient to reveal selection especially if it acts on traits determined by a few genes. Eight outliers were however identified within the native range, underlining a genetic singularity congruent with a well-known biogeographic break along the Florida. Our results call into question the relevance of AFLP genome-scans in detecting adaptation on the time-scale of biological invasions: genome-scans often reveal long-term adaptation involving numerous genes throughout the genome but seem less effective in detecting recent adaptation from pre-existing variation on polygenic traits. This study advocates other methods to detect selection effects during biological invasions – on phenotypic traits, although genome-scans may remain useful for elucidating introduction histories.
Data from: Signatures of divergence, invasiveness and terrestralization revealed by four apple snail genomes
The family Ampullariidae includes both aquatic and amphibious apple snails. They are an emerging model for evolutionary studies due to the high diversity, ancient history and wide geographical distribution. Insight into drivers of ampullariid evolution is hampered, however, by the lack of genomic resources. Here we report the genomes of four ampullariids spanning the Old World (Lanistes nyassanus) and New World (Pomacea canaliculata, Pomacea maculata and Marisa cornuarietis) clades. The ampullariid genomes have conserved ancient bilaterial karyotype features and a novel Hox gene cluster rearrangement, making them valuable in comparative genomic studies. They have expanded gene families related to environmental sensing and cellulose digestion, which may have facilitated some ampullarids to become notorious invasive pests. In the amphibious Pomacea, novel acquision of an egg neurotoxin and a protein for making the calcareous eggshell may have been key adaptations enabling their transition from underwater to terrestrial egg deposition.
Data from: Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex
The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genome-wide genetic markers are still lacking. Here we characterized a large set of genome-wide gene-associated microsatellite markers for C. intestinalis spA (= C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24 - 48) and Cape Town, South Africa (N = 24 - 33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from two to 11, 0 to 0.833 and 0.021 to 0.818, and from two to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genome-wide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genome-wide resource for ecological and evolutionary studies using C. intestinalis as a model.
Data from: Population genomics of a symbiont in the early stages of a pest invasion
Invasive species often depend on microbial symbionts, but few studies have examined the evolutionary dynamics of symbionts during the early stages of an invasion. The insect Megacopta cribraria and its bacterial nutritional symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in 2009. While M. cribraria was initially discovered on wild kudzu plants, it was found as a pest on soybeans within 1 year of infestation. Because prior research suggests Ishikawaella confers the pest status—that is, the ability to thrive on soybeans—in some Megacopta species, we performed a genomic study on Ishikawaella from US. Megacopta cribraria populations to understand the role of the symbiont in driving host plant preferences. We included Ishikawaella samples collected in the first days of the invasion in 2009 and from 23 locations across the insect's 2011 US range. The 0.75 Mb symbiont genome revealed only 47 fixed differences from the pest-conferring Ishikawaella in Japan, with only one amino acid change in a nutrition-provisioning gene. This similarity, along with a lack of fixed substitutions in the US symbiont population, indicates that Ishikawella likely arrived in the US capable of being a soybean pest. Analyses of allele frequency changes between 2009 and 2011 uncover signatures of both positive and negative selection and suggest that symbionts on soybeans and kudzu experience differential selection for genes related to nutrient provisioning. Our data reveal the evolutionary trajectory of an important insect-bacteria symbiosis in the early stages of an invasion, highlighting the role microbial symbionts may play in the spread of invasive species.
Data from: Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern US
Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in the invasive riparian shrub saltcedar (Tamarix L.) by analyzing 1,997 genome-wide SNP markers for 259 individuals from 25 populations collected throughout the southwestern US. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers, and founder effects during range expansion.
Rattus population genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management
<p><a name="_Hlk13067419"></a><a name="_Hlk16009716">Invasive species have led to precipitous declines in biodiversity, especially in island systems. Brown (<i>Rattus norvegicus</i>) and black rats (<i>R. rattus</i>) are among the most invasive animals on the planet, with eradication being the primary tool for established island populations. The need for increased research for defining eradication units and monitoring outcomes has been highlighted as a means to maximize success. Haida Gwaii is an archipelago ~100 km off the northern coast of British Columbia, Canada that hosts globally significant breeding populations of seabirds that are at risk due to invasive rats. Here, we paired sampling of brown (n=287) and black (n=291) rats across the Haida Gwaii archipelago (British Columbia, Canada) with genotyping-by-sequencing (10,770-27,686 SNPs) to investigate patterns of population connectivity and infer levels/direction of gene flow among invasive rat populations in Haida Gwaii. We reconstructed three regional clusters for both species (north, central, south), with proximate populations within regions being largely more related than those that were more distant, consistent with predictions from island biogeography theory. Population assignment of recently detected individuals post-eradication on Faraday, Murchison, and the Bischof Islands revealed all were re-invaders from Lyell Island, rather than being on-island survivors. Based on these results, we identified six eradication units constituting single or clusters of islands that would limit the potential for re-invasion, some of which will need to be combined with biosecurity measures. Overall, our results highlight the importance of targeted research prior to conducting eradications and demonstrates a framework for applying population genomics for guiding invasive species management in island systems.</a></p>
Supplementary Info for manuscript "A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae)" - F1000 Research
Open the record for dataset details and reuse information.
Data from: Population genomics shed light on the demographic and adaptive histories of European invasion in the Pacific oyster, Crassostrea gigas
Open the record for dataset details and reuse information.
Data from: Signatures of divergence, invasiveness and terrestralization revealed by four apple snail genomes
Open the record for dataset details and reuse information.
Data from: Population genomics of a symbiont in the early stages of a pest invasion
Open the record for dataset details and reuse information.
Data from: Mixed population genomics support for the central marginal hypothesis across the invasive range of the cane toad (Rhinella marina) in Australia
Open the record for dataset details and reuse information.
Data from: Contrasting patterns of genome-wide polymorphism in the native and invasive range of the marine mollusk Crepidula fornicata
Open the record for dataset details and reuse information.
Data from: Rattus population genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management
Open the record for dataset details and reuse information.
Data from: Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern US
Open the record for dataset details and reuse information.
Data from: Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex
Open the record for dataset details and reuse information.
Data from: The genomic ancestry, landscape genetics, and invasion history of introduced mice in New Zealand
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.