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Dataset results
29 results for “salmon conservation”
Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci
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Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms
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Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies
A novel application of genome-wide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha), and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site-associated markers and Random Forest, an approach suitable for polygenic traits. Mapping of trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to, or more divergent in, the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated – and potentially adaptive – loci. The results will promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.
Supplementary material 1 from: Shaffer JA, Parks D, Campbell K, Moragne A, Hueske B, Adams P, Bauman JM (2023) Coastal beaver, Chinook, coho, chum salmon and trout response to nearshore changes resulting from diking and large-scale dam removals: synergistic ecosystem engineering and restoration in the coastal zone. Nature Conservation 53: 61-83. https://doi.org/10.3897/natureconservation.53.85421
Mean woody plant abundance surveyed from the riparian and shrub-emergent marsh vegetation
Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies
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Sex-Biased Gene Expression and Sequence Conservation in Pacific and Atlantic Salmon Lice (Lepeophtheirus salmonis)
GEO Series GSE73734. Lepeophtheirus salmonis. 40 samples. Type: Expression profiling by array.
Conservation genomics of Atlantic salmon (Year One)
GEO Series GSE19111. Oncorhynchus mykiss; Oncorhynchus tshawytscha; Salmo salar; Coregonus clupeaformis; Osmerus mordax. 20 samples. Type: Expression profiling by array.
Conservation genomics of Atlantic salmon
GEO Series GSE19170. Osmerus mordax; Oncorhynchus tshawytscha; Coregonus clupeaformis; Oncorhynchus mykiss; Salmo salar. 54 samples. Type: Expression profiling by array.
Conservation genomics of Atlantic salmon (Year Two)
GEO Series GSE19119. Osmerus mordax; Salmo salar; Coregonus clupeaformis; Oncorhynchus mykiss; Oncorhynchus tshawytscha. 34 samples. Type: Expression profiling by array.
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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.