Galeorhinus galeus
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ABSTRACT:
PROVIDER: PRJNA1121340 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Galeorhinus galeus (School Shark) genome, sGalGal3, haplotype 2
| PRJNA1121341 | ENA
Project description:Galeorhinus galeus (School Shark), sGalGal3, sequence data
| PRJNA1121342 | ENA
Project description:ORG.one project Galeorhinus galeus whole genome
| PRJEB57096 | ENA
Project description:ORG.one project Galeorhinus galeus conservation genomics
| PRJEB70712 | ENA
Project description:Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Dependent within Australia. Individuals are known to move between both countries, but it is disputed whether the stocks are reproductively linked. Accurate and unbiased determination of stock and population connectivity is crucial to inform effective management. In this study, we assess the genetic composition and population connectivity between Australian and New Zealand school sharks using genome-wide SNPs, while accounting for non-random kin sampling. Between 2009 and 2013, 88 neonate and juvenile individuals from Tasmanian and New Zealand nurseries were collected and genotyped. Neutral loci were analyzed to detect fine-scale signals of reproductive connectivity. Seven full-sibling groups were identified and removed for unbiased analysis. Based on 6,587 neutral SNPs, pairwise genetic differentiation from Tasmanian and New Zealand neonates was non-significant (F ST = 0.0003, CI95 = [-0.0002, 0.0009], p = 0.1163; D est = 0.0006 ± 0.0002). This pattern was supported by clustering results. In conclusion, we show a significant effect of non-random sampling of kin and identify fine-scale reproductive connectivity between Australian and New Zealand school sharks.Open research badgesThis article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.pd8612j.
| S-EPMC6476751 | biostudies-literature
Project description:The tope shark (Galeorhinus galeus Linnaeus, 1758) is a temperate, coastal hound shark found in the Atlantic and Indo-Pacific oceans. In this study, the population structure of Galeorhinus galeus was determined across the entire Southern Hemisphere, where the species is heavily targeted by commercial fisheries, as well as locally, along the South African coastline. Analysis was conducted on a total of 185 samples using 19 microsatellite markers and a 671 bp fragment of the NADH dehydrogenase subunit 2 (ND2) gene. Across the Southern Hemisphere, three geographically distinct clades were recovered, including one from South America (Argentina, Chile), one from Africa (all the South African collections) and an Australia-New Zealand clade. Nuclear data revealed significant population subdivisions (FST = 0.192 to 0.376, p<0.05) indicating limited gene flow for tope sharks across ocean basins. Marked population connectivity was however evident across the Indian Ocean based on Bayesian clustering analysis. More locally in South Africa, F-statistics and multivariate analysis supported moderate to high gene flow across the Atlantic/Indian Ocean boundary (FST = 0.035 to 0.044, p<0.05), with exception of samples from Struisbaai and Port Elizabeth which differed significantly from the rest. Discriminant and Bayesian clustering analysis indicated admixture in all sampling populations, decreasing from west to east, corroborating possible restriction to gene flow across regional oceanographic barriers. Mitochondrial sequence data recovered seven haplotypes (h = 0.216, π = 0.001) for South Africa, with one major haplotype shared by 87% of the individuals and at least one private haplotype for each sampling location except Port Elizabeth. As with many other coastal shark species with cosmopolitan distribution, this study confirms the lack of both historical dispersal and inter-oceanic gene flow while also implicating contemporary factors such as oceanic currents and thermal fronts to drive local genetic structure of G. galeus on a smaller spatial scale.
| S-EPMC5589243 | biostudies-literature
Project description:Background Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. Methods We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. Conclusions Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
2017-03-24 | GSE96683 | GEO
Project description:Stegostoma tigrinum (zebra shark) genome, sSteFas4, haplotype 2
| PRJNA986594 | ENA