Assembly and annotation of the grey reef shark (Carcharhinus amblyrhynchos) genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB89872 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Skin microbiome of black-tip reef shark (Carcharhinus melanopterus)
| PRJNA498626 | ENA
Project description:Whole genome sequencing of Carcharhinus amblyrhynchos
| PRJEB90057 | ENA
Project description:For broadly distributed, often overexploited species such as elasmobranchs (sharks and rays), conservation management would benefit from understanding how life history traits change in response to local environmental and ecological factors. However, fishing obfuscates this objective by causing complex and often mixed effects on the life histories of target species. Disentangling the many drivers of life history variability requires knowledge of elasmobranch populations in the absence of fishing, which is rarely available. Here, we describe the growth, maximum size, sex ratios, size at maturity, and offer a direct estimate of survival of an unfished population of grey reef sharks (Carcharhinus amblyrhynchos) using data from an eight year tag-recapture study. We then synthesized published information on the life history of C. amblyrhynchos from across its geographic range, and for the first time, we attempted to disentangle the contribution of fishing from geographic variation in an elasmobranch species. For Palmyra's unfished C. amblyrhynchos population, the von Bertalanffy growth function (VBGF) growth coefficient k was 0.05 and asymptotic length L∞ was 163.3 cm total length (TL). Maximum size was 175.5 cm TL from a female shark, length at maturity was estimated at 116.7-123.2 cm TL for male sharks, maximum lifespan estimated from VBGF parameters was 18.1 years for both sexes combined, and annual survival was 0.74 year-1. Consistent with findings from studies on other elasmobranch species, we found significant intraspecific variability in reported life history traits of C. amblyrhynchos. However, contrary to what others have reported, we did not find consistent patterns in life history variability as a function of biogeography or fishing. Ultimately, the substantial, but not yet predictable variability in life history traits observed for C. amblyrhynchos across its geographic range suggests that regional management may be necessary to set sustainable harvest targets and to recover this and other shark species globally.
| S-EPMC5313192 | biostudies-literature
Project description:Globally, the frequency of shark bites is rising, resulting in an increasing demand for shark deterrents and measures to lessen the impact of shark bites on humans. Most existing shark protection measures are designed to reduce the probability of a bite, but fabrics that minimise injuries when a shark bite occurs can also be used as mitigation devices. Here, we assessed the ability of the Ocean Guardian Scuba7 and Kevlar material to reduce the likelihood of blacktip reef sharks, Carcharhinus melanopterus, from feeding, and to minimise injuries from shark bites. Sharks were enticed to consume a small piece of local reef fish (bait) placed between the two Scuba7 electrodes with the deterrents randomly being turned on or kept off. In the second experiment, the bait was attached to a small pouch made of either standard neoprene or neoprene with a protective layer of Kevlar around it. The Scuba7 reduced the proportion of baits being taken by 67%, (from 100% during control trials to 33%). Sharks also took more time to take the bait when the device was active (165 ± 20.40 s vs. 38.9 ± 3.35 s), approached at a greater distance (80.98 ± 1.72 cm vs. 38.88 ± 3.20 cm) and made a greater number of approaches per trial (19.38 ± 2.29 vs. 3.62 ± 0.53) than when the Scuba7 was inactive. The sizes of punctures from shark bites were significantly smaller on neoprene with Kevlar compared to standard neoprene (3.64 ± 0.26 mm vs. 5.88 ± 0.29 mm). The number of punctures was also fewer when Kevlar was used (14.92 ± 3.16 vs. 74.1 ± 12.44). Overall, the Ocean Guardian Scuba7 and Kevlar reduced the impact of blacktip reef shark bites. These findings may help consumers make informed decisions when purchasing shark deterring and protective products.
| S-EPMC7046715 | biostudies-literature
Project description:With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.
| S-EPMC5555095 | biostudies-literature
Project description:The Caribbean reef shark (Carcharhinus perezi; Poey, 1876) is a medium to large-bodied coastal and reef-associated predator found throughout the subtropical and tropical waters of the Atlantic Ocean and Caribbean Sea, although its populations are increasingly threatened by overfishing. We describe the first mitochondrial genome sequence for this species, using Illumina MiSeq sequencing of an individual from The Bahamas. We report the mitogenome sequence of the Caribbean reef shark to be 16,709 bp and composed two rRNA genes, 22 tRNA genes, 13 protein-coding genes, 2 non-coding regions; the D-loop control region and the origin of light-strand replication. We discuss the implications of this new information on future monitoring efforts and conservation measures such as marine protected areas, and urge for greater application of mitochondrial studies of sharks in the Atlantic Ocean.
| S-EPMC8381894 | biostudies-literature