The complete mitochondrial genome of a gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae), from the Western Indian Ocean.
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ABSTRACT:
SUBMITTER: Patel E
PROVIDER: S-EPMC7782100 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We report the first mitochondrial genome sequences for the gray reef shark, Carcharhinus amblyrhynchos. Two specimens from the British Indian Ocean Territory were sequenced independently using two different next generation sequencing methods, namely short read sequencing on the Illumina HiSeq and long read sequencing on the Oxford Nanopore Technologies' MinION sequencer. The two sequences are 99.9% identical and are 16,705 base pairs (bp) and 16,706 bp in length. The mitogenome contains 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two non-coding regions; the control region and the origin of light-strand replication (OL).
| S-EPMC7782339 | biostudies-literature
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-other
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
Project description:The Chagos archipelago in the British Indian Ocean Territory (BIOT) has been lacking in detailed genetic studies of its chondrichthyan populations. Chondrichthyes in Chagos continue to be endangered through illegal fishing operations, necessitating species distribution and abundance studies to facilitate urgent monitoring and conservation of the species. Here, we present a complete mitochondrial genome of the Silvertip Shark, Carcharhinus albimarginatus sampled in the Chagos archipelago. The mitochondrial genome of C. albimarginatus was 16,706 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a replication origin and a D-loop region. GC content was at 38.7% and the control region was 1,065 bp in length. We expect that mitogenomes presented here will aid development of molecular assays for species distribution studies. Overall these studies will promote effective conservation of marine ecosystemes in the BIOT.
| S-EPMC7782225 | biostudies-literature
Project description:Grey reef sharks (Carcharhinus amblyrhynchos) can be one of the numerically dominant high order predators on pristine coral reefs, yet their numbers have declined even in the highly regulated Australian Great Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine scale genetic connectivity of grey reef sharks is essential for their effective management, but no genetic data are yet available. We investigated grey reef shark genetic structure in the GBR across a 1200?km latitudinal gradient, comparing empirical data with models simulating different levels of migration. The empirical data did not reveal any genetic structuring along the entire latitudinal gradient sampled, suggesting regular widespread dispersal and gene flow of the species throughout most of the GBR. Our simulated datasets indicate that even with substantial migrations (up to 25% of individuals migrating between neighboring reefs) both large scale genetic structure and genotypic spatial autocorrelation at the reef scale were maintained. We suggest that present migration rates therefore exceed this level. These findings have important implications regarding the effectiveness of networks of spatially discontinuous Marine Protected Areas to protect reef sharks.
| S-EPMC4551972 | biostudies-literature
Project description:We present the first mitochondrial genome of Trianenodon obesus from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area. The mitogenome was 16,702 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 38.9%. The control region was 1064 bp in length. This mitogenome for the BIOT MPA T. obesus differed from the previously published T. obesus genome by 15 bp and the differences include a 2 bp insertion and 13 single nucleotide polymorphisms distributed across the mitogenome in the BIOT MPA sequence. Whole mitogenome sequence of T. obesus from the Chagos archipelago presented here fills existing gaps in genetic information on marine species from the BIOT MPA and provides additional tools for species specific assessments as to the effectiveness of MPA management. In addition, methods presented here lay the framework for genetic studies in remote locations with limited infrastructure.
| S-EPMC7783066 | biostudies-literature
Project description:We present the first mitochondrial genome of Carcharhinus falciformis from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area (MPA). The mitochondrial genome of C. falciformis is 16,701 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 1063 bp in length. The complete mitogenome sequence of C. falciformis from the BIOT MPA will enable improved conservation measures of the CITES listed species through studies of species distribution, population abundance, fishing pressure and wildlife trade.
| S-EPMC7782099 | 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:Aim:Understanding the drivers of the structure of coral reef fish assemblages is vital for their future conservation. Quantifying the separate roles of natural drivers from the increasing influence of anthropogenic factors, such as fishing and climate change, is a key component of this understanding. It follows that the intrinsic role of historical biogeographical and geomorphological factors must be accounted for when trying to understand the effects of contemporary disturbances such as fishing. Location:Comoros, Madagascar, Mozambique and Tanzania, Western Indian Ocean (WIO). Methods:We modeled patterns in the density and biomass of an assemblage of reef-associated fish species from 11 families, and their association with 16 biophysical variables. Results:Canonical analysis of principal coordinates revealed strong country affiliations of reef fish assemblages and distance-based linear modeling confirmed geographic location and reef geomorphology were the most significant correlates, explaining 32% of the observed variation in fish assemblage structure. Another 6%-8% of variation was explained by productivity gradients (chl_a), and reef exposure or slope. Where spatial effects were not significant between mainland continental locations, fishing effects became evident explaining 6% of the variation in data. No correlation with live coral was detected. Only 37 species, predominantly lower trophic level taxa, were significant in explaining differences in assemblages between sites. Main Conclusions:Spatial and geomorphological histories remain a major influence on the structure of reef fish assemblages in the WIO. Reef geomorphology was closely linked to standing biomass, with "ocean-exposed" fringing reefs supporting high average biomass of ~1,000 kg/ha, while "lagoon-exposed fringing" reefs and "inner seas patch complex" reefs yielded substantially less at ~500kg/ha. Further, the results indicate the influence of benthic communities on fish assemblages is scale dependent. Such insights will be pivotal for managers seeking to balance long-term sustainability of artisanal reef fisheries with conservation of coral reef systems.
| S-EPMC6468081 | biostudies-other