ORCID Profile
0000-0002-3579-7094
Current Organisation
University of California Merced
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Publisher: Frontiers Media SA
Date: 05-05-2021
DOI: 10.3389/FMARS.2021.619695
Abstract: Chondrichthyes, an ancient and erse class of vertebrates, are crucial to the health of marine ecosystems. Excessive demand for chondrichthyan products has increased fishing pressure, threatening ∼30% of species with extinction in recent decades. India is the second-largest shark landing nation globally and the province of Gujarat, is the largest contributor to its shark exports. Despite their significant contribution to global fish supplies, chondrichthyan fisheries in Gujarat remain understudied and many species, data deficient, posing challenges to the conservation of remaining populations in the region. Here, we report results from taxonomic assessment of elasmobranchs at four key landing sites in Gujarat. We identified thirty-one species of sharks and rays with a significant bias toward capture of females and juveniles by fisheries. Our data indicate the presence of nursery areas for species such as Sphyrna lewini and Rhynchobatus laevis in the neritic areas off Gujarat. Further, we discovered extensions of the current distribution range for three species - Torpedo sinuspersici , Carcharhinus sorrah , and Rhinobatos punctifer . Taxonomic identities for a subset of species were confirmed using genomic analyses conducted with portable DNA sequencing tools. We present assessments for six data deficient species in the region – Rhinobatos annandalei , Rhinoptera jayakari , Maculabatis bineeshi, Pateobatis bleekeri, T. sinuspersici , and Carcharhinus amboinensis. Our investigation underscores species with urgent conservation needs and reduces data deficiencies. These data will inform and pivot future scientific and conservation efforts to protect remaining populations of some of the most vulnerable Chondrichthyes in the Arabian Seas Region.
Publisher: Springer Science and Business Media LLC
Date: 14-03-2019
DOI: 10.1038/S41598-019-40940-9
Abstract: Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis , a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus , suggesting the need for taxonomic reassignment of P . glauca . We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for bio ersity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of lification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.
Publisher: Elsevier BV
Date: 06-2020
No related grants have been discovered for Sam Fellows.