Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Molecular species identification and population genetics of chondrichthyans in South Africa: current challenges, priorities and progress

Molecular species identification and population genetics of chondrichthyans in South Africa:... Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South Africa's chondrichthyans are threatened with extinction. South Africa's commercial shark fisheries have increased over the last decade and there is a need to ensure sustainable utilisation and conservation of this fisheries resource. Here, we give an overview of the molecular techniques that are used to assist in the identification of species, cryptic speciation and possible interspecific hybridisation, as well as the assessment of population structure and reproductive behaviour of endemic and commercially important chondrichthyan species of southern Africa. We discuss the potential application of these techniques for management and conservation of several species affected by South African fisheries. Acquiring baseline barcode data of all chondrichthyans in southern African waters and assessing the population structure of exploited species on a local and greater regional scale are recommended as research priorities. Future prospects should also include high-throughput molecular marker development and investigation of intraspecies functional variation using next generation sequencing technology. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png African Zoology Taylor & Francis

Molecular species identification and population genetics of chondrichthyans in South Africa: current challenges, priorities and progress

Download PDF
13 pages

Molecular species identification and population genetics of chondrichthyans in South Africa: current challenges, priorities and progress

Abstract

Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South Africa's chondrichthyans are threatened with extinction. South Africa's commercial shark fisheries have increased over the last decade and there is a need to ensure...
Loading next page...
 
/lp/taylor-francis/molecular-species-identification-and-population-genetics-of-8AzLqzpFaS
Publisher
Taylor & Francis
Copyright
© 2015 Zoological Society of Southern Africa
ISSN
2224-073X
eISSN
1562-7020
DOI
10.1080/15627020.2015.1063408
Publisher site
See Article on Publisher Site

Abstract

Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South Africa's chondrichthyans are threatened with extinction. South Africa's commercial shark fisheries have increased over the last decade and there is a need to ensure sustainable utilisation and conservation of this fisheries resource. Here, we give an overview of the molecular techniques that are used to assist in the identification of species, cryptic speciation and possible interspecific hybridisation, as well as the assessment of population structure and reproductive behaviour of endemic and commercially important chondrichthyan species of southern Africa. We discuss the potential application of these techniques for management and conservation of several species affected by South African fisheries. Acquiring baseline barcode data of all chondrichthyans in southern African waters and assessing the population structure of exploited species on a local and greater regional scale are recommended as research priorities. Future prospects should also include high-throughput molecular marker development and investigation of intraspecies functional variation using next generation sequencing technology.

Journal

African Zoology – Taylor & Francis

Published: Jul 3, 2015

Keywords: chondrichthyans; conservation; fisheries; genetics; sharks; southern Africa

References

  • Global-scale genetic identification of hammerhead sharks: application to assessment of the international fin trade and law enforcement
  • Nuclear and mitochondrial DNA reveals isolation of imperilled grey nurse shark populations (Carcharias taurus
  • A new legskate (Rajoidei: genus Cruriraja) from southern Africa
  • You could be eating shark meat and not even know it
  • Bycatch in South Africa's inshore trawl fishery as determined from observer records
  • DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp
  • Phylogeography of the copper shark Carcharhinus brachyurus in the southern hemisphere: implications for the conservation of a coastal apex predator
  • Chondrichthyan occurrence and abundance trends in False Bay, South Africa, spanning a century of catch and survey records
  • Agulhas leakage dynamics affects decadal variability in Atlantic overturning circulation
  • Differential gene flow patterns for two commercially exploited shark species, tope (Galeorhinus galeus) and common smoothhound (Mustelus mustelus) along the south-west coast of South Africa
  • Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes
  • Genetic divergence, speciation and biogeography of Mustelus (sharks) in the central Indo-Pacific and Australasia
  • Frequency of multiple paternity in gummy shark, Mustelus antarcticus, and rig, Mustelus lenticulatus, and the implications of mate encounter rate, post-copulatory influences, and reproductive mode
  • Rapid isolation of the first set of polymorphic microsatellite loci from the Australian gummy shark, Mustelus antarcticus and their utility across divergent shark taxa
  • Genetic mating system of the brown smoothhound shark Mustelus henlei, including a literature review of multiple paternity in other elasmobranch species
  • DNA barcoding reveals a high incidence of fish species misrepresentation and substitution on the South African market
  • Global population structure of the tope Galeorhinus galeus inferred by mitochondrial control region sequence data
  • Characterization of 13 microsatellite loci for the tope shark, Galeorhinus galeus, discovered with next-generation sequencing and their utility for eastern Pacific smooth-hound sharks (Mustelus
  • A streamlined, bi-organelle, multiplex PCR approach to species identification: application to global conservation and trade monitoring of the great white shark, Carcharodon carcharias
  • There and back again: a review of residency and return migrations in sharks, with implications for population structure and management
  • Genetic diversity despite population collapsein a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata
  • Estimates of shark species composition and numbers associated with the shark fin trade based on Hong Kong auction data
  • Global estimates of shark catches using trade records from commercial markets
  • Social, economic and regulatory drivers of the shark fin trade
  • An overview of chondrichthyan systematics and biodiversity in southern Africa. Transactions of the Royal Society of South Africa
  • First identification of interspecies hybridization in the freshwater stingrays Potamotrygon motoro and P. falkneri (Myliobatiformes, Potamotrygonidae
  • National Plan of Action for the conservation and management of sharks (NPOA-Sharks
  • Genetic catch verification to support recovery plans for deepsea gulper sharks (genus Centrophorus, family Centrophoridae) – an Australian example using the 16S gene
  • Is multiple mating beneficial or unavoidable? Low multiple paternity and genetic diversity in the shortspine spurdog Squalus mitsukurii
  • Global phylogeography with mixed marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini
  • A description and updated overview of the status and management of South Africa's chondrichthyan fisheries In
  • South Africa's demersal shark meat harvest
  • Quantifying the degree of protection afforded by a no-take marine reserve on an exploited shark
  • Special features of RAD sequencing data: implications for genotyping
  • Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff
  • The unholy trinity: taxonomy, species delimitation and DNA barcoding
  • Are indirect genetic benefits associated with polyandry? Testing predictions in a natural population of lemon sharks
  • First observations of young of the year and juvenile great white sharks (Carcharodon carcharias) scavenging from a whale carcass
  • Species identification, distribution and reproductive interactions of common smooth-hound and blackspotted smooth-hound shark (genus Mustelus) in the Adriatic Sea
  • Applying genetic techniques to study remote shark fisheries in northeastern Madagascar
  • A review of the application of molecular genetics for fisheries management and conservation of sharks and rays
  • IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific
  • Population status of 14 shark species caught in the protective gillnets off KwaZulu–Natal beaches, South Africa, 1978–2003
  • You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks
  • Extinction risk and conservation of the world's sharks and rays
  • Global phylogeography of the scalloped hammerhead shark Sphyrna lewini
  • Pristiophorus nancyae, a new species of sawshark (Chondrichthyes: Pristiophoridae) from southern Africa
  • Biodiversity and systematics of skates (Chondrichthyes: Rajiformes: Rajoidei
  • A new lanternshark (Squaliformes: Etmopteridae
  • Tetronarce cowleyi, sp. nov., a new species of electric ray from southern Africa (Chondrichthyes: Torpediniformes: Torpedinidae
  • Beyond Jaws: rediscovering the ‘lost sharks’ of southern Africa
  • Applications of next generation sequencing in molecular ecology of non-model organisms
  • Local de novo assembly of RAD paired-end contigs using short sequencing reads
  • A simple genetic identification method for northeast Atlantic smoothhound sharks (Mustelus spp
  • The breeding biology of lemon sharks at a tropical nursery lagoon
  • Population genetic structure of the lemon shark Negaprion brevirostris in the western Atlantic: DNA microsatellite variation
  • Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks
  • Susceptibility of sharks, rays and chimaeras to global extinction
  • Molecular barcoding reveals mislabelling of commercial fish products in Italy
  • Global population genetic structure of the pelagic blue shark (Prionace glauca
  • Sharks, rays and chimaeras: the status of the chondrichthyan fishes. Status survey
  • Population expansion and genetic structure in Carcharhinus brevipinna in the southern Indo-Pacific
  • Marine biodiversity in South Africa: an evaluation of current states of knowledge
  • DNA barcodes distinguish species of tropical Lepidoptera
  • Biological identifications through DNA barcodes
  • Mitochondrial DNA diversity and divergence among sharpnose sharks, Rhizoprionodon terraenovae, from the Gulf of Mexico and mid-Atlantic Bight
  • SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus
  • Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing
  • Evolutionary mechanisms shaping the genetic population structure of marine fishes; lessonsfrom the European flounder (Platichthys flesus L
  • Incipient genetic isolation of a temperate migratory coastal sciaenid fish (Argyrosomus inodorus) within the Benguela Cold Current system
  • Evidence of deep genetic divergence between populations of an important recreational fishery species, Lichia amia L. 1758, around southern Africa
  • Low worldwide genetic diversity in the basking shark (Cetorhinus maximus
  • Identification of shark and ray fins using DNA barcoding
  • Identifying Canadian freshwater fishes through DNA barcodes
  • Taxonomy and molecular phylogeny of some southern African catsharks (Scyliorhinidae; Chondrichthyes
  • A taxonomic revision of the catshark genus Haploblepharus Garman 1913 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae
  • Testing morphologically based phylogenetic theories within the cartilaginous fishes with molecular data, with special reference to the catshark family (Chondrichthyes; Scyliorhinidae) and the interrelationships within them
  • Nursery grounds, movement patterns and growth rates of dusky sharks, Carcharhinus obscurus: a long-term tag and release study in South African waters
  • The Benguela Current: an ecosystem of four components
  • IUCN Red List of Threatened Species
  • The effect of multiple paternity on the genetically effective size of a population
  • Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA
  • Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal
  • Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea
  • New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus
  • Development of a FINS-based method for the identification of skates species of commercial interest
  • White sharks and other chondrichthyan interactions with the beach-seine (treknet) fishery in False, Bay, South Africa
  • DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan
  • Global diversity hotspots and conservation priorities for sharks
  • Genetic diversity and population genetic structure in the South African commercially important shark species, the common smoothhound (Mustelus mustelus
  • Microsatellite cross-species amplification and utility in southern African elasmobranchs: a valuable resource for fisheries management and conservation
  • Genetic tracking of basking shark products in international trade
  • RNA-seq: from technology to biology
  • Rates of mitochondrial DNA evolution in sharks are slow compared with mammals
  • Commercialization of a critically endangered species (largetooth sawfish, Pristis perotteti) in fish markets of northern Brazil: authenticity by DNA analysis
  • Identification of the shark species Rhizoprionodon lalandii and R. porosus (Elasmobranchii, Carcharhinidae) by multiplex PCR and PCR-RFLP techniques
  • Classification of sharks in the Egyptian mediterranean waters using morphological and DNA barcoding approaches
  • Detection of interspecies hybridisation in Chondrichthyes: Hybrids and hybrid offspring between Australian (Carcharhinus tilstoni) and common (C. limbatus) blacktip shark found in an Australian fishery
  • Assessing statistical power of SNPs for population structure and conservation studies
  • Barcoding deep-water chondrichthyans from mainland Portugal
  • Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia
  • Management of sharks and their relatives Elasmobranchii
  • Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini
  • A DNA sequence-based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology
  • Ocean's eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries
  • The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago
  • Negligible evidence for regional genetic population structure for two shark species Rhizoprionodon acutus (Rüppell, 1837) and Sphyrna lewini (Griffith & Smith, 1834) with contrasting biology
  • Vigorous exchange between the Indian and Atlantic oceans at the end of the past five glacial periods
  • Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs
  • Effective size closely approximates the census size in the heavily exploited western Atlantic population of the sandbar shark, Carcharhinus plumbeus
  • Marine Living Resources Act (Act No. 18 of 1998
  • National Environmental Management: Biodiversity Act, 2004 (Act No. 10 of 2004) Draft Shark Biodiversity Management Plan
  • Microsatellite analysis of population structure in the shortfin mako (Isurus oxyrinchus
  • DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia
  • Occurrence of Carcharias taurus in nursery areas of the Eastern and Western Cape, South Africa
  • Life history and diet of two southern African smoothhound sharks, Mustelus mustelus (Linnaeus, 1758) and Mustelus palumbes Smith, 1957 (Pisces: Triakidae
  • First megamouth shark from the western Indian Ocean and South Africa
  • Inclusion of South American samples reveals new population structuring of the blacktip shark (Carcharhinus limbatus) in the Western Atlantic
  • Barcoding Nemo: DNA-based identifications for the ornamental fish trade
  • The effects of fishing on sharks, rays, and chimaeras (chondrichthyans), and the implications for marine ecosystems
  • Molecular phylogeny and node time estimation of bioluminescent lantern sharks (Elasmobranchii: Etmopteridae
  • Two sides of the same coin: extinctions and originations across the Atlantic/ Indian Ocean boundary as consequences of the same climate oscillation
  • Accuracy of species identification by fisheries observers in a north Australian shark fishery
  • Evidence for reproductive philopatry in the bull shark Carcharhinus leucas
  • Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops ocellatus
  • Biogeography and the selection of priority areas for conservation of South African coastal fishes
  • A weaker Agulhas Current leads to more Agulhas leakage
  • What barcode sequencing reveals about the shark fishery in Peru
  • First record of living Manta alfredi×
  • Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species
  • Shark fin identification through DNA barcoding
  • DNA barcoding of shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species
  • DNA barcoding Australia's fish species
  • Description of two new species of smoothhounds, Mustelus widodoi and M. ravidus (Carcharhiniformes: Triakidae) from the Western Central Pacific
  • Description of two new species of gummy sharks, genus Mustelus (Carcharhiniformes: Triakidae), from Australian waters
  • Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach
  • Global catches, exploitation rates, and rebuilding options for sharks
  • Widespread utility of highly informative AFLP molecular markers across divergent shark species