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

References

• Abercrombie DL, Clarke SC, Shivji MS. 2005. Global-scale genetic identification of hammerhead sharks: application to assessment of the international fin trade and law enforcement. Conservation Genetics 6: 775–788.
   Google Scholar
• Ahonen H, Harcourt RG, Stow AJ. 2009. Nuclear and mitochondrial DNA reveals isolation of imperilled grey nurse shark populations (Carcharias taurus). Molecular Ecology 18: 4409–4421.
   Google Scholar
• Aschliman NC, Ebert DA, Compagno LJ. 2010. A new legskate (Rajoidei: genus Cruriraja) from southern Africa. Copeia 3: 364–372.
   Google Scholar
• Atkins H. 2010. You could be eating shark meat and not even know it. Cape Times, 14 May.
   Google Scholar
• Attwood CG, Petersen SL, Kerwath SE. 2011. Bycatch in South Africa's inshore trawl fishery as determined from observer records. ICES Journal of Marine Science 68: 2163–2174.
   Google Scholar
• Barbuto M, Galimberti A, Ferri E, Labra M, Malandra R, Galli P, Casiraghi M. 2010. DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp.). Food Research International 43: 376–381.
   Google Scholar
• Benavides MT, Feldheim KA, Duffy CA, Wintner S, Braccini JM, Boomer J, Huveneers C, Rogers P, Mangel JC, Alfaro-Shigueto J, Cartamil DP, Chapman DD. 2011. Phylogeography of the copper shark Carcharhinus brachyurus in the southern hemisphere: implications for the conservation of a coastal apex predator. Marine and Freshwater Research 62: 861–869.
   Google Scholar
• Best LN, Attwood CG, da Silva CD, Lamberth SJ. 2013. Chondrichthyan occurrence and abundance trends in False Bay, South Africa, spanning a century of catch and survey records. African Zoology 48: 201–227.
   Google Scholar
• Biastoch A, Böning CW, Lutjeharms JRE. 2008. Agulhas leakage dynamics affects decadal variability in Atlantic overturning circulation. Nature 456: 489–492.
   Google Scholar
• Bitalo DN, Maduna SN, da Silva C, Roodt-Wilding R, Bester-van der Merwe AE. In press. 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. Fisheries Research. DOI: 10.1016/j.fishres.2015.07.003.
   Google Scholar
• Blower DC, Pandolfi JM, Bruce BD, Gomez-Cabrera MDC, Ovenden JR. 2012. Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes. Marine Ecology Progress Series 455: 229–244.
   Google Scholar
• Boomer JJ, Harcourt RG, Francis MP, Stow AJ. 2012. Genetic divergence, speciation and biogeography of Mustelus (sharks) in the central Indo-Pacific and Australasia. Molecular Phylogenetics and Evolution 64: 697–703.
   Google Scholar
• Boomer JJ, Harcourt RG, Francis MP, Walker TI, Braccini JM, Stow AJ. 2013. 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. Journal of Heredity 104: 371–379.
   Google Scholar
• Boomer JJ, Stow AJ. 2010. Rapid isolation of the first set of polymorphic microsatellite loci from the Australian gummy shark, Mustelus antarcticus and their utility across divergent shark taxa. Conservation Genetic Resources 3: 393–395.
   Google Scholar
• Byrne RJ, Avise JC. 2012. Genetic mating system of the brown smoothhound shark Mustelus henlei, including a literature review of multiple paternity in other elasmobranch species. Marine Biology 159: 749–756.
   Google Scholar
• Cawthorn DM, Steinman HA, Witthuhn RC. 2012. DNA barcoding reveals a high incidence of fish species misrepresentation and substitution on the South African market. Food Research International 46: 30–40.
   Google Scholar
• Chabot CL, Allen LG. 2009. Global population structure of the tope Galeorhinus galeus inferred by mitochondrial control region sequence data. Molecular Ecology 18: 545–552.
   Google Scholar
• Chabot CL, Nigenda S. 2011. 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). Conservation Genetic Resources 3: 553–555.
   Google Scholar
• Chapman DD, Abercrombie DL, Douady CJ, Pikitch EK, Stanhopen MJ, Shivji MS. 2003. A streamlined, bi-organelle, multiplex PCR approach to species identification: application to global conservation and trade monitoring of the great white shark, Carcharodon carcharias. Conservation Genetics 4: 415–425.
   Google Scholar
• Chapman DD, Feldheim KA, Papastamatiou YP, Hueter RE. 2015. There and back again: a review of residency and return migrations in sharks, with implications for population structure and management. Annual Review of Marine Science 7: 547–570.
   Google Scholar
• Chapman DD, Simpfendorfer CA, Wiley TR, Poulakis GR, Curtis C, Tringali M, Carlson JK, Feldheim KA. 2011. Genetic diversity despite population collapsein a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata). Journal of Heredity 102: 643–652.
   Google Scholar
• Clarke SC, McAllister MK, Michielsens CGJ. 2005. Estimates of shark species composition and numbers associated with the shark fin trade based on Hong Kong auction data. Journal of Northwest Atlantic Fishery Science 35: 453–465.
   Google Scholar
• Clarke SC, McAllister MK, Milner-Gulland EJ, Kirkwood GP, Michielsens CGJ, Agnew DJ, Pikitch EK, Nakano H, Shivji MS. 2006. Global estimates of shark catches using trade records from commercial markets. Ecology Letters 9: 1115–1126.
   Google Scholar
• Clarke SC, Milner-Gulland EJ, Bjørndal T. 2007. Social, economic and regulatory drivers of the shark fin trade. Marine Resource Economics 22: 305–327.
   Google Scholar
• Compagno LJV. 1999. An overview of chondrichthyan systematics and biodiversity in southern Africa. Transactions of the Royal Society of South Africa 54: 75–120.
   Google Scholar
• Compagno LJV, Dando M, Fowler S. 2005. Sharks of the world. Princeton: Princeton University Press.
   Google Scholar
• Cruz VP, Vera M, Mendonça FF, Pardo BG, Martinez P, Oliveira C, Foresti F. 2015. First identification of interspecies hybridization in the freshwater stingrays Potamotrygon motoro and P. falkneri (Myliobatiformes, Potamotrygonidae). Conservation Genetics 16: 241–245.
   Google Scholar
• DAFF (Department of Agriculture, Forestry and Fisheries). 2013. National Plan of Action for the conservation and management of sharks (NPOA-Sharks). Pretoria: DAFF.
   Google Scholar
• Daley RK, Appleyard, SA, Koopman, M. 2012. Genetic catch verification to support recovery plans for deepsea gulper sharks (genus Centrophorus, family Centrophoridae) – an Australian example using the 16S gene. Marine and Freshwater Research 63: 708–714.
   Google Scholar
• Daly-Engel TS, Grubbs RD, Feldheim KA, Bowen BW, Toonen RJ. 2010. Is multiple mating beneficial or unavoidable? Low multiple paternity and genetic diversity in the shortspine spurdog Squalus mitsukurii. Marine Ecology Progress Series 403: 255–267.
   Google Scholar
• Daly-Engel TS, Seraphin KD, Holland KN, Coffey JP, Nance HA, Toonen RT, Bowen BW. 2012. Global phylogeography with mixed marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini). PLoS ONE 7: e29986.
   Google Scholar
• da Silva C, Booth AJ, Dudley SFJ, Kerwath SE, Lamberth SJ, Leslie RW, McCord ME, Sauer WHH, Zweig T. 2015. A description and updated overview of the status and management of South Africa's chondrichthyan fisheries In: Ebert DA, Huveneers C, Dudley SFJ (eds), Advances in shark research. African Journal of Marine Science 37. DOI: 10.2989/1814232X.2015.1044471.
   Google Scholar
• da Silva C, Bürgener M. 2007. South Africa's demersal shark meat harvest. TRAFFIC Bulletin 21: 55–56.
   Google Scholar
• da Silva C, Kerwath SE, Attwood CG, Thorstad EB, Cowley PD, Økland F, Wilke CG, Næsje TF. 2013. Quantifying the degree of protection afforded by a no-take marine reserve on an exploited shark. African Journal of Marine Science 35: 57–66.
   Google Scholar
• Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML. 2013. Special features of RAD sequencing data: implications for genotyping. Molecular Ecology 22: 3151–3164.
   Google Scholar
• DeSalle R. 2006. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conservation Biology 20: 1545–1547.
   Google Scholar
• DeSalle R, Egan MG, Siddall M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1905–1916.
   Google Scholar
• DiBattista JD, Feldheim KA, Gruber SH, Hendry AP. 2008. Are indirect genetic benefits associated with polyandry? Testing predictions in a natural population of lemon sharks. Molecular Ecology 17: 783–795.
   Google Scholar
• Dicken ML. 2008. First observations of young of the year and juvenile great white sharks (Carcharodon carcharias) scavenging from a whale carcass. Marine and Freshwater Research 59: 596–602.
   Google Scholar
• Di Francesco N. 2011. Species identification, distribution and reproductive interactions of common smooth-hound and blackspotted smooth-hound shark (genus Mustelus) in the Adriatic Sea. MSc thesis, University of Bologna, Italy.
   Google Scholar
• Doukakis P, Hanner R, Shivji M, Bartholomew C, Chapman D, Wong E, Amato G. 2011. Applying genetic techniques to study remote shark fisheries in northeastern Madagascar. Mitochondrial DNA 22: 15–20.
   Google Scholar
• Dudgeon CL, Blower DC, Broderick D, Giles JL, Holmes BJ, Kashiwagi T, Krück NC, Morgan JAT, Tillett BJ, Ovenden JR. 2012. A review of the application of molecular genetics for fisheries management and conservation of sharks and rays. Journal of Fish Biology 80: 1789–1843.
   Google Scholar
• Dudgeon CL, Broderick D, Ovenden JR. 2009. IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific. Molecular Ecology 18: 248–261.
   Google Scholar
• Dudley SF, Simpfendorfer CA. 2006. Population status of 14 shark species caught in the protective gillnets off KwaZulu–Natal beaches, South Africa, 1978–2003. Marine and Freshwater Research 57: 225–240.
   Google Scholar
• Dulvy NK, Baum JK, Clarke S, Compagno LJV, Cortés E, Domingo A, Fordham S, Fowler S, Francis MP, Gibson C, Martínez J, Musick JA, Soldo A, Stevens JD, Valenti S. 2008. You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks. Aquatic Conservation: Marine and Freshwater Ecosystems 18: 459–482.
   Google Scholar
• Dulvy NK, Fowler SL, Musick JA, Cavanagh RD, Kyne PM, Harrison LR, Carlson JK, Davidson LNK, Fordham SV, Francis MP, Pollock CM, Simpfendorfer CA, Burgess GH, Carpenter KE, Compagno LJV, Ebert DA, Gibson C, Heupel MR, Livingstone SR, Sanciangco JC, Stevens JD, Valenti S, White W. 2014. Extinction risk and conservation of the world's sharks and rays. eLife 3: e00590.
   Google Scholar
• Duncan KM, Martin AP, Bowen BW, De Couet HG. 2006. Global phylogeography of the scalloped hammerhead shark Sphyrna lewini. Molecular Ecology 15: 2239–2251.
   Google Scholar
• Ebert DA, Cailliet GM. 2011. Pristiophorus nancyae, a new species of sawshark (Chondrichthyes: Pristiophoridae) from southern Africa. Bulletin of Marine Science 87: 501–512.
   Google Scholar
• Ebert DA, Compagno LJ. 2007. Biodiversity and systematics of skates (Chondrichthyes: Rajiformes: Rajoidei). Environmental Biology of Fishes 80: 111–124.
   Google Scholar
• Ebert DA, Compagno LJ. 2009. Chlamydoselachus africana, a new species of frilled shark from southern Africa (Chondrichthyes, Hexanchiformes, Chlamydoselachidae). Zootaxa 2173: 1–18.
   Google Scholar
• Ebert DA, Compagno LJ, De Vries MJ. 2011. A new lanternshark (Squaliformes: Etmopteridae: Etmopterus) from southern Africa. Copeia 3: 379–384.
   Google Scholar
• Ebert DA, Haas DL, de Carvalho MR. 2015. Tetronarce cowleyi, sp. nov., a new species of electric ray from southern Africa (Chondrichthyes: Torpediniformes: Torpedinidae). Zootaxa 3936: 237–250.
   Google Scholar
• Ebert DA, van Hees KE. 2015. Beyond Jaws: rediscovering the ‘lost sharks’ of southern Africa. In: Ebert DA, Huveneers C, Dudley SFJ (eds), Advances in shark research. African Journal of Marine Science 37. DOI: 10.2989/1814232X.2015.1048730.
   Google Scholar
• Ekblom R, Galindo J. 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107: 1–15.
   Google Scholar
• Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA. 2011. Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE 6: e18561.
   Google Scholar
• FAO (Food and Agriculture Organization of the United Nations). 2011. Review of the state of world marine fishery resources. FAO Fisheries and Aquaculture Technical Paper no. 569. Rome: FAO.
   Google Scholar
• Farrell ED, Clarke MW, Mariani S. 2009. A simple genetic identification method for northeast Atlantic smoothhound sharks (Mustelus spp.). ICES Journal of Marine Science 66: 561–565.
   Google Scholar
• Feldheim KA, Gruber SH, Ashley MV. 2002. The breeding biology of lemon sharks at a tropical nursery lagoon. Proceedings of the Royal Society B: Biological Sciences 269: 1655–61.
   Google Scholar
• Feldheim KA, Gruber SH, Ashley MV. 2010. Population genetic structure of the lemon shark Negaprion brevirostris in the western Atlantic: DNA microsatellite variation. Molecular Ecology 10: 295–303.
   Google Scholar
• Feldheim KA, Gruber SH, DiBattista JD, Babcock EA, Kessel SA, Hendry AP, Pikitch EK, Ashley MV, Chapman DD. 2014. Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks. Molecular Ecology 23: 110–117.
   Google Scholar
• Field IC, Meekan MG, Buckworth RC, Bradshaw CJ. 2009. Susceptibility of sharks, rays and chimaeras to global extinction. Advances in Marine Biology 56: 275–363.
   Google Scholar
• Filonzi L, Chiesa S, Vaghi M, Marzano FN. 2010. Molecular barcoding reveals mislabelling of commercial fish products in Italy. Food Research International 43: 1383–1388.
   Google Scholar
• Fitzpatrick SF. 2012. Global population genetic structure of the pelagic blue shark (Prionace glauca). PhD thesis, Queen's University Belfast, Ireland.
   Google Scholar
• Fowler SL, Cavanagh RD, Camhi M, Burgess GH, Cailliet GM, Fordham SV, Simpendorfer CA, Musick JA (eds). 2005. Sharks, rays and chimaeras: the status of the chondrichthyan fishes. Status survey. Gland: IUCN/SSC Shark Specialist Group.
   Google Scholar
• Geraghty PT, Williamson JE, Macbeth WG, Wintner SP, Harry AV, Ovenden JR, Gillings MR. 2013. Population expansion and genetic structure in Carcharhinus brevipinna in the southern Indo-Pacific. PloS ONE 8: e75169.
   Google Scholar
• Griffiths CL, Robinson TB, Lange L, Mead A. 2010. Marine biodiversity in South Africa: an evaluation of current states of knowledge. PloS ONE 5: e12008.
   Google Scholar
• Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the USA 103: 968–971.
   Google Scholar
• Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270: 313–321.
   Google Scholar
• Heist EJ, Musick JA, Graves JE. 1996. Mitochondrial DNA diversity and divergence among sharpnose sharks, Rhizoprionodon terraenovae, from the Gulf of Mexico and mid-Atlantic Bight. Fishery Bulletin 94: 664–668.
   Google Scholar
• Helyar SJ, Limborg MT, Bekkevold D, Babbucci M, van Houdt J, Maes GE, Bargelloni L, Nielsen RO, Taylor MI, Ogden R, Cariani A, Carvalho GR, FishPopTrace Consortium, Panitz F. 2012. SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus). PloS ONE 7: e42089.
   Google Scholar
• Helyar SJ, Lloyd HAD, de Bruyn M, Leake J, Bennett N, Carvalho GR. 2014. Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing. PloS ONE 9: e98691.
   Google Scholar
• Hemmer-Hansen J, Nielsen EEG, Gronkjaer P, Loeschcke V. 2007. Evolutionary mechanisms shaping the genetic population structure of marine fishes; lessonsfrom the European flounder (Platichthys flesus L.). Molecular Ecology 16: 3104–3118.
   Google Scholar
• Henriques R, Potts WM, Sauer WHH, Santos CV, Shaw PW. 2014. Incipient genetic isolation of a temperate migratory coastal sciaenid fish (Argyrosomus inodorus) within the Benguela Cold Current system. Marine Biology Research 11: 423–429.
   Google Scholar
• Henriques R, Potts WM, Sauer WHH, Shaw PW. 2012. Evidence of deep genetic divergence between populations of an important recreational fishery species, Lichia amia L. 1758, around southern Africa. African Journal of Marine Science 34: 585–591.
   Google Scholar
• Hoelzel AR, Shivji MS, Magnussen J, Francis MP. 2006. Low worldwide genetic diversity in the basking shark (Cetorhinus maximus). Biology Letters 2: 639–642.
   Google Scholar
• Holmes BH, Steinke D, Ward RD. 2009. Identification of shark and ray fins using DNA barcoding. Fisheries Research 95: 280–288.
   Google Scholar
• Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P, Zhang J, April J, Bernatchez L. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PloS ONE 3: e2490.
   Google Scholar
• Human BA. 2003. Taxonomy and molecular phylogeny of some southern African catsharks (Scyliorhinidae; Chondrichthyes). PhD thesis, University of Cape Town, South Africa.
   Google Scholar
• Human BA. 2007. A taxonomic revision of the catshark genus Haploblepharus Garman 1913 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae). Zootaxa 40: 1–40.
   Google Scholar
• Human BA, Owen P, Compagno LJV, Harley EH. 2006. 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. Molecular Phylogenetics and Evolution 39: 384–391.
   Google Scholar
• Hussey NE, McCarthy ID, Dudley SF, Mann BQ. 2009. Nursery grounds, movement patterns and growth rates of dusky sharks, Carcharhinus obscurus: a long-term tag and release study in South African waters. Marine and Freshwater Research 60: 571–583.
   Google Scholar
• Hutchings L, van der Lingen CD, Shannon LJ, Crawford RJM, Verheye HMS, Bartholomae CH, van der Plas AK, Louw D, Kreiner A, Ostrowski M, Fidel Q, Barlow RG, Lamont T, Coetzee J, Shillington F, Veitch J, Currie JC, Monteiro PMS. 2009. The Benguela Current: an ecosystem of four components. Progress in Oceanography 83: 15–32.
   Google Scholar
• IUCN (International Union for Conservation of Nature and Natural Resources). 2009. IUCN Red List of Threatened Species, Version 2009.2. Available at http://www.iucnredlist.org [accessed 20 May 2014].
   Google Scholar
• Karl SA. 2008. The effect of multiple paternity on the genetically effective size of a population. Molecular Ecology 17: 3973–3977.
   Google Scholar
• Karl SA, Castro ALF, Lopez JA, Charvet P, Burgess GH. 2011. Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA. Conservation Genetics 12: 371–382.
   Google Scholar
• Keeney DB, Heist EJ. 2006. Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal. Molecular Ecology 15: 3669–3679.
   Google Scholar
• Keeney DB, Heupel MR, Hueter RE, Heist EJ. 2005. 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. Molecular Ecology 14: 1911–1923.
   Google Scholar
• Kemper JM, Ebert DA, Compagno LJ, Didier DA. 2010. Chimaera notafricana sp. nov. (Chondrichthyes: Chimaeriformes: Chimaeridae), a new species of chimaera from southern Africa. Zootaxa 2532: 55–63.
   Google Scholar
• Krück NC, Innes DI, Ovenden JR. 2013. New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus). Molecular Ecology Resources 13: 715–725.
   Google Scholar
• Lago FC, Vietites JM, Espineira M. 2012. Development of a FINS-based method for the identification of skates species of commercial interest. Food Control 24: 38–43.
   Google Scholar
• Lamberth SJ. 2006. White sharks and other chondrichthyan interactions with the beach-seine (treknet) fishery in False, Bay, South Africa. African Journal of Marine Science 28: 723–727.
   Google Scholar
• Liu S-YV, Chan C-LC, Lin O, Hu C-S, Chen CA. 2013. DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan. PLoS ONE 8: e79373.
   Google Scholar
• Lucifora LO, García VB, Worm B. 2011. Global diversity hotspots and conservation priorities for sharks. PLoS ONE 6: e19356.
   Google Scholar
• Maduna SN. 2014. Genetic diversity and population genetic structure in the South African commercially important shark species, the common smoothhound (Mustelus mustelus). MSc thesis, Stellenbosch University, South Africa.
   Google Scholar
• Maduna SN, Rossouw C, Roodt-Wilding R, Bester-van der Merwe AE. 2014. Microsatellite cross-species amplification and utility in southern African elasmobranchs: a valuable resource for fisheries management and conservation. BMC Research Notes 7: 352.
   Google Scholar
• Magnussen JE, Pikitch EK, Clarke SC, Nicholson C, Hoelzel AR, Shivji MS. 2007. Genetic tracking of basking shark products in international trade. Animal Conservation 10: 199–207.
   Google Scholar
• Marguerat S, Bähler J. 2010. RNA-seq: from technology to biology. Cellular and Molecular Life Sciences 67: 569–579.
   Google Scholar
• Martin AP, Naylor GJP, Palumbi SR. 1992. Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357: 153–155.
   Google Scholar
• Melo Palmeira CA, da Silva Rodrigues-Filho LF, de Luna Sales JB, Vallinoto M, Schneider H, Sampaio I. 2013. Commercialization of a critically endangered species (largetooth sawfish, Pristis perotteti) in fish markets of northern Brazil: authenticity by DNA analysis. Food Control 34: 249–252.
   Google Scholar
• Mendonça FF, Hashimoto DT, Porto-Foresti F, Oliveira C, Gadig OBF, Foresti F. 2009. Identification of the shark species Rhizoprionodon lalandii and R. porosus (Elasmobranchii, Carcharhinidae) by multiplex PCR and PCR-RFLP techniques. Molecular Ecology Resources 9: 771–773.
   Google Scholar
• Moftah M, Abdel Aziz SH, Elramah S, Favereaux, A. 2011. Classification of sharks in the Egyptian mediterranean waters using morphological and DNA barcoding approaches. PLoS ONE 6: e27001.
   Google Scholar
• Morgan JT, Harry AV, Welch DJ, Street R, White J, Geraghty PT, Macbeth WG, Tobin A, Simpfendorfer CA, Ovenden JR. 2012. 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. Conservation Genetics 13: 455–463.
   Google Scholar
• Morin PA, Martien KK, Taylor BL. 2009. Assessing statistical power of SNPs for population structure and conservation studies. Molecular Ecology Resources 9: 66–73.
   Google Scholar
• Moura T, Silva MC, Figueiredo I. 2015. Barcoding deep-water chondrichthyans from mainland Portugal. Marine and Freshwater Research 66: 508–517.
   Google Scholar
• Mourier J, Planes S. 2013. Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia. Molecular Ecology 22: 201–214.
   Google Scholar
• Musick JA, Burgess G, Cailliet G, Camhi M, Fordham S. 2000. Management of sharks and their relatives Elasmobranchii. Fisheries 25: 9–13.
   Google Scholar
• Nance HA, Klimley P, Galván-Magaña F, Martínez-Ortíz J, Marko PB. 2011. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini. PLoS ONE 6: e21459.
   Google Scholar
• Naylor GJP, Caira JN, Jensen K, Rosana KAM, White WT, Last PR. 2012. A DNA sequence-based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology. Bulletin of the American Museum of Natural History 367: 1–262.
   Google Scholar
• Ovenden JR, Berry O, Welch DJ, Buckworth RC, Dichmont CM. 2015. Ocean's eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish and Fisheries 16: 125–159.
   Google Scholar
• Ovenden JR, Kashiwagi T, Broderick D, Giles J, Salini JP. 2009. The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago. BMC Evolutionary Biology 9: 40.
   Google Scholar
• Ovenden JR, Morgan JA, Street R, Tobin A, Simpfendorfer C, Macbeth W, Welch D. 2011. Negligible evidence for regional genetic population structure for two shark species Rhizoprionodon acutus (Rüppell, 1837) and Sphyrna lewini (Griffith & Smith, 1834) with contrasting biology. Marine Biology 158: 1497–1509.
   Google Scholar
• Peeters FJ, Acheson R, Brummer GJA, de Ruijter WP, Schneider RR, Ganssen GM, Ufkes E, Kroon D. 2004. Vigorous exchange between the Indian and Atlantic oceans at the end of the past five glacial periods. Nature 430: 661–665.
   Google Scholar
• Portnoy DS, Heist EJ. 2012. Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs. Journal of Fish Biology 80: 1120–1140.
   Google Scholar
• Portnoy DS, McDowell JR, McCandless CT, Musick JA, Graves JE. 2009. Effective size closely approximates the census size in the heavily exploited western Atlantic population of the sandbar shark, Carcharhinus plumbeus. Conservation Genetics 10: 1697–1705.
   Google Scholar
• RSA (Republic of South Africa). 1998. Marine Living Resources Act (Act No. 18 of 1998). Government Gazette, South Africa 395 (18930).
   Google Scholar
• RSA (Republic of South Africa). 2014. National Environmental Management: Biodiversity Act, 2004 (Act No. 10 of 2004) Draft Shark Biodiversity Management Plan. Government Gazette, South Africa 37586.
   Google Scholar
• Schrey AW, Heist EJ. 2003. Microsatellite analysis of population structure in the shortfin mako (Isurus oxyrinchus). Canadian Journal of Fisheries and Aquatic Sciences 60: 670–675.
   Google Scholar
• Sembiring A, Pertiwi NPD, Mahardini A, Wulandari R, Kurniasih EM, Kuncoro AW, Cahyani NKD, Anggoro A, Ulfa M, Madduppa H, Carpenter KE, Barber PH, Mahardika GN. 2015. DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia. Fisheries Research 164: 130–134.
   Google Scholar
• Smale MJ. 2002. Occurrence of Carcharias taurus in nursery areas of the Eastern and Western Cape, South Africa. Marine and Freshwater Research 53: 551–556.
   Google Scholar
• Smale MJ, Compagno LJV. 1997. Life history and diet of two southern African smoothhound sharks, Mustelus mustelus (Linnaeus, 1758) and Mustelus palumbes Smith, 1957 (Pisces: Triakidae) South African Journal of Marine Science 18: 229–248.
   Google Scholar
• Smale MJ, Compagno LJV, Human BA. 2002. First megamouth shark from the western Indian Ocean and South Africa. South African Journal of Science 98: 349–350.
   Google Scholar
• Sodré D, Rodrigues-Filho LFS, Souza RFC, Rêgo PS, Schneider H, Sampaio I, Vallinoto M. 2012. Inclusion of South American samples reveals new population structuring of the blacktip shark (Carcharhinus limbatus) in the Western Atlantic. Genetics and Molecular Biology 35: 752–760.
   Google Scholar
• Steinke D, Zemlak TS, Hebert PDN. 2009. Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS ONE 4: e6300.
   Google Scholar
• Stevens JD, Bonfil R, Dulvy NK, Walker PA. 2000. The effects of fishing on sharks, rays, and chimaeras (chondrichthyans), and the implications for marine ecosystems. ICES Journal of Marine Science 57: 476–494.
   Google Scholar
• Straube N, Iglésias SP, Sellos DY, Kriwet J, Schliewen UK. 2010. Molecular phylogeny and node time estimation of bioluminescent lantern sharks (Elasmobranchii: Etmopteridae). Molecular Phylogenetics and Evolution 56: 905–917.
   Google Scholar
• Teske PR, Zardi GI, McQuaid CD, Nicastro KR. 2013. Two sides of the same coin: extinctions and originations across the Atlantic/ Indian Ocean boundary as consequences of the same climate oscillation. Frontiers of Biogeography 5: 48–59.
   Google Scholar
• Tillett BJ, Field IC, Bradshaw CJA, Johnson G, Buckworth RC, Meekan MG, Ovenden JR. 2012a. Accuracy of species identification by fisheries observers in a north Australian shark fishery. Fisheries Research 127: 109–115.
   Google Scholar
• Tillett BJ, Meekan MG, Field IC, Thorburn DC, Ovenden JR. 2012b. Evidence for reproductive philopatry in the bull shark Carcharhinus leucas. Journal of Fish Biology 80: 2140–2158.
   Google Scholar
• Turner TF, Wares JP, Gold JR. 2002. Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops ocellatus). Genetics 162: 1329–1339.
   Google Scholar
• Turpie JK, Beckley LE, Katua SM. 2000. Biogeography and the selection of priority areas for conservation of South African coastal fishes. Biological Conservation 92: 59–72.
   Google Scholar
• van Sebille E, Biastoch A, van Leeuwen PJ, de Ruijter WPM. 2009. A weaker Agulhas Current leads to more Agulhas leakage. Geophysical Research Letters 363: 3.
   Google Scholar
• Velez-Zuazo X, Alfaro-Shigueto J, Mangel J, Papa R, Agnarsson I. 2015. What barcode sequencing reveals about the shark fishery in Peru. Fisheries Research 161: 34–41.
   Google Scholar
• Walter RP, Kessel ST, Alhasan N, Fisk AT, Heath DD, Chekchak T, Klaus R, Younis M, Hill G, Jones B, Braun CD, Berumen ML, DiBattista JD, Priest MA, Hussey NE. 2013. First record of living Manta alfredi×jManta birostris hybrid. Marine Biodiversity 44: 1–2.
   Google Scholar
• Waples RS. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity 89: 438–450.
   Google Scholar
• Ward RD. 2009. Shark fin identification through DNA barcoding. Endangered Species Update 26: 3–9.
   Google Scholar
• Ward RD, Costa FO, Holmes BH, Steinke D. 2008. 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. Aquatic Biology 3: 71–78.
   Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1847–1857.
   Google Scholar
• White WT, Last PR. 2006. Description of two new species of smoothhounds, Mustelus widodoi and M. ravidus (Carcharhiniformes: Triakidae) from the Western Central Pacific. Cybium 30: 235–246.
   Google Scholar
• White WT, Last PR. 2008. Description of two new species of gummy sharks, genus Mustelus (Carcharhiniformes: Triakidae), from Australian waters. In: Last PR, White WT, Pogonoski JJ (eds), Descriptions of new Australian chondrichthyans. CSIRO Marine and Atmospheric Research Paper 022. Canberra: CSIRO Marine and Atmospheric Research. pp 189–202.
   Google Scholar
• Wong EH-K, Shivji MS, Hanne RH. 2009. Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Molecular Ecology Resources 9: 243–256.
   Google Scholar
• Worm B, Davis B, Kettemer L, Ward-Paige CA, Chapman D, Heithaus MR, Kessel ST, Gruber SH. 2013. Global catches, exploitation rates, and rebuilding options for sharks. Marine Policy 40: 194–204.
   Google Scholar
• Zenger KR, Stow AJ, Peddemors V, Briscoe DA, Harcourt RG. 2006. Widespread utility of highly informative AFLP molecular markers across divergent shark species. Journal of Heredity 97: 607–611.
   Google Scholar