SPECIES IDENTIFICATION IN THE AMERICAN SHARK FIN MARKET AUSTIN AYER MAY 2016 SPECIES IDENTIFICATION IN THE AMERICAN SHARK FIN MARKET An Honors Thesis Submitted to the Department of Biology in partial fulfillment of the Honors Program STANFORD UNIVERSITY by AUSTIN AYER MAY 2016 Species Identification in the American Shark Fin Market by Austin Ayer Approved for submittal to the Department of Biology for consideration of granting graduation with honors: Research Sponsor Stephen Palumbi ____________________________ Date _ May 5th 2016_________ (signature) Second Reader Giulio De Leo _____________________________ Date _May 5th 2016__________ (signature) Ayer 1 Species Identification in the American Shark Fin Market TABLE OF CONTENTS TABLES AND FIGURES ........................................................................................................................... 2 ABSTRACT ................................................................................................................................................... 3 INTRODUCTION ........................................................................................................................................ 4 METHODS ................................................................................................................................................. 10 RESULTS ................................................................................................................................................... 13 DISCUSSION ............................................................................................................................................. 20 CONCLUSIONS ........................................................................................................................................ 27 REFERENCES .......................................................................................................................................... 28 Ayer 2 TABLES AND FIGURES _________________________________________________________________________________________________ Table 1: Primers used for amplification of mitochondrial shark DNA (Page 11) Table 2: Identifications of shark fin products purchased in the San Francisco market between 2003 and 2008 (Page 16) Table 3: Unique identifications of shark fin products purchased in the Las Vegas market in 2015 made using a newly developed partial DNA-barcoding assay (Page 20) Table 4: Species composition of a sample of 92 shark fins sampled from the San Francisco market (Page 23) _________________________________________________________________________________________________ Figure 1: Map of a shark mitochondrial COI gene and primer sets (Page 13) Figure 2: Partial phylogenetic tree generated from the full COI gene for various known shark species and CITES listed test sequences from the San Francisco market (Page 15) Figure 3: An ambiguous portion of the phylogenetic tree generated from the full COI gene for various known shark species and test sequences from the San Francisco market (Page 16) Figure 4: Partial phylogenetic tree generated using the Mini-barcoding assay developed by Fields et al. for various known shark species and Las Vegas soup test sequences (Page 19) Ayer 3 ABSTRACT With a lucrative trade in shark fins driving the unsustainable exploitation of the global shark fishery, tighter regulation of both the fishery and the fin market is needed. Given the important, apex predator role that many sharks play in marine ecosystems, as well as the precarious conservation status of certain species, there is a pressing need for more information regarding the species composition of shark fin imports. Because the removal and processing of shark fins can hinder identification based on morphological characteristics, a molecular approach to species identification has gained popularity. Here, genetic surveys of the San Francisco shark fin market and the Las Vegas shark fin soup market are described, including the discovery of CITES listed endangered species in both. Additionally, a novel, partial-COI DNA-barcoding assay is developed to improve identification potential from the highly degraded DNA found in shark fin soup. Ayer 4 INTRODUCTION The Global Shark Fishery As in many of the world’s most important fisheries, the global shark fishery is being exploited at an unsustainable rate. The expansion and industrialization of fishing practices over the last half century have led to an overall decline in shark populations. 1 Targeted shark fisheries, as well as bycatch (much of it from long line, purse-seine, and gillnet fisheries targeting tuna and billfish), pull millions of sharks from the ocean each year.1, 2 However, quantifying the precise extent of the shark fishery and its decline is difficult, due to the incomplete and under reporting of shark catches, as well as the likelihood of high levels of illegal, unregulated, and unreported (IUU) catch.3 Using data on reported catch, discarded sharks (finned or not), and estimated IUU catch, Worm et al. estimated total global shark catch for the year 2000 at 1.44 million metric tons, and for 2010 at 1.41 million metric tons. Generalizing based on average shark weights, these catch levels represent 100 million and 97 million individual sharks, respectively. The removal of an estimated one billion sharks from the world’s oceans in a decade has profound implications for the future of these fish. Using published stock assessments, the same researchers estimated the exploitation rate for all sharks at between 6.4% and 7.9% annually. Although this may seem to be a relatively low exploitation rate, it is much higher that the average rebound rate of 4.9% per year calculated from a compilation of life histories of 62 shark species.1 The staggering number of sharks being fished becomes even more daunting when the life history strategies of sharks are considered. Life history strategies of members of the class Condrichthyes, which includes sharks, rays, skates, and chimaeras, are characterized by slower growth rates, later attainment of sexual maturity, and lower fecundity compared to most bony fish.4,5 These factors combine to make sharks more vulnerable at a species level to fishing pressures than other fish, exacerbating the consequences of the high catch numbers for sharks. The over- exploitation of shark stocks, combined with their vulnerability to fishing-induced Ayer 5 population decline, indicates that global shark populations are declining rapidly. Without intensive management, current fishing practices are likely to cause the collapse of shark fisheries whose target species have lower rebound potential.6 The apex predator status of most sharks confers them great influence over the ecosystems in which they live. Large shark species exert heavy top-down predation influence, both through consumptive and behavioral mechanisms, on species of lower trophic levels.4 The removal of large sharks releases smaller elasmobranch predators, marine mammals, and marine reptiles from their principal source of predation, causing cascading effects throughout the ecosystem.4 For example, Bascompte et al. modeled trophic interactions for hundreds of species in the Caribbean, and found that sharks were present in 48% of trophic chains. The model suggested that the removal of sharks could have contributed to an observed shift from coral- to seaweed-dominated reefs via an increase in populations of fish consumers.7 Additionally, some studies have placed large sharks in the role of keystone predator, although others suggest that supporting evidence for these claims are lacking.8 While it is still unclear whether certain individual shark species qualify as keystone predators, the removal of large sharks from the oceans has the potential to cause cascading ecological effects, and highlights the importance of understanding which species are being brought to market. The 1973 Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) provides an international legal framework for the recognition of the conservation status of individual species, as well as the enforcement of regulations regarding the sale of products from those species.9 Currently, there are eight species of shark listed by CITES: whale shark, Rhincodon typus, basking shark, Cetorhinus maximus, white shark, Carcharodon carcharias, porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus, scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. zygaena, and great hammerhead, S. mokarran. Each of these species is listed in CITES Appendix II, described as a list of species that may become threatened with extinction in the absence of trade controls. Within the United States, these species have special management status that criminalizes the unpermitted sale of their parts and Ayer 6 products under the Endangered Species Act. Parties can apply for export permits to engage in the trade of CITES Appendix II listed species, provided a “Scientific Authority of the State of export has advised that such export will not be detrimental to the survival of that species,” among other requirements.9 The Shark Fin Market The high price demanded by shark fins around the world confers a large responsibility on the shark fin market as a driver of the global shark fishery. Finning, or the practice of removing a shark’s cartilaginous fins and discarding the rest of the animal, is a major factor in the unsustainable harvesting of sharks. The global market for shark fin soup, an Asian delicacy,