THE APPLICATION OF GENETICS AND PROTEOMICS FOR THE CONSERVATION OF SHARKS AND THEIR RELATIVES

Abstract

Sharks, rays and skates (elasmobranchs) are a group of cartilaginous fishes currently facing mass declines from overfishing. As of 2014, 25% of elasmobranch species were classified as threatened with extinction by The International Union of the Conservation of Nature (IUCN) Red List. It is estimated that 100 million are killed every year through illegal, unregulated and unreported (IUU) fishing, often for their fins which are in high demand for shark fin soup. As elasmobranchs have been on the planet for nearly 450 million years, the function that each species has within the environment is vital for the marine food web structure and function which ultimately regulates biomass density and therefore balancing ecosystem functions. However, more information is still required on the general biology and population structure of most elasmobranch species, which will assist in management at in-situ and ex-situ sites, to conserve populations. To address some of these issues, this thesis uses a range of molecular techniques to investigate species identification and population dynamics by genetics and non-invasive/non-intrusive tagging methodologies. All samples collected and analysed were either a discard elasmobranch product from fish markets or from non-invasive/non-intrusive mucus swabs, which ensures each chapter has not contributed to the decline of wild populations. By focusing on non-invasive techniques, the thesis developed a new method of collecting non-intrusive DNA samples by mucus swabbing individuals underwater, collected by scuba divers. Non-intrusive and invasive discard product samples from the undulate ray Raja undulata revealed 6 new distinct genetic clusters throughout their distribution and the application of capture mark-recapture using photographs and recognition software provided consistent population sizes and evidence of female to female or female to male pairing between individuals. Photo recognition was also successfully applied to the small-spotted catshark Scyliorhinus canicula in early-stage development (within the first 60 weeks of life) as an alternative for invasive tagging, especially focusing on ex-situ conservation. Genetic analysis using microsatellite markers was applied to two species of captive sharks for ex-situ management and found genetically diverse populations with little signs of inbreeding. Wild samples of discard products of elasmobranchs and chimaeras (chondrichthyans) caught in Morocco in June 2015 and 2016 were utilized for two chapters. By employing DNA barcoding methods and observational field methods, the first analysis of the diversity of chondrichthyans was conducted and provided evidence of targeted fishing for elasmobranchs and IUU fishing. These samples were also used to investigate the ability of identifying the proteins in elasmobranch fins, which could possibly be applied as an alternative method of identifying species. We found that 5 main protein groups define the composition of elasmobranch fins; collagen, actin, tubulin, tropomyosin and myosin. Finally, the use of genetics found the first evidence of twins and heteropaternal superfecundation, whereby twins were formed from two different fathers in the same egg. Following the outcomes of the thesis, further research is advised to focus on revealing and understanding the full genome sequence of species to better understand individual characteristics and population differences, which may influence the their success or demise for future conservation. As elasmobranchs continue to decline, it is imperative that further studies are not only conducted but applied in order to conserve elasmobranchs for the future. The outcomes of this thesis have successfully generated a deeper understanding of the biology, connectivity and utilisation of elasmobranch populations in both in-situ and ex-situ sites. However, it is the responsibility of scientists and governments to continue the research into elasmobranch biology and population structure, to influence management, conservation and social change.

Date of Award	1 Aug 2020
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Michael Buckley (Supervisor), Catherine Walton (Supervisor) & Holly Shiels (Supervisor)