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Genetic Diversity of Antarctic Fish

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GENETIC DIVERSITY OF ANTARCTIC FISH Elaine M. Fitzcharles A Thesis Submitted for the Degree of PhD at the University of St Andrews 2014 Full metadata for this item is available in Research@StAndrews:FullText at: http://research-repository.st-andrews.ac.uk/ Please use this identifier to cite or link to this item: http://hdl.handle.net/10023/6860 This item is protected by original copyright Genetic Diversity of Antarctic Fish Elaine M. Fitzcharles This thesis is submitted in partial fulfilment for the degree of PhD at the University of St Andrews May 2014 Supervisor of studies Prof. Alex Rogers (University of Oxford) Dr Melody Clark (British Antarctic Survey) Prof. Andrew Brierley (University of St Andrews) Sponsoring establishment British Antarctic Survey Natural Environment Research Council High Cross Madingley Road Cambridge CB3 0ET United Kingdom ii DECLARATIONS 1. Candidate’s declarations: I, Elaine Fitzcharles, hereby certify that this thesis, which is approximately 35000 words in length, has been written by me, and that it is the record of work carried out by me, or principally by myself in collaboration with others as acknowledged, and that it has not been submitted in any previous application for a higher degree. I was admitted as a research student in September 2005 and as a candidate for the degree of Doctor of Philosophy in April 2007; the higher study for which this is a record was carried out in the University of St Andrews between 2005 and 2014. Date 23/5/11 Signature of candidate …………………….............. 2. Supervisor’s declaration: I hereby certify that the candidate has fulfilled the conditions of the Resolution and Regulations appropriate for the degree of Doctor of Philosophy in the University of St Andrews and that the candidate is qualified to submit this thesis in application for that degree. Date 23/5/11 Signature of supervisor …………………….............. 3. Permission for publication: (to be signed by both candidate and supervisor) In submitting this thesis to the University of St Andrews I understand that I am giving permission for it to be made available for use in accordance with the regulations of the University Library for the time being in force, subject to any copyright vested in the work not being affected thereby. I also understand that the title and the abstract will be published, and that a copy of the work may be made and supplied to any bona fide library or research worker, that my thesis will be electronically accessible for personal or research use unless exempt by award of an embargo as requested below, and that the library has the right to migrate my thesis into new electronic forms as required to ensure continued access to the thesis. I have obtained any third-party copyright permissions that may be required in order to allow such access and migration, or have requested the appropriate embargo below. The following is an agreed request by candidate and supervisor regarding the publication of this thesis: PRINTED COPY a) No embargo on print copy ELECTRONIC COPY a) No embargo on electronic copy Date 23/5/11 Signature of candidate ……… Signature of supervisor …………………….............. i Acknowledgements This part-time PhD was funded by the British Antarctic Survey. First and foremost I have to thank my supervisors, Alex Rogers and Melody Clark, for having enough faith in me as a scientist to let me begin this journey, and Andy Brierley for having enough faith in Alex to agree to take me on. It has been a longer journey than any of us intended so thank you, especially to Melody, for your continued support when life, work and unplanned distractions got in the way. Special thanks go to Martin Collins and Mark Belchier for the fish samples, advice and support over the years. Your interest in the results has helped to keep me going. Also, to the number of fisheries scientists who have kindly collected me samples over the years; Sue Gregory, Judith Brown and Katie Brigden to name just a few. Thanks to Peter Smith, Steve Parker and Peter McMillan for the samples from the Far Side (Ross Sea), and Sarah Helyar for the ones from the North and the microsatellite collaboration. I have to thank Will Goodall-Copestake for the technical help and training in phylogenetic analysis, as well as general support and encouragement, Huw Griffiths for the assistance with the GIS maps and Michelle Taylor for her last minute advice and reassurance. My BAS management has changed over the year but particular thanks go to Tim Moffat for recognising the importance of this work and giving me the time to finish it. I also need to thank my colleagues in the biology lab management team, Guy Hillyard, Paul Geissler and Michelle King, for continued support over the years but particularly these last few months. Taking on a part-time PhD and a full-time job is not an easy task and would not have been possible without the support of my work colleagues in the Angel lab and fellow PhD students (too many to mention). Particular thanks go to Katrin Linse and Sandra ii McInnes for their advice, support and friendship, and to Natalie Ensor and Mags Wallace for being there and understanding. On a personal note I have to thank my brother, Colin Mitchell, for helping to keep me sane, Ria (Bob) Kishen for the shared frustrations over molecular biology (we never had these problems with McGregor’s cakes) and Leanne Hulse for giving me a home from home on my visits to St Andrews. Most of all I have to thank my husband, Scott Fitzcharles, for agreeing to let me do this and being there for me throughout. There have been some tough times during the course of this PhD but also the happiest times. Thank you for Frewin and Caelan. Having two boys while trying to juggle the job and PhD probably wasn’t the most sensible idea but it was the best one. They may add to the frustrations, exhaustion and general chaos but they make everything worthwhile. Finally, thank you to my mother for the continued support in everything I decide to do in life (even the bad ideas) and always being there when I need her. To my father, I know how proud you would have been. iii Abstract Correct species identification is fundamental to all areas of biology, but particularly the policy related areas of conservation and fisheries management. To enable guidelines to be developed for environmental management and conservation, such identifications need links to studies of the evolutionary history, biological factors and environmental influences driving species divergence and population dynamics for the target species. This study concerns two genera of gadiform fish, Muraenolepis and Macrourus, found in southern temperate and Antarctic waters, with a single species, Macrourus berglax, present in the North Atlantic. With similar distribution patterns to toothfish species, Dissostichus eleginoides and D. mawsoni, they are a major food source and by-catch of the toothfish fishery. Both are slow growing and long lived, with different evolutionary histories, life expectancies and strategies for reproduction. For both genera, the accuracy of morphological keys, number of described species and their distribution is under debate. This study has identified specimens to species level using both morphological and genetic techniques, redefining the range for morphological features and taxonomic keys. For Muraenolepis, this has clarified confusion over Mu. marmoratus and Mu. microps being a single species, confirmed some mis-identification from sexual dimorphism and provided genetic evidence for the recently described species Mu. evseenkoi. For Macrourus, this work has identified a new species, now named Ma. caml, and found that Ma. holotrachys and Ma. berglax are genetically identical, raising the question of bipolar distribution or recent divergence. The low level of genetic variation within both species suggests a recent evolution and expansion into Antarctic waters. Similar geographic species limits imply common processes influencing divergence, with the oceanographic fronts as potential barriers. Further investigation of niche overlap and fine scale population structure are required to fully understand the processes driving speciation and provide the underlying data required for fisheries management. iv Contents CHAPTER 1 .................................................................................................................................. 1 General introduction ...................................................................................................................... 1 1.1 Introduction ............................................................................................................................. 1 1.2 Antarctica and the Southern Ocean ......................................................................................... 1 1.3 Evolution of Antarctic Fish ..................................................................................................... 5 1.4 Study Fish Species .................................................................................................................. 6 1.5 Antarctic Fisheries................................................................................................................... 8 1.5 The role of genetics in conservation...................................................................................... 10 1.6 Aims and objectives .............................................................................................................. 12 1.7 This thesis .............................................................................................................................
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