i Conservation Genetics and Reproduction in Three Australian Marsupial Species © J. Gould Emily J. Miller 2008 A dissertation presented to the University of New South Wales in fulfillment of requirement for the degree of Doctorate of Philosophy in Biological Sciences ii “…on [the two largest] these islands are large numbers of cats, which are creatures of miraculous form, as big as a hare; the Head is similar to [that] of a Civet cat, the forepaws are very short, about a finger long. Whereon they have five small Nails, or small fingers, as an ape’s fore-paw, and the two hind legs are at least half an ell long, they run on the flat of the joint of the leg, so that they are not quick in running. The tail is very long, the same as a Meerkat [lemur]; if they are going to eat they sit on their hind legs and take the food with their fore-paws and eat exactly the same as squirrels or apes do.” - Description of the first sighting of a tammar wallaby in the Abrolhos Islands, Western Australia by Francisco Pelsaert from the translation of Heeres (1899) (originally published 1648) “DNA…doesn’t lie.” - Mark D. B. Eldridge For my Family Image on front cover: Macropus eugenii (Tammar wallaby), reproduced from John Gould, The Mammals of Australia, 1863. iii Declaration of Originality I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged. Signed: ……………………………………… Date: …………………………….. Emily J. Miller iv Copyright Statement I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation. Signed: ……………………………………… Date: …………………………….. Emily J. Miller v Authenticity Statement I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format. Signed: ……………………………………… Date: …………………………….. Emily J. Miller vi Preface This thesis consists of five stand-alone papers (Chapters two to six) that are being prepared for submission to international journals of high standing. Each chapter is therefore self-contained and some repetition occurs. To prevent unnecessary duplication a single reference list is provided at the end of the thesis formatted in the style for Conservation Biology. This thesis is a compilation of my own work, with guidance from my principal supervisors, Catherine Herbert and Mark Eldridge. The contributions of co-authors are detailed below. Chapter 1 2 3 4 5 6 7 Conception EJM EJM, EJM, EJM, EJM, EJM, EJM CAH, CAH, CAH, CAH, CAH, MDBE MDBE MDBE MDBE RJ Sample/data NA EJM, EJM, EJM, EJM, EJM, NA Collection CAH, CAH, CAH, CAH, CAH, NT, NT, MDBE, MDBE, JC, BM, BM, KM, JC, JN, MC, MC, NT, JN MW, HR, NM PO, TF NN, BJ NM, KM Analysis NA EJM EJM EJM EJM EJM NA Writing EJM EJM EJM EJM EJM EJM EJM EJM – Emily J. Miller; CAH – Catherine A. Herbert; MDBE – Mark D. B. Eldridge; RJ – Robert Johnson; NT – Neil Thomas; BM – Brian MacMahon; MC – Martin Clarke; HR – Howard Robinson; NN – Nicole Noakes; NM – Nicola Marlow; KM – Keith Morris; PO – Peter Orell; BJ – Brent Johnson; JC – James Cook; JN – Jan Nedved; MW – Michelle Wilson; TF – Terry Fletcher. vii Abstract Many Australian marsupial species require active population management to ensure their survival in the wild. Such management should be based on a sound understanding of species biology. This thesis explores how knowledge of reproduction and genetics can be applied to the management of three Australian marsupial species faced with contrasting management scenarios. The ‘vulnerable’ greater bilby is the sole remaining desert bandicoot in Australia. They are a secretive, solitary species whose mating system is unclear. This research examined temporal changes in genetic diversity within two captive breeding programs utilising different management strategies. Using seven microsatellite loci, this study found the regular translocation of new individuals into the population maintained genetic diversity. Parentage analysis revealed the bilby to have a promiscious mating system. Sires and non-sires could not be distinguished by morphological traits. The tammar wallaby is a polygynous, solitary species that is threatened on mainland Australia, but overabundant on some offshore islands. The population genetics of tammars from the Abrolhos Islands in Western Australia were examined using nine autosomal and four Y-linked microsatellite loci, and mitochondrial DNA. There was a relationship between island size, population size and genetic diversity. The Abrolhos populations have significantly lower genetic diversity and are more inbred than mainland tammars and all sampled populations were significantly differentiated. The Abrolhos and mainland populations should be treated as separate Management Units. The eastern grey kangaroo is a gregarious, polygynous species that is often locally overabundant. To determine traits influencing male reproductive success, behavioural, morphological, physiological and genetic data were examined and showed dominance status, body size and testosterone concentrations were important factors. Sires were also significantly more heterozygous and genetically dissimilar to females, than non- sires. As body condition influences individual fitness, and management decisions; five body condition indices (BCI) calculated from morphological data were validated using viii serum biochemistry and haematology in two kangaroo populations with contrasting body condition. Blood parameters were found to be more reliable indicators of condition, questioning the credibility of BCIs currently used in management. These studies demonstrate the importance of reproductive and genetic data in assisting wildlife management, regardless of a species conservation status. ix Acknowledgements A career in biology was unexpected and arose from a friend (Joanna Gurung) insisting I attend a biology lecture conducted by Professor David Briscoe, as it was apparently unlike anything else. Eight years later the journey has been incredible and I have experienced so much personal and professional growth, travelled to amazing places and worked with fantastic people. However, none of this would have been possible without the love, support and encouragement from my supervisors, family, friends and colleagues. I am indebted to my supervisors Dr Cath Herbert, Dr Mark Eldridge and Professor Des Cooper. I am privileged to have had the opportunity to work with you all. I am grateful to Cath for her friendship and giving me the opportunity to do a PhD and sparking my initial curiosity in the biology of marsupials. Cath’s passion, enthusiasm and sheer brilliance have enabled me to learn and experience incredible opportunities. I solely credit Cath for my introduction to the art of ‘fondling testicles’ – all in the name of science of course! Without Cath this PhD would not exist. Mark Eldridge inspired my passion for genetics, as well as broadening my interests/hobbies to include other taxa. From the very first time we did laboratory work together and discovered sneaky copulations occurring in tammar wallabies, I have never looked back. Mark has been a pillar of support for me during my PhD through continual encouragement and teaching me to appreciate the eccentricities that come with being a biologist. Mark has provided me very useful insights at times of crisis such as “there is something fundamentally wrong with the universe” and “there is nothing worse than a bit of integer overflow”. Professor Des Cooper has enlightened me over the years learning the intricacies of cricket, and cricket players and possesses inspiring wisdom and knowledge. This PhD involved much fieldwork. James Cook and Jan Nedved dedicated a large amount of their time and energy into capturing kangaroos and wallabies so I could ‘fondle their testicles’, as James puts it. James provided much support, particularly when dealing with spiders. A big thankyou to all the volunteers who have assisted with fieldwork. x To Lee Ann Rollins, Joachim Elenz, and the Elenz clan (Mischa, Adam and Klara) who have become dear friends and a second family to me. Thank you all for keeping me sane, particularly Lee who always help me keep things in perspective and company in the lab. The Rollins/Elenz family has treated me as one of their own and words cannot express my gratitude and how much you have all come to mean to me. To my dear friends, Richard (Dr Dick) Lane, Ryan (no name) Moore, (Ranger) Dan Tilbury, without your love, support and shenanigans I would not have stayed “sane”.