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General copyright and disclaimer In addition to the above conditions, authors give their consent for the digital copy of their work to be used subject to the conditions specified on the Library Thesis Consent Form and Deposit Licence. Phylogeography of the commensal Rattus exulans with implications for its use as bioproxy for human migrations Melanie Hingston A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in Biological Sciences, University of Auckland, 2015 ABSTRACT The Pacific rat, Rattus exulans, or Kiore as it is called by Maori, is a small human commensal associated with the human settlement of the Pacific. Archaeological evidence from Island Melanesia connects the distribution of the species with the presumed ancestors of all Polynesians, the so-called Lapita. Excavations have uncovered artefacts unprecedented in the region, comprising a style of distinctively dentate-stamped pottery, fish hooks and animal remains among others. The earliest animal remains are from pigs and R. exulans, which was clearly introduced into this region by the people as part of their cultural complex. On these grounds R. exulans has previously been used as proxy to infer human migration pathways throughout the Pacific. Accessibility of human archaeological material is scarce and by way of proxy a much higher sampling resolution for the commensal allows more specific inferences. While the origin of the Lapita is still widely disputed among disciplines from archaeology over linguistics and genetics, attention is focused on the Bismarck Archipelago, as an essential stepping stone for the distribution of these human migrants into the Pacific. The genetics of R. exulans might contribute to an assessment of the established theories of the Lapita origin. However, to make inferences regarding human migration based on the species, more knowledge is needed about its population structure and distribution history. In this thesis I establish the current population structure of R. exulans by extensive sampling of mitochondrial D-loop sequences across its distributional range with a strong focus on the Bismarck Archipelago. The population is deeply divided into three major geographic regions with more recent regional substructures. With the help of a chronology-based reconstruction of ancestral regional distribution I infer the geographic origin of these observed haplogroups and evaluate the chronology in the light of palaeoclimatic events to distinguish natural dispersal events from those that are human mediated. The marked differentiation of the Philippines and of Remote Oceania is almost certainly connected to a I Pleistocene interglacial. And while further differentiation within the Philippines can also be associated with palaeoclimatic events, evidence for dispersal of the species to the east into Near Oceania and the Pacific supports a human-mediated distribution. These results of a dual introduction of lineages into Near and Remote Oceania support a minimum of two separate migration waves of human settlers. One was possibly Lapita- associated, spreading the Near Oceanic lineage, and a second one passed only tangentially through the Bismarcks but distributed the Remote Oceanic lineage throughout the Pacific. Two competing theories for the origin of R. exulans have been proposed based on morphological studies on previously distinguished subtypes of the species. Here I use the population genetic data and the results of the ancestral area reconstruction to independently infer an origin for the species. Genetic evidence is incompatible with an origin on the Southeast Asian mainland, while it supports the theory of a Lesser Sunda origin. II In memory of Martin, my best friend, husband and partner in crime. III IV ACKNOWLEDGEMENTS Life tried to teach me patience, because this journey was led along quite a few detours. But I am here now and I am thankful to everyone who has accompanied me in one way or another. You have made a difference and allowed me to finish what I started in a different life so long ago. I would like to begin with sincerely thanking my supervisors, Howard Ross and Lisa Matisoo-Smith. You have not only stood by me with professional guidance but also supported me personally throughout this rollercoaster; no one could be prepared for the unexpected. For their moral support and assistance in the Lab I would like to give my special thanks to my friend Judith Robins and the late Vernon Tintinger. Judith, we can have a really long coffee break now! The crazy bunch, Danushka, Alana, Jess, Steven, Bonbon, and Louis, made me feel at home in the lab round 01. Finally I am catching up with you. My lab buddies round 02, Peter, Louis and Kevin, were invaluable help in all Perl or R questions, even better than google. Also, without our continuous chocolate supply, I could never have made it. Thanks also to Vicky and Patricia, particularly for reminding me to take breaks. Thanks to my friends Lorna, Gabby, Katie and Ken, who shared much of the PhD experience and more; Emma & Leah, who are the best concert company; Steffen & Jess, who have grown to be Kiwi family, and additionally answered yet another statistics question from this humble Biologist; Ben, who’s Nerd-Nites and Irregulars have provided me with much needed distraction and lots of people to discuss life, the universe and everything with. You all rock! Well apart from everyone who left New Zealand before I could finish . I am grateful for funding by the Marsden Fund Council administered by the Royal Society of New Zealand, the Allan Wilson Centre for Molecular Ecology and Evolution and the V University of Auckland. Additional thanks to the University of Auckland for having such a supportive and flexible system, that allowed me to finish this work despite various suspension times, and personal thanks to Sue Skelly, who made the paperwork ‘go away’ in moments of need. For permission to sample museum skins I would like to thank Mike Carleton, Linda Gordon and the National Museum of Natural History at the Smithsonian Institution, DC, Chris Conroy and the Museum of Vertebrate Zoology Berkeley, CA, Larry Heaney and the Field Museum of Natural History, IL, Ken Aplin and the South Australian Museum, as well as the National Research and Development Centre for Archaeology in Indonesia along with the University of Wollongong for the provision of the Liang Bua Cave sample. For kindly providing me with additional field samples, my thanks go to my fellow researchers Marie Pagès, INRA, France and Russell Palmer, Australia. Additionally I would like to thank Kelly Ananga & family, Herman Mandui, Matt Leavesley, Irene, Agnes & Segunda, who supported me in my quest to catch rats during my stay in Kavieng and on Emirau. My biggest thanks however goes to my families. Besides the obvious, you have supported me with countless skype calls and parcels, so I would not feel lonely and despair. You gave me the strength to go on. Still, most of all I am thankful to Martin, who has believed in me like nobody else. I wish our journey together could have included this and many more years of traveling. Thanks for all the fish! Now and forever. On closing, I thank Aotearoa for all the beautiful rainbows and all people whom I have crossed paths with and did not mention explicitly. I remember. VI CONTENTS Abstract ......................................................................................................................... I Acknowledgements ............................................................................................................. V List of Figures .................................................................................................................... XI List of Tables .................................................................................................................. XV Abbreviations ............................................................................................................... XVII Chapter 01 General introduction .......................................................................................... 1 1.1 Rattus exulans, the Pacific rat or Kiore .......................................................... 4 1.1.1 Appearance ..................................................................................................... 5 1.1.2 Population dynamics ....................................................................................... 6 1.1.3 Nutrition .......................................................................................................... 7 1.1.4 Habitat ............................................................................................................ 8 1.1.5 Behaviour .......................................................................................................