Probosciger Aterrimus), the Legacy of Landscape and Biogeographic History
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Cultural diversity and meta-population dynamics in Australian palm cockatoos (Probosciger aterrimus), the legacy of landscape and biogeographic history. Miles V. Keighley Thesis submitted for the degree of Doctorate of Philosophy at the Fenner school of Environment and Society, Australian National University Photo credit: Luke Burnett © Copyright by Miles Vernon Keighley 2017 All Rights Reserved I certify that the majority of this thesis is my own original work. I have acknowledged all cases where contributions have been made by others in the Author contribution sections of each chapter. A significant contribution was made by another author who wrote the supplementary methods section of Chapter 4 (2150 words) and conducted these methods and analyses. Signed: Miles Vernon Keighley Date: September 21, 2017 Acknowledgements This thesis would not have neared completion if it wasn’t for the encouragement and support of the wonderful people surrounding me; first and foremost, my patient and infectiously enthusiastic supervisors Rob Heinsohn and Naomi Langmore. Big thank you to Christina Zdeneck for passing on so much useful knowledge about palm cockatoo vocal behaviour and accommodating us during visits to Iron Range. My family deserve much of the credit for the piece presented before you. My mum, Carol encouraged me to accept the position that I had applied for in the first place, and Dad helped to support me through my off-scholarship year. Through long phone calls, my brother James helped align my perspective keeping me functioning mentally and emotionally during fieldwork, and my other brother Matthew did the same during write-up in Denmark. I owe much to Xénia for helping support me during most of my final year, and encouraging me over the significant hurdles involved with moving overseas and a nasty back injury. I also thank my super smart office-mates/co-sufferers for setting a good example; Ben, Darren, Nélida, Keshab, Wendy, and especially Claire Foster for pulling me back to the office from working at home. I am especially grateful to Claudia Benham for her support and for helping me adjust to PhD life. I thank also the Fenner School of Environment and Society for holding weekly morning teas, which are excellent. Chris Sanderson, Maddie Castles, Zoe Reynolds, Richie Southerton and Andrew Neilen were high quality companions and skilled assistants for many weeks camping on Cape York Peninsula, and Piers Bairstow and Mauro Devanzo provided logistical equipment and advice, and a fully loaded four-wheel driving course. 1 Baz and Shelley Lyon provided the ‘Palmy army’ with a second home at Boulder Bend and a second family. Thanks Terry Irwin and Australia Zoo for putting me on a crocodile twice, and for generally being eager to help with the project. And thanks to the Australian Wildlife Conservancy, Graham Woods and Sally Gray and Eridani Mulder for such professional assistance with fieldwork on Piccaninny Plains. A big thanks to Steve Murphy, for his hard work collecting demographic data on this special but difficult study species, and to my co-authors Josh Penalba and Steve Haslett for their respective contributions and abundant skill. Brian Venables’ kind offer of a beer turned into emergency post-prang accommodation and assistance in Cairns. Thanks also John Pritchard for sharing your idyllic home among the canopy, and of course for all the fish. I also thank my Danish hosts Torben Dabelsteen, Nina Simonsen, Concalo Cordoso, Thomas Læssøe and Ulrik Søchting for conversation, an office with a view and the all important ‘hæve sinke bord’ (height adjustable table). I thank the Australian Government for my Australian Postgraduate Award, Birdlife Australia, the Hermon Slade Foundation and the National Geographic Society for the valuable funding they provided for field and lab work. I also thank the staff at the Australian, Western Australian, South Australian and Queensland Museums as well as at the Australian National Wildlife Collection for providing valuable palm cockatoo tissue samples to the project. 2 Overall abstract Understanding dispersal dynamics is important for conservation of vulnerable species because they effect whether populations recover or disappear following decline or disturbance, especially in species with slow life-histories that cannot replenish quickly. Palm cockatoos have one of the slowest reproductive rates for any parrot, and likely face steep decline in at least one location on Cape York Peninsula (CYP), north-eastern Australia. Traditional methods of measuring dispersal, such as capture and fitting of tracking devices, identification markers or tissue sampling for genetic analyses, are inappropriate in this species due to their susceptibility to stress. While handling chicks for DNA sample collection does not cause harm, locating nests requires too much focused effort at spatial scales relevant for conservation. In this thesis, I assess the utility of cultural methods for determining population connectivity based on published literature, and employ a combination of cultural and genetic methods to assess connectivity among Australian palm cockatoo populations. I then use a landscape ‘resistance’ modelling approach based on electrical circuit theory to identify connectivity corridors. Finally, I use population viability analysis (PVA) to determine the effects of dispersal dynamics on viability for both individual populations and the combined meta-population in Australia. Based on the literature I concluded that geographic variation in cultural behaviour among populations of a species can help fill important knowledge gaps about their population level processes, especially when comparisons to similar species and alternative data are available. My assessments of vocal and genetic variation among populations revealed differentiation among populations on Cape York Peninsula, separating east coast palm cockatoos at Iron Range from other Australian populations with some evidence of gene flow between them. My landscape ‘resistance’ analysis 3 identified the Great Dividing Range as a barrier, and rainforest patches as important corridors for interaction among separate populations. However, the level of connectivity we determined appears not to provide enough support via dispersal to buffer the decline predicted for Iron Range. Furthermore, other populations require much better reproductive success than data suggests for Iron Range if individuals dispersing to there are to be replenished. I emphasise the importance of managing local declines for the preservation of genetic and behavioural diversity in Australian palm cockatoos. 4 Table of Contents Acknowledgements 1 Overall abstract 3 Table of Contents 5 Chapter 1: Introduction 9 Assessing connectivity through population structure and dispersal 10 Thesis structure and rationale 13 Conservation of a small inter-connected meta-population: the case of Australian palm cockatoos. 14 Context statement 16 References 21 Chapter 2: Parrots as non-human models for cultural evolution 22 Abstract 22 Introduction 23 1. Communication 26 Vocal learning 26 Visual communication 30 2. Tool manufacture 32 Tool use in parrots: spontaneous or cultural? 32 3. Musical parrots 35 Parrot rhythm and sound tools 36 4. Geographic variation and change over time 37 Applications of cultural information 40 Conclusion 42 Acknowledgements 43 Author contributions 43 References 44 Chapter 3: Geographic variation in vocal characteristics of Australian palm cockatoos (Probosciger aterrimus). 54 Abstract 54 Introduction 55 Methods 58 Study sites 58 Recordings 59 Call Classification 62 Geographic variation in palm cockatoo calls 64 Common call sharing 66 5 Structural differences in contact calls 68 Results 70 Population differences in common call types 70 Within population analyses on contact calls 71 Between population scale analyses on contact calls 73 Discussion 76 Within population analyses on common contact calls 77 Between population analyses of common contact calls 77 Vocalization patterns and biogeography 78 Acknowledgements 80 Funding 80 Author contributions 81 References 81 Chapter 4: Genomic population structure supports vocal dialect boundaries in palm cockatoos (Probosciger aterrimus) and a refugial late-Quaternary distribution model. 86 Abstract 86 Funding details 87 Introduction 87 Methods 92 Sampling 92 DNA sequencing 93 Data processing 94 Population structure and statistics 95 Species distribution modeling 95 Results 96 Population structure and admixture 96 Population genetics statistics 98 Species distribution modeling 98 Discussion 103 Genetic similarity between Cape York Peninsula and Papua New Guinea 103 Genetic distinctiveness of Iron Range 105 Contemporary population connectivity 106 Culture and connectivity 108 Conclusion 109 Acknowledgements 110 Author contributions 110 6 References 111 Supplementary methods section 116 DNA sequencing 116 Data processing 118 Population structure and statistics 120 References 121 Chapter 5: Genetic and vocal data show that topography and restricted habitat corridors determine population connectivity in a large parrot. 124 Abstract 124 Introduction 125 Methods 127 Study species 127 Study sites 129 Recordings 129 Genetic structure 131 Distribution prediction 131 Landscape connectivity predictions 133 Results 135 Range and habitat preferences 135 Testing landscape level connectivity 138 Discussion 139 Distribution and habitat 140 Landscape level connectivity 142 Acknowledgements 145 Author contributions 146 References 146 Chapter 6: Slow