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Palaeoecological Changes in Populations of Antarctic Ice-Dependent Predators and Their Environmental Drivers

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Palaeoecological Changes in Populations of Antarctic Ice-Dependent Predators and Their Environmental Drivers PALAEOECOLOGICAL CHANGES IN POPULATIONS OF ANTARCTIC ICE-DEPENDENT PREDATORS AND THEIR ENVIRONMENTAL DRIVERS Jane Younger BSc (Nanotechnology) (Hons), BAntSt (Hons) Submitted in fulfilment for the requirements for the degree of Doctor of Philosophy Institute for Marine and Antarctic Studies June 2015 DECLARATION OF ORIGINALITY This thesis contains no material which has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledged in the thesis, and to the best of my knowledge and belief no material previously published or written by another person except where due acknowledgement is made in the text of the thesis, nor does the thesis contain any material that infringes copyright. Jane Younger 22/06/2015 AUTHORITY OF ACCESS The publishers of the papers comprising Chapters 1, 2, 3 & 4 hold the copyright for that content, and access to the material should be sought from the journals, Global Change Biology (Chapters 1 &2) and BMC Evolutionary Biology (Chapters 3 & 4). The remaining non published content of the thesis may be made available for loan and limited copying and communication in accordance with the Copyright Act 1968.” CONTENTS List of figures ............................................................................................................................... vi List of tables ............................................................................................................................... vii Abbreviations ............................................................................................................................ viii Time periods referred to in text .................................................................................................... ix Types of ice referred to in text ..................................................................................................... ix Statement of ethical conduct ........................................................................................................ x Statement of co-authorship ......................................................................................................... xi Acknowledgements ................................................................................................................... xiii Abstract ..................................................................................................................................... xvi Map of Antarctica ...................................................................................................................... xix Chapter 1 - A review of palaeoecological changes in Southern Ocean marine predator populations and their environmental drivers .................................................................................................... 1 1.1 Introduction ................................................................................................................................... 2 1.2 An overview of Southern Ocean palaeoclimate............................................................................. 3 1.3 Palaeoecology of the Southern Ocean ........................................................................................... 7 1.4 Ice-free breeding species – the sub-Antarctic ............................................................................... 8 1.4.1 King penguins .......................................................................................................................... 9 1.4.2 Southern elephant seals .......................................................................................................... 9 1.5 Ice-free breeding species – the Pygoscelis penguins ................................................................... 13 1.5.1 Chinstrap penguins ................................................................................................................ 14 1.5.2 Gentoo penguins ................................................................................................................... 14 1.5.3 Adélie penguins ..................................................................................................................... 15 1.6 Ice-free breeding species – flying seabirds of the Antarctic continent........................................ 17 1.6.1 Snow petrels .......................................................................................................................... 17 1.7 Antarctic sea ice breeders ............................................................................................................ 18 1.7.1 Emperor penguins ................................................................................................................. 18 1.8.1 Weddell, crabeater and Ross seals ........................................................................................ 19 i 1.9 Key long-term drivers of Southern Ocean predator populations ................................................ 20 1.10 Statement of thesis aims ........................................................................................................... 23 1.11 References ................................................................................................................................. 24 Chapter 2 - Too much of a good thing: sea ice extent may have forced emperor penguins into refugia during the last glacial maximum ...................................................................................... 33 2.1 Abstract........................................................................................................................................ 34 2.2 Introduction ................................................................................................................................. 34 2.3 Methods ....................................................................................................................................... 37 2.3.1 Sample collection .................................................................................................................. 37 2.3.2 DNA extraction, amplification and sequencing .................................................................... 38 2.3.3 Data analysis – summary statistics and population structure .............................................. 40 2.3.4 Data analysis - demographic histories .................................................................................. 40 2.4 Results.......................................................................................................................................... 41 2.4.1 Present day population structure ......................................................................................... 41 2.4.2 Population history with respect to climate change .............................................................. 44 2.5 Discussion .................................................................................................................................... 46 2.6 References ................................................................................................................................... 51 2.7 Appendices .................................................................................................................................. 59 Appendix 2.1 Haplotype networks of phylogenetic relationships ................................................. 59 Appendix 2.2 Table of primer sequences. ...................................................................................... 60 Chapter 3 - Contrasting responses to a climate regime change by sympatric meso-predators ........ 62 3.1 Abstract........................................................................................................................................ 63 3.2 Introduction ................................................................................................................................. 63 3.3 Methods ....................................................................................................................................... 66 3.3.1 Sample collection .................................................................................................................. 66 3.3.2 Molecular laboratory ............................................................................................................ 68 3.3.3 Genetic diversity and present day population structure ....................................................... 68 3.3.4 Reconstructions of demographic history .............................................................................. 69 ii 3.4 Results .......................................................................................................................................... 70 3.4.1 Genetic diversity .................................................................................................................... 70 3.4.2 Extant population structure .................................................................................................. 71 3.4.3 Trends in effective female population size ............................................................................ 72 3.5 Discussion ..................................................................................................................................... 74 3.5.1 Ecological niche ..................................................................................................................... 74 3.5.2 Adaptive capacities ..............................................................................................................
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