http://researchcommons.waikato.ac.nz/ Research Commons at the University of Waikato Copyright Statement: The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). The thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: Any use you make of these documents or images must be for research or private study purposes only, and you may not make them available to any other person. Authors control the copyright of their thesis. You will recognise the author’s right to be identified as the author of the thesis, and due acknowledgement will be made to the author where appropriate. You will obtain the author’s permission before publishing any material from the thesis. Diversity of New Zealand Deep-sea Amphipoda A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy at The University of Waikato by MATTHEW ANDREW KNOX 2012 i ABSTRACT Biodiversity and the ecological and evolutionary processes which influence faunal distributions are poorly understood in deep-sea habitats. This thesis assesses diversity of deep-sea amphipod crustaceans at three taxonomic levels (family, species, genetic) on continental margins of New Zealand relative to environmental variables. Sampling was undertaken at 20 stations located on Chatham Rise and Challenger Plateau, two major geomorphic features with contrasting environmental conditions. In Chapter 1, total diversity of the >12,500 amphipods assessed at the family-level revealed high abundance (range: 44 – 2074 individuals 1000 m-2) and taxonomic richness (27 families). Amphipod assemblages at all stations were largely dominated by the same families. Chatham Rise stations were mostly similar in family composition to one another and to the two closest Challenger Plateau stations. Overall, amphipod community composition correlated most strongly with surface chlorophyll a, suggesting strong benthic- pelagic coupling. In Chapter 2, I used molecular methods (COI DNA sequence thresholds of 6%) to estimate species diversity in the dominant amphipod family identified from Chapter 1 - the Phoxocephalidae. Analyses revealed 49 putative species-level taxa, which greatly exceeds the current number (n=17) of formally described New Zealand phoxocephalid species. A cluster of stations with highly similar taxa was identified, broadly distributed over the crest of the Chatham Rise, in association with elevated food availability. Similar to the family-level analyses of Chapter 1 multivariate analysis of phoxocephalid assemblages and environmental parameters revealed a strong correlation with measures of food supply. ii Analyses of inter-station assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions on eastern and western continental margins. Chapter 3 examined genetic connectivity among deep-sea habitats. A phylogenetic analyses of three relatively abundant and widespread taxa; cf. Ampelisca chiltoni, cf. Oediceroides apicalis and Phoxocephalidae sp., was combined with available genetic data from a further 61 taxa collected from the same stations, to examine mean levels of inter- station genetic divergences. Nearly identical levels of genetic divergence were found between eastern and western regions for all three taxa. Furthermore, inter-station analysis of the wider amphipod community revealed similar patterns of genetic structure in most taxa. Based on molecular clock estimates, genetic divergences most likely corresponded to isolation following landmass changes during the Pleistocene. This thesis research has revealed a biodiversity hotspot on New Zealand continental margins. I conclude that Cook Strait and the subtropical front are important structures responsible for shaping benthic communities on New Zealand continental margins and that vicariance is likely to have played an important role in the evolutionary radiation of the New Zealand deep-sea fauna. iii ACKNOWLEDGEMENTS Firstly, I wish to thank my supervisory panel, Ian Hogg, Conrad Pilditch and Anne-Nina Lörz. Thanks for your unfaltering willingness to provide encouragement, advice, ideas, and critique on the many, many manuscripts, PowerPoint presentations and progress reports which I have sent you. Thanks also for giving me the opportunity to join voyages and expeditions to such amazing and interesting places! Getting to go to Antarctica (twice) AND feature in TV guide were two major highlights which I’ll never forget. To the team at Guelph, notably Dirk Steinke and Paul Hebert, thanks for welcoming me into your lab. The work carried out during my time in Guelph allowed me to analyse a much greater number of samples, at a more accelerated rate than would have otherwise been possible. Thanks also to Kareen Schnabel and Sadie Mills at NIWA Invertebrate Collection, and to all the other people with whom I shared the RV Tangoroa with during sampling. To all my fellow students in ecology at the University of Waikato, thanks for the daily morning tea distractions and for occasionally letting me excel against you during touch games. To everyone who has worked in PBRL over the last few years, thanks for sharing your skills and knowledge and making lab work here an enjoyable, productive experience. To Ian and Chrissen, thanks for helping me to blossom into ‘technician Matt’. This job has not only helped support me financially, but has broadened my lab skills and also been pretty fun. To my Mum, Dad and my in laws Allen and Lorraine, thanks for your support throughout this period and for not asking me THE question too often and for finally iv learning how to say am-phi-pod (Allen). Delphi, thanks for letting me finish this thing without too many problems and for reminding me of the important things in life. Finally, the biggest thanks of all must go to my lovely lady, Annaleise. I know that this PhD has been just as much of a wait for you and I promise I’ll never do one again. Thanks for all your love and patience. v TABLE OF CONTENTS ABSTRACT…………………………………………………………………………………………………………………………….. ii ACKNOWLEDGEMENTS………………………………………………………………………………………………………… iv TABLE OF CONTENTS………………………………………………………………………………………………………….… vi LIST OF TABLES…………………………………………………………………………………………………………….….…… ix LIST OF FIGURES……………………………………………………………………………………………………………...…… x LIST OF APPENDICES…………………………………………………………………………………………………….….……xii THESIS INTRODUCTION………………………………………………………………………………………..……...…..... 1 Organisation of Thesis............................................................................................................... 7 References…………………………………………………………………………………………………………...……...…..... 9 CHAPTER 1. ABUNDANCE AND DIVERSITY OF EPIBENTHIC AMPHIPODS (CRUSTACEA) IN CONTRASTING BATHYAL HABITATS…………………………………………………………..……….... 16 Abstract…………………………………………………………………………………………………………….... 17 Introduction……………………………………………………………………………………………..……….... 18 Methods……………………………………………………………………………………………………..…….... 23 Station selection and sampling protocol………………………………………..…….... 23 Sample sorting and taxonomic identification……………………………………….... 25 Statistical analyses……………………………………………………………………………….... 25 Results……………………………………………………………………………………………………………...... 29 Amphipod biodiversity: univariate……………………………………………………….... 29 Amphipod biodiversity: multivariate…………………………………………………...... 30 vi Discussion………………………………………………………………………………………………………….... 36 Amphipod biodiversity………………………………………………………………………….... 36 Relationship between biodiversity and environmental factors…….…….…... 38 Conclusions……………………………………………………………………………………………………..….. 41 Acknowledgements……………………………………………………………………………………….….... 42 References…………………………………………………………………………………………………………... 43 CHAPTER 2. GREATER AMPHIPOD DIVERSITY ASSOCIATED WITH ENVIRONMENTAL HETEROGENEITY IN DEEP-SEA HABITATS……………………………………………………………... 53 Abstract……………………………………………………………………………………………………………….. 54 Introduction………………………………………………………………………………………………………... 55 Methods………………………………………………………………………………………………………….…... 61 Study sites and sampling methods…………………………………………………………. 61 Sample sorting and taxonomic identification……………………………………….…. 61 Genetic analyses…………………………………………………………………………………..… 62 Statistical analyses…………………………………………………………………………………. 63 Results……………………………………………………………………………………………………………….... 68 Phoxocephalid diversity………………………………………………………………………..… 68 Community analyses…………………………………………………………………………….... 69 Discussion………………………………………………………………………………………………………….… 72 Phoxocephalid diversity……………………………………………………………………..…… 72 Community analyses and relationships with environmental parameters… 74 Acknowledgements…………………………………………………………………………………………..…. 77 References…………………………………………………………………………………………………………... 78 vii CHAPTER 3. EVIDENCE FOR VICARIANT DIVERGENCE AMONG POPULATIONS OF DEEP-SEA AMPHIPODS FROM NEW ZEALAND……………………………………………………………………… 88 Abstract………………………………………………………………………………………………………..……… 89 Introduction………………………………………………………………………………………………….…….. 90 Methods………………………………………………………………………………………………………..…….. 95 Study sites and sampling methodology……………………………………………….…. 95 Genetic protocols……………………………………………………………………………….….. 96 Statistical analyses………………………………………………………………………….…….. 97 Results…………………………………………………………………………………………………..……………..100 Discussion…………………………………………………………………………………………………….……… 107 Acknowledgements………………………………………………………………………………………..…….111 References…………………………………………………………………………………………………..……….112 THESIS CONCLUSION………………………………………………………………………………….…………………….. 123 Future directions.......................................................................................................125