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Spatial and Temporal Genetic Structure of The SPATIAL AND TEMPORAL GENETIC STRUCTURE OF THE NEW ZEALAND SCALLOP Pecten novaezelandiae: A MULTIDISCIPLINARY PERSPECTIVE BY CATARINA NUNES SOARES SILVA A thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Doctor of Philosophy Victoria University of Wellington Te Whare Wānanga o te Ūpoko o te Ika a Māui 2015 This thesis was conducted under the supervision of Prof. Jonathan Gardner & A. Prof. James Bell Victoria University of Wellington Wellington, New Zealand ii Abstract Knowledge about the population genetic structure of species and the factors shaping such patterns is crucial for effective management and conservation. The complexity of New Zealand’s marine environment presents a challenge for management and the classification of its marine biogeographic areas. As such, it is an interesting system to investigate marine connectivity dynamics and the evolutionary processes shaping the population structure of marine species. An accurate description of spatial and temporal patterns of dispersal and population structure requires the use of tools capable of incorporating the variability of the mechanisms involved. However, these techniques are yet to be broadly applied to New Zealand marine organisms. This study used genetic markers to assess the genetic variation of the endemic New Zealand scallop, Pecten novaezelandiae, at different spatial and temporal scales. A multidisciplinary approach was used integrating genetic with environmental data (seascape genetics) and hydrodynamic modelling tools. P. novaezelandiae supports important commercial, recreational and customary fisheries but there is no previous information about its genetic structure. Therefore, twelve microsatellite markers were developed for this study (Chapter 2). Samples (n=952) were collected from 15 locations to determine the genetic structure across the distribution range of P. novaezelandiae. The low genetic structure detected in this study is expected given the recent evolutionary history, the large reproductive potential and the pelagic larval duration of the species (approximately 3 weeks). A significant isolation by distance signal and a degree of differentiation from north to south was apparent, but this structure conflicted with some evidence of panmixia. A latitudinal genetic diversity gradient was observed that might reflect the colonisation and extinction events and insufficient time to reach migration-drift equilibrium during a recent range expansion (Chapter 3). A seascape genetic approach was used to test for associations between patterns of genetic variation in P. novaezelandiae and environmental variables (three geospatial and six environmental variables). Although the geographic distance between populations was an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of distance. Evidence suggests iii that some environmental factors such as freshwater discharge and suspended particulate matter can be contributing to the patterns of genetic differentiation of P. novaezelandiae in New Zealand (Chapter 4). Dispersal of P. novaezelandiae was investigated at a small spatial and temporal scale in the Coromandel fishery using genetic markers integrated with hydrodynamic modelling. For the spatial analysis, samples (n=402) were collected in 2012 from 5 locations and for the temporal analysis samples (n=383) were collected in 2012 and 2014 from 3 locations. Results showed small but significant spatial and temporal genetic differentiation, suggesting that the Coromandel fishery does not form a single panmictic unit with free gene flow and supporting a model of source-sink population dynamics (Chapter 5). The importance of using multidisciplinary approaches at different spatial and temporal scales is widely recognized as a means to better understand the complex processes affecting marine connectivity. The outcomes of this study highlight the importance of incorporating these different approaches, provide vital information to assist in effective management and conservation of P. novaezelandiae and contribute to our understanding of evolutionary processes shaping population structure of marine species. iv Acknowledgments I would like to thank my primary supervisor Professor Jonathan Gardner for the opportunity to do this research in such a beautiful corner of the world and for his contribution to the work contained herein. I also greatly appreciate the support of my secondary supervisor Associate Professor James Bell shortly after my arrival and his helpful feedback on the content of this thesis. Thank you to the members of my committee Dr. Peter Ritchie, Dr. Shane Lavery, Associate Professor Joe Zuccarello and Dr. Martin Cryer (MPI) for the valuable advice and input in the early stages of my studies. This research would not have been possible without the enormous generosity of everyone who helped with sample collection. I would like to thank Dr. James Williams (NIWA) for all the support and for connecting me with fishermen for sample collection (Karl Aislabie from Scallop Coromandel Fishery and Donna and Ewan MacMillan from Sodablast Northland ltd). Thank you to Daniel McNaughtan and Paul Mensink for assisting and collecting scallops from Wellington Harbour. Dr. Shane Geange kindly collected scallops from Fiordland, Dr. Debbie Freeman and Brenton Twist provided tissue of scallops from Stewart Is (thanks to Dr. Chris Hepburn for putting me in contact with Brenton), David Middleton and Oliver Wilson provided scallops from Coromandel and Reid Forrest provided scallops from the Marlborough sounds. I would also like to thank Dr. Shane Lavery for putting me in contact with students and staff during my time at Auckland University; thanks to Paul Caiger for helping with sample collection and everyone at Auckland University who welcomed me so warmly. I would also like to thanks Dr. Matt Pinkerton for generating the variables from the ocean colour satellite data MODIS project. I would like to thank my lab mates for sharing their knowledge with me and for their friendship, especially Danielle Hannan and Heather Constable for all the valuable advice and support in the beginning of this research. I would also like to thank the staff from the School of Biological Sciences and the Faculty of Sciences, specially Mary Murray, Sandra Taylor, Patricia Stein, Paul Marsden and Mark Stephen for all the logistical support and infinite patience. I am also thankful for the helpful feedback that Dr. Simon Davy, Dr. Ian Hogg and Dr. Jennifer Ovenden gave on my thesis and for the time and effort they spent in the examination process. v The Ministry for Primary Industries provided funding for this research (Biodiversity Research Advisory Group project ZBD2009-10), which gave me the privilege to work on this research. I also received considerable funding from Victoria University of Wellington; I am grateful for the Victoria Doctoral Scholarship, Victoria PhD Submission Scholarship, Victoria University of Wellington Students Association Sponsorship, VUW Faculty of Science Strategic Research Grant and Kathleen Stewart Postgraduate Scholarship that allowed me to pursue my studies and to attend international conferences. I am thankful for the opportunity to volunteer as Vice-President of the Society for Conservation Biology VUW Chapter. Thanks to the committee and other members for all the valuable knowledge and for our stimulating discussions. I am very grateful for the financial support of the Society for Conservation Biology to attend international conferences. This journey would not have been so rewarding without the support of my Wellingtonian family. I am very grateful to have made such good friends, thank you all for the good moments. I would also like to thank many good friends overseas for their support and their special sense of humour. Last but not least, a very special thank you to my parents, Madalena and António, who always encouraged my decisions and fuelled my passion for biology and to my partner João for all the support and for ensuring my healthy levels of insanity. vi “One planet, one experiment.” E. O. Wilson vii Table of contents Abstract ........................................................................................................................... iii Acknowledgments ............................................................................................................. v Table of contents ........................................................................................................... viii List of Figures ................................................................................................................... x List of Tables................................................................................................................. xiii CHAPTER 1 Introduction ................................................................................................ 1 Marine connectivity and fisheries genetics ...................................................................... 2 Environmental factors affecting genetic variation ........................................................... 6 The New Zealand marine environment ............................................................................ 7 Study species ................................................................................................................... 8 Aims and thesis structure .............................................................................................
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