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Patterns of Genetic Connectivity in Deep-Sea Vulnerable Marine Ecosystems and Implications for Conservation

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Patterns of Genetic Connectivity in Deep-Sea Vulnerable Marine Ecosystems and Implications for Conservation PATTERNS OF GENETIC CONNECTIVITY IN DEEP-SEA VULNERABLE MARINE ECOSYSTEMS AND IMPLICATIONS FOR CONSERVATION BY CONG ZENG A thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Biology. Victoria University of Wellington 2016 Abstract Knowledge about and understanding of population structure and connectivity of deep- sea fauna decreases with increasing depth, but such information is crucial for the management of vulnerable marine ecosystems (VMEs) in particular. As such, research using genetic markers, which does not require knowledge of ecological or environmental processes as a prerequisite for the analysis, is a practical method to investigate population connectivity of VME indicator taxa. However, population genetics studies are yet to be broadly conducted in the deep sea around New Zealand. To provide background information and develop hypothesises for this research, 196 population genetic studies of deep-sea fauna were reviewed and analysed. Based on the collected studies, four different patterns of spatial genetic structure were observed: global homogeneous, oceanic, regional, and fine structure. These different structures were reported that they were related to depth, topography, distance between populations, temperature and other biological factors. Quantification of the relationship between these factors and the detection of barriers to gene flow (barrier detection) showed that depth, currents and topography contributed significantly to barrier detection and depth and topography were acting as a barrier to gene flow in the deep sea. Furthermore, different sampling strategies and different genetic marker types significantly influenced genetic barrier detection. Comparison amongst different habitats suggested that different conservation strategies should be developed for different habitat types (Chapter 2). This study used different genetic markers to assess the genetic connectivity amongst VME indicator taxa Vulnerable Marine Ecosystems (VME). Seven VME indicator taxa were selected: 4 sponges (Neoaulaxinia persicum, Penares sp., Pleroma menoui and Poecillastra laminaris) and 3 corals (Goniocorella dumosa, Madrepora oculata and Solenosmilia variabilis), at different spatial scales. Due to lack of genetic information for these species, genetic markers were developed for Poecillastra laminaris (0) and S. variabilis (Chapter 4). A geographic province (northern-southern province), region (north-central-south), and geomorphic feature hierarchical testing framework was employed to examine species-specific I genetic variation in mitochondrial (COI, Cytb and 12S) and nuclear markers (microsatellites) amongst populations of four deep-sea sponges within the New Zealand region. For Poecillastra laminaris, significant mitochondrial and nuclear DNA genetic differences were revealed amongst biogeographic provinces. In contrast, no significant structure was detected across the same area for Penares sp. Both Neoaulaxinia persicum and Pleroma menoui were only available from the northern province, in which Pleroma menoui showed no evidence of genetic structure, but N. persicum exhibited a geographic differentiation in 12S. No depth- related isolation was observed for any of the four species at the mitochondrial markers, nor at the microsatellite loci for Poecillastra laminaris. Genetic connectivity in Poecillastra laminaris is likely to be influenced by oceanic sub-surface currents that generate routes for gene flow and may also act as barriers to dispersal. Although data are limited, these results suggest that the differences in patterns of genetic structure amongst the species can be attributed to differences in life history and reproductive strategies. The results are discussed in the context of existing marine protected areas, and the future design of spatial management measures for protecting VMEs in the New Zealand region (Chapter 5). To better understand the vulnerability of stony corals (Goniocorella dumosa, Madrepora oculata and Solenosmilia variabilis) to disturbance within the New Zealand region, and to guide marine protected area design, genetic structure and connectivity were determined using microsatellite loci and DNA sequencing. Analyses compared population genetic differentiation between two biogeographic provinces, amongst three sub-regions (north-central-south), and amongst geomorphic features. Population genetic differentiation varied amongst species and between marker types. For G. dumosa, genetic differentiation existed amongst regions and populations on geomorphic features, but not between provinces. For M. oculata, only a north-central-south regional structure was observed. For S. variabilis, genetic differentiation was observed between provinces, amongst regions and amongst geomorphic features based on microsatellite variation. Multivariate analyses indicated that populations on the Kermadec Ridge were genetically different from Chatham Rise populations in all three coral species. Furthermore, a significant isolation-by-depth pattern was observed for both marker types in G. dumosa, and also in ITS of M. oculata. An isolation-by-distance pattern was found in microsatellites of S. variabilis. Migrate analysis showed that medium to high self-recruitment were detected in all geomorphic feature populations, and different species presented different genetic connectivity patterns. These different patterns of population genetic structure and connectivity at a range of spatial scales II indicate that flexible spatial management is required for the conservation of deep-sea corals around New Zealand (Chapter 6). Understanding the deep-sea ecological processes that shape spatial genetic patterns of species is critical for predicting evolutionary dynamics and defining significant evolutionary and/or management units. In this study, the potential role of environmental factors in shaping the genetic structure of the 7 deep-sea habit-providing study species was investigated using a seascape genetics approach. The genetic data were acquired from nuclear and mitochondrial sequences and microsatellite genotype data, and 25 environmental variables (5 topographic, 17 physiochemical and 3 biological variables). The results indicated that environmental factors affected genetic variation differently amongst the species. However, factors related to current and food source explained the north-central-south genetic structure in sponges and corals, and environmental variation in these parameters may be acting as a barrier to gene flow. At the geomorphic feature level, the DistLM and dbRDA analysis showed that factors related to the food source and topography were most related to genetic variation in microsatellites of sponge and corals. This study highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms (Chapter 7). The outcomes of this study provide vital information to assist in effective management and conservation of VME indicator taxa and contribute to an understanding of evolutionary and ecological processes in the deep sea (Chapter 8). III IV Acknowledgments Four years is not a long time on the journey of life, but these four years in New Zealand will be one of the most-cherished periods in my lifetime. Since I started my New Zealand life, I have received many munificent assistances in both academic and living aspects, and here I express my appreciation to these people in this thesis. Firstly, I am extremely indebted to my primary supervisor Professor Jonathan Gardner for bringing me here. This is an important milestone in this one-way journey, because this opportunity not only shifts my research interests into marine biology but also offers me a fabulous experience in such a beautiful and peaceful country. Besides, his great effects and contributions to my PhD project contained herein are indelible. I also greatly appreciate my secondary supervisors, Dr Ashley Rowden and Dr Malcolm Clark, for guiding me in the researches, providing logistical support for my research and their helpful feedback on the content of this thesis and other publications, and an opportunity to participate in research cruise TAN1402. I am also grateful to members of my committee Dr Peter Ritchie and Professor Phil Lester for the valuable advice and input in the early stages of my studies. Also, I am grateful that Associate Professor Joe Zuccarello who provided practical advice for my experiments. This research would not have been possible without the enormous generosity of everyone who helped with sample collection. I would like to thank Ms Sadie Mills (NIWA) for supporting and caring for me in the Invertebrate Collection (NIC). Many appreciations are given to Ms Dianne Tracey for coral identifications and providing chances for academic training and an international conference. I am also thankful to Dr Michelle Kelly who is responsible for the sponge taxonomical work for my thesis. Additional thanks are for kindly assistances from other staff in NIWA. Great thanks to Dr Karen Miller (UTAS) and Dr Sophie Arnaud Haond (Ifremer) for sharing the data and sending the specimens, and Dr Mike Williams (NIWA) for generating the environmental data as well. Thank you to Dr Everett Meredith (NOAA) and Dr Cheryl Morrison (USGS) for connecting me with other coral experts. I would like to thank my lab mates for sharing their knowledge with me and for their friendship, especially Dr Leighton Thomas and Dr Catarina
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