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Trophic Structure Through the History of Exploitation in New Zealand Fish Communities

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Trophic structure through the history of exploitation in New Zealand fish communities _________________________________ A thesis submitted in partial fulfilment of the requirements for the Doctor of Philosophy diploma in Marine Sciences at University of Otago by Leonardo Maia Durante _________________________________ University of Otago 2020 Abstract of a thesis submitted in partial fulfilment of the requirements for the Doctor of Philosophy diploma in Marine Sciences Trophic structure through the history of exploitation in New Zealand fish communities by Leonardo Maia Durante Marine ecosystems have been under a considerable amount of stress due to human activities, especially after industrialization. The abundance and ecological interactions of exploited fishes are influenced by fishing activities, climate change, and natural environmental variability, but there is a lack of knowledge on how these community parameters have changed over time. In the present study, temporal shifts in the trophic structure and composition of an important commercial fish community along the east coast of the South Island of New Zealand was investigated. The Marine Trophic Index (MTI) and species composition of the reported commercial fisheries landings for the whole country were used to identify periods of fisheries expansion and shifts in the trophic architecture of the landings. A stable isotope approach was used to estimate resource use and trophic level of fishes, comparing these parameters spatially and temporally. It was demonstrated that it is possible to access carbon and nitrogen stable isotope values from preserved fishes, for both bulk tissues and specific amino acids, which enabled this work to access ecological information from specimens stored in museum samples. The results demonstrate that fisheries industrialization occurred between 1970 and 2000 in New Zealand, increasing MTI values and shifting the relative landings composition from inshore to offshore and deep-water species over time. Regional comparisons demonstrated that modern fish communities from Otago relied more heavily on macroalgae production when compared to those from Kaikoura, linked to higher fishery yields in the former. When analyzing the same parameters from museum specimens collected before the full expansion of industrialized fisheries, modern species inhabiting the outer shelf and slope also showed a reduced reliance on macroalgae production, together with an increased trophic level. When considering continuous changes in the trophic parameters, environmental factors and prey abundance had a significant relationship with the variation of trophic parameters for most fish assemblages. Trophic parameters of the inner shelf assemblage also showed a relationship with MTI throughout time, indicating the earlier effects of coastal fisheries. Although Kaikoura and modern communities showed a wider niche breadth compared to Otago and historical samples, respectively, tarakihi was the only species to show both regional and temporal trends. Tarakihi stocks in the region have been overexploited and are sensitive to habitat degradation, which could be linked to the shift in trophic structure observed here. Furthermore, temporal changes in community composition towards a relatively higher abundance of lower trophic level species were observed from the analysis of long-term trawl survey data. Species with decreasing abundance that presented shifts in trophic parameters with time, such as red cod, had their trophic level and resource use occupied by species with increasing abundance, like spiny dogfish. The present study demonstrates how the trophic structure and composition of important commercial communities have changed over time and how they are related to natural and anthropogenic effects, with the potential to alter regional fishery yields. This study highlights how uncovering ecological baselines before human impacts is an important step towards the implementation of an ecosystem-based management approach to fisheries resources. Keywords: Quota Management System, fisheries, exploitation, isotopes, isotopic ecology, compound specific isotopic analysis, amino acids, history, ecosystem-based management, sustainability, kelp forest, food web, resource use, trophic level, museum collection, oceanography, fish community, ecological baselines, fishing down marine food webs Life is only a snapshot of the ever-changing nature iv Acknowledgements I would like to thank my family for all the support throughout my studies, especially my mom who taught me from a young age the importance of education in a person’s life. She showed me that I had the capabilities to follow my dreams, as long as I was willing to put in the necessary effort to achieve them. I would like to give special thanks to my sister Leticia and my wife Erica, which are my biggest examples of dedication and endurance, both professionally and in their personal lives, I could not have completed this thesis without their support. I would also like to show my gratitude to all my supervisors, for all the time they have put into the development of this thesis and myself as a researcher. I would like to express an especial thanks to Steve Wing, who took me as a Ph.D. student and provided financial, professional, and moral support for the completion of this thesis. I thank all the staff from NIWA, Fisheries New Zealand and Sea Around Us, as well as Stina Kolodzey, Tomo, Rex, Tania King, Monique Ladds, Sorrel O'Connell-Milne, Max Williams and Alex Connolly who assisted with data and sample acquisition for this work. I would also like to show my gratitude to Neil Bagley, Mike Beentjes, Rosemary Hurst, Rich Ford, Peter Russel, Rob Smith, Carl Struthers, Clive Roberts and Andrew Stewart for their expertise, contribution, and support of this work. Technical support was provided by Robert van Hale, Dianne Clark, Doug Mackie, Linda Groenewegen, Reuben Pooley and from the Departments of Marine Science, Chemistry and Zoology at Otago University, which I am grateful for. Monetary support was provided from a National Science Challenge: Sustainable Seas (4.1.1 Ecosystem Connectivity) grant to Stephen Richard Wing, while I was additionally supported by a University of Otago Ph.D. scholarship. 5 Table of Contents Acknowledgements .................................................................................................................... 5 List of Tables ............................................................................................................................ 11 List of Figures .......................................................................................................................... 13 General introduction ................................................................................................................. 18 Chapter 1 Shifting trophic architecture of marine fisheries in New Zealand: implications for guiding effective ecosystem-based management .................................................................................. 23 Abstract ................................................................................................................................ 23 1.1. Introduction ................................................................................................................... 24 1.1.1. New Zealand and global fisheries .......................................................................... 24 1.1.2. A brief overview of the fishery and management history in New Zealand ........... 28 1.1.3. Fish landings and ecological trends of New Zealand fish stocks ........................... 31 1.2. Methods ......................................................................................................................... 34 1.3. Results ........................................................................................................................... 37 1.4. Discussion ..................................................................................................................... 43 Chapter 2 Oceanographic transport along frontal zones forms carbon, nitrogen, and oxygen isoscapes on the east coast of New Zealand: implications for food web studies .......................................... 51 Abstract ................................................................................................................................ 51 2.1. Introduction ................................................................................................................... 52 2.2. Methods ......................................................................................................................... 57 2.2.1. Samples and data collection ................................................................................... 57 2.2.2. Sample preparation and laboratory analysis ........................................................... 58 2.2.3. Data analysis and statistical framework ................................................................. 59 2.3. Results ........................................................................................................................... 61 2.3.1. Oceanography of the ECSI ..................................................................................... 61 2.3.2. ECSI marine isoscapes ........................................................................................... 67 2.4. Discussion ....................................................................................................................
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