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Canning Estuary DDeevveellooppmmeenntt ooff bbiioottiicc iinnddiicceess ffoorr eessttaabblliisshhiinngg aanndd mmoonniittoorriinngg eeccoossyysstteemm hheeaalltthh ooff tthhee SSwwaann-- CCaannnniinngg EEssttuuaarryy FINAL TECHNICAL REPORT May 2011 Valesini, F.J., Hallett, C.S., Cottingham, A., Hesp, S.A., Hoeksema, S.D., Hall, N.G., Linke, T.E., Buckland, A.J. Prepared for the Swan River Trust, Department of Water and Department of Fisheries 1 2 Development of biotic indices for establishing and monitoring ecosystem health of the Swan- Canning Estuary FINAL TECHNICAL REPORT May 2011 Valesini, F.J., Hallett, C.S., Cottingham, A., Hesp, S.A., Hoeksema, S.D., Hall, N.G., Linke, T.E., Buckland, A.J. Prepared for the Swan River Trust, Department of Water and Department of Fisheries 3 4 Disclaimer The authors have prepared this report in accordance with the usual care and thoroughness of the Centre for Fish and Fisheries Research (CFFR) for the use by the Swan River Trust (SRT), Department of Water (DoW) and Department of Fisheries (DoF) and only those third parties who have been authorised in writing by the CFFR to rely on the report. It is based on generally accepted practices and standards at the time it was prepared. No other warranty, expressed or implied, is made as to the professional advice included in this report. It is prepared in accordance with the scope of work and for the purpose required by the SRT, DoW and DoF. The methodology adopted and sources of information used by the authors are outlined in this report. The authors have made no independent verification of this information beyond the agreed scope of works, and they assume no responsibility for any inaccuracies or omissions. No indications were found during our investigations that information contained in this report as provided to the authors was false. This report was prepared between July 2007 and September 2010, and is based on the information reviewed at the time of preparation. The authors disclaim any responsibility for changes that may have occurred after this time. This report should be read in full. No responsibility is accepted for use of any part of this report in any other context or for any other purpose or by third parties. This report does not purport to give legal advice. Legal advice can only be given by qualified legal practitioners. 5 6 Acknowledgements Funds for this project were kindly provided by the Swan River Trust, Department of Fisheries, Department of Water and Murdoch University. Gratitude is also expressed to the many colleagues at the Centre for Fish and Fisheries Research, Murdoch University, who have helped with sampling the fish fauna of the Swan-Canning Estuary, both historically and during the current study. We are also indebted to Professors Norm Hall, Ken Pollock and Bob Clarke for their extensive help with many aspects of the statistical approaches adopted during this study. We also thank the Department of Water for supplying water quality data from the Swan-Canning Estuary and the various anonymous reviewers whose comments have helped to improve earlier drafts of this report. 7 8 Table of Contents Acknowledgements .................................................................................................................. 7 Chapter 1. General Introduction .......................................................................................... 13 Chapter 2. Changes in the characteristics of the fish fauna of the Swan-Canning Estuary since the late 1970s and development of a fish-based biotic index of ecosystem health ....................................................................................................................................... 17 Executive Summary ................................................................................................................. 17 2.1 Introduction ........................................................................................................................ 25 2.2 Materials and Methods ....................................................................................................... 29 2.2.1 Changes in the characteristics of the fish fauna of the Swan-Canning Estuary since the late 1970s ................................................................................................................................. 29 2.2.1.1 Fish sampling regime ................................................................................................... 29 2.2.1.1.1 Nearshore waters ....................................................................................................... 33 2.2.1.1.2 Offshore waters ......................................................................................................... 35 2.2.1.2 Water quality parameters ............................................................................................. 36 2.2.1.3 Statistical analyses – nearshore fish fauna ................................................................... 36 2.2.1.3.1 Data standardisation .................................................................................................. 38 2.2.1.3.2 Data analysis ............................................................................................................. 40 2.2.1.4 Statistical analyses – offshore fish fauna ..................................................................... 43 2.2.1.4.1 Data standardisation .................................................................................................. 43 2.2.1.4.2 Data analysis ............................................................................................................. 43 2.2.1.5 Relationships between fish faunal composition and water quality in nearshore and offshore waters ......................................................................................................................... 44 2.2.2 Development of a biotic index of estuarine health ......................................................... 47 2.2.2.1 Selection of metrics for constructing estuarine health indices..................................... 47 2.2.2.1.1 Allocation of fish to ecological guilds ...................................................................... 47 2.2.2.1.2 Candidate fish metrics ............................................................................................... 50 2.2.2.1.3 Selection of metrics sensitive to spatial changes in habitat quality .......................... 51 2.2.2.1.4 Selection of metrics sensitive to temporal changes .................................................. 58 2.2.2.2 Establishing reference conditions for estuarine health indices .................................... 63 2.2.2.2.1 Reference data sets .................................................................................................... 63 2.2.2.2.2 Establishing reference conditions and scoring metrics ............................................. 63 2.2.2.3 Index calculation and validation .................................................................................. 64 2.2.2.3.1 Index calculation ....................................................................................................... 64 2.2.2.3.2 Preliminary interpretation of index performance ...................................................... 65 2.2.2.3.3 Index validation ........................................................................................................ 65 2.2.2.3.4 Random sampling variability .................................................................................... 67 2.3 Results ................................................................................................................................ 68 2.3.1 Changes in the characteristics of the fish fauna of the Swan-Canning Estuary between 1978 and 2009 .......................................................................................................................... 68 2.3.1.1 Seine net comparison ................................................................................................... 68 2.3.1.2 Differences in the nearshore fish fauna among periods ............................................... 70 2.3.1.2.1 Mean species densities .............................................................................................. 70 2.3.1.2.2 Mean overall density and taxonomic distinctness .................................................... 76 2.3.1.2.3 Species composition of fish assemblages among periods ........................................ 79 9 2.3.1.3 Differences in the offshore fish fauna among periods ................................................. 93 2.3.1.3.1 Mean species catch-rates........................................................................................... 93 2.3.1.3.2. Mean overall number of species, catch-rates and taxonomic distinctness ............... 95 2.3.1.3.3 Species composition of fish assemblages among periods ........................................ 98 2.3.1.4 Relationships between fish faunal composition and water quality in nearshore and offshore waters ....................................................................................................................... 104 2.3.1.4.1 Nearshore (surface) waters ..................................................................................... 104 2.3.1.4.2 Offshore (surface and bottom) waters..................................................................... 114 2.3.2 Development of a biotic index of estuarine health ......................................................
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