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Investigating the Physical and Ecological Drivers of Change in a Coastal Ecosystem: from Individual- to Population-Scale Impacts

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INVESTIGATING THE PHYSICAL AND ECOLOGICAL DRIVERS OF CHANGE IN A COASTAL ECOSYSTEM: FROM INDIVIDUAL- TO POPULATION-SCALE IMPACTS By Kathryn Elizabeth Ross A thesis submitted in partial fulfilment of the requirements of Bournemouth University for the degree of Doctor of Philosophy September 2013 Bournemouth University In collaboration with HR Wallingford 1 This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with its author and due acknowledgement must always be made of the use of any material contained in, or derived from, this thesis. 2 Declaration I confirm that the work presented in this thesis is my own, with the exception of: In Chapter 2, the collection, processing and identification of benthic samples from 2009 was a collaborative effort led by Dr Roger Herbert, and part of a condition survey for Poole Harbour, funded by Natural England. The full output of this study is reported in: Herbert, R.J.H., Ross, K., Hübner, R., Stillman, R.A., 2010. Intertidal invertebrates and biotopes of Poole Harbour SSSI and survey of Brownsea Island Lagoon: Report to Natural England, Poole, UK. The collection and processing of benthic samples from 2002 was conducted by the Centre for Ecology and Hydrology and the data were collated by Dr Richard Caldow. Species-level identification of a subset of the benthic fauna of Brownsea Island Lagoon, reported in Chapter 3, was conducted by Dr Roger Bamber and funded by the EDRF Interreg IVB project EcoSal: “Ecotourism in saltworks of the Atlantic: a strategy for integral and sustainable development” (UK partner, Bournemouth University). The individual-based model presented in Chapter 6 was developed in collaboration with Prof. Richard Stillman. Data on the nektonic prey abundance of Brownsea Island Lagoon were collected by Ross Wheeler. Kathryn E. Ross 3 Investigating the physical and ecological drivers of change in a coastal ecosystem: from individual- to population-scale impacts Kathryn E. Ross Abstract Coastal ecosystems are undergoing unprecedented rates of environmental change. Many of these changes are anthropogenically-driven and linked to long-term, climate-related phenomena. This thesis focusses on ecological change in soft sediment intertidal habitats. One of the largest harbours in Europe, Poole Harbour, is used as a case study. It contains a variety of important habitats including intertidal mudflat and non-tidal saline lagoon. The two main themes of the thesis are 1) assessing the physical and ecological factors that determine benthic invertebrate abundance, distribution and community structure, which is examined at the scale of the whole harbour, and at the scale of individual habitats: an intertidal mudflat and a saline lagoon; and 2) predicting the response of an overwintering shorebird population, the pied avocet (Recurvirostra avosetta), to future environmental changes, such as sea-level rise and habitat loss. This is achieved by development of an individual-based model (IBM) and consideration of the species’ unique foraging behaviour. This study contributes to the understanding of the factors structuring soft sediment benthic communities, including the use of data from fine-scale hydrodynamic models. It offers a unique comparison of the spatial and temporal variables driving community structure of a saline lagoon and an intertidal mudflat. It also provides insight into the foraging ecology of the pied avocet at a level of detail that has not previously been considered, including a comparison of foraging behaviour in a tidal and non-tidal habitat, the importance of social foraging, and the novel application of an IBM to this species. 4 Acknowledgements I am indebted to my primary supervisors, Richard Stillman and Roger Herbert, for the knowledge and skills they have imparted, and their support and enthusiasm for my project; also to my secondary supervisor, Jay Willis, for always providing a fresh perspective and helpful comments. My project was part-funded by HR Wallingford, and I am grateful for guidance and expertise from Diane Jones, John Baugh and Tom Benton. I kindly acknowledge the contributions of the following organisations and individuals: Natural England commissioned the 2009 benthic survey, with support from Sue Burton. Andrew Woods and colleagues at the Royal National Lifeboat Institute (RNLI) provided the exhilarating experience of sample collection by hovercraft. Additional sample collection was aided by Frank Elston of Dorset Workboats and John Humphreys of JH Consulting (who also generously provided use of his back garden for mud sieving). Roger Bamber at Artoo Consulting identified a subset of my lagoon samples to species level. Robert Gifford and the Stour Ringing Group’s expertise in mist-netting shorebirds allowed me to collect precious avocet faecal samples. Toby Branston, Craig Daters and colleagues at Arne RSPB Reserve and Chris Thain of the Dorset Wildlife Trust, Brownsea Island, provided access to my study sites (I am particularly grateful for the use of the overnight facilities at the villa on Brownsea Island). Hein van Grow at the Natural History Museum, Tring, provided access to the preserved avocet specimens. The British Trust for Ornithology (BTO), the Dorset Environmental Records Centre (DERC) and Dorset Bird Club (DBC) provided bird count data. My work has benefited from enlightening discussions with the following people: Ralph Clarke, Duncan Golicher, Rob Britton and Dan Franklin at Bournemouth University; Steven Pearce at the Poole Harbour Commission; Richard Caldow of Natural England; Richard Barnes at Cambridge University; David and Pat Wileman; and John Goss-Custard. Credit must go also to the kind souls who provided laboratory and field assistance (especially on the really cold, wet days): Ralf Hübner, Duncan Golicher, Sally Keith, Ann Thornton, Jen Morgan, Kevin Nakonechny, Elizabeth White, Jon Mace, Sam Cottingham, Reece Woolgar, Jane Wilkin, Sarah Kerr, Steven Colledge, Christopher Butler, Stephen Treby, David Bray, Christopher Ranford, Michael Strowger, Matt Harris, Clare Dean, Carolina Castro, Sam Manning, Alex Lovegrove, David Fletcher, Kat Evans, David Pearce, Jessica Tasker, Lee Broderick, Tristan Chekkaba, Thomas Haley, Gary Hedges, Robert Bennett, Dan Gracias, Gary White, Ross Wheeler, and Joanne Clarke. I am most grateful to the Moody family for their support in my final year, and particularly to Chris for daily sustenance and encouragement. Last, but not least, I am grateful to my mum for a lifetime of support and inspiration, my dad for encouraging me to keep an open mind and a full toolbox, and the friends and family who make it all worthwhile. 5 Table of Contents Title page 1 Copyright statement 2 Declaration 3 Abstract 4 Acknowledgements 5 Table of contents 6 List of tables 11 List of figures 12 List of appendices 17 List of abbreviations 19 Chapter 1: Introduction 20 1.1 Abstract 20 1.2 Wider context and rationale 21 1.2.1 The extent and importance of coastal habitats 21 1.2.2 Threats to coastal ecosystems 22 1.2.3 Ecological impacts of environmental change in coastal habitats 23 (i) Invertebrate communities 23 (ii) Coastal bird populations 23 1.2.4 Policy governing coastal habitats 24 1.3 Predictive modelling of species distributions: a review of approaches 26 1.3.1 Species distribution modelling (SDM) 26 (i) Niche-based models 26 (ii) Demographic models 28 (iii) Process-based models 28 1.4 Study site: Poole Harbour 30 1.4.1 General geography 30 1.4.2 Ecological significance 31 1.4.3 Brownsea Island Lagoon 32 1.5 Focal species: the pied avocet (Recurvirostra avosetta) 33 1.5.1 Population trends 33 1.5.2 Wintering behaviour 33 1.5.3 The Poole Harbour avocet population 34 1.6 Scope of thesis 36 1.6.1 Aims and objectives 36 1.6.2 Thesis structure 36 6 Chapter 2: Explaining broad-scale invertebrate distribution in soft sediment intertidal habitats: insights from machine learning 39 2.1 Abstract 39 2.2 Introduction 40 2.3 Methods 42 2.3.1 Study site 42 2.3.2 Benthic community and sediment data collection 42 2.3.3 Macrofaunal processing 43 2.3.4 Sediment processing 43 2.3.5 Hydrodynamic modelling 43 2.3.6 Statistical models 45 2.4 Results 47 2.4.1 Environmental variables 47 (i) Hydrodynamics 47 (ii) Salinity 47 (iii) Sediment 47 2.4.2 Benthic community data 50 (i) How well did environmental variables explain species distribution for each year? 52 (ii) Which environmental variables were important? 54 (iii) Which species were driving the changes in community structure? 55 (iv) Spatial structuring of data 55 2.5 Discussion 58 2.5.1 Comparison of methods 60 2.5.2 Explaining species associations with environmental gradients 60 2.5.3 Spatial structure 61 2.5.4 Future research directions 61 Chapter 3: Spatial and temporal variation in lagoon macrobenthic communities 63 3.1 Abstract 63 3.2 Introduction 64 3.2.1 The importance of lagoon and estuary habitats to coastal birds 64 3.2.2 The conservation importance of lagoons 65 3.2.3 Lagoon macrobenthic communities 65 3.2.4 Aims and objectives 67 3.3 Methods and materials 68 3.3.1 Study sites 68 3.3.2 Study design 68 3.3.3 Sampling 68 3.3.4 Biomass quantification 70 3.3.5 Data analysis 71 3.4 Results 72 3.4.1 Macrobenthic communities 72 3.4.2 Seasonal variation in invertebrate abundance 74 3.4.3 Spatial variation in invertebrate abundance 75 3.4.4 Seasonal variation in biomass 76 3.4.5 Spatial variation in biomass 78 3.4.6 Size-frequency distributions of selected taxa 79 3.4.7 The annelid-gastropod biomass
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