ASSESSING THE IMPACTS OF INTENSIVE FOREST PRACTICES ON BIODIVERSITY IN FRAGMENTED LANDSCAPES IN PORTUGAL Maria Joana Gonçalves Pereira da Cruz Doctor of Philosophy University of York Environment January 2014 ABSTRACT The Mediterranean basin is a biodiversity hotspot which is being threatened by land abandonment and afforestation, most notably with eucalypt plantations, but little research has been done to assess their impact. This study evaluated the impact of eucalypt plantations on biodiversity in the Mediterranean area, taking Portugal as a case study and amphibians, bats and carnivores as the target groups. The impact of eucalypt cover and other landscape, stand and local variables was evaluated in relation to: species richness and species occurrence for amphibians, namely if amphibian species occurrence is influenced by local characteristics (micro- scale), land-use cover (migration and dispersion-scale) or a mix of both and whether the effects differ if the main cover is eucalypt plantations or montado; species richness, bat activity, Kuhl’s bat Pipistrellus kuhlii (the most abundant bat species in the area) activity, for bats; and species occupancy and detection and spatial and temporal co-occurrence patterns for carnivores. Amphibian species occurrence was, generally, not influenced by eucalypt cover, with the exception of the newt Lissotriton boscai, which was negatively affected, and Salamandra salamandra, which was positively affected. Overall, eucalypt plantations had a negative impact on bat activity, species richness and Pipistrellus kuhlii activity and negatively influenced carnivore detection probability across all species in both single and co-occurrence models. Eucalypt plantations had a negative effect on red fox (Vulpes vulpes) occupancy, whilst stone marten (Martes foina) and badger (Meles meles) preferred native land covers. However, eucalypt plantations had no effect on the interactions within this carnivore community. This study confirms the negative impact of eucalypt plantations on bats and carnivores and suggests forest management guidelines to improve biodiversity at the stand and landscape scale. Namely, at a local scale, the implementation of a pond network of different hydroperiods and the exclusion/removal of exotic fish and promotion of understorey vegetation on eucalypt stands; at a landscape scale, it is suggested a multi-functional landscape, promoting eucalypt plantations with diverse age stands and the maintenance/promotion of native and patchy habitats. 2 CONTENTS ABSTRACT 2 CONTENTS 3 LIST OF TABLES 7 LIST OF FIGURES 8 ACKNOWLEDGEMENTS 9 AUTHOR’S DECLARATION 10 CHAPTER 1 ............................................................................................................. 11 Introduction 11 1.1. Forest plantations 11 1.1.1 Effects of forest plantations on biodiversity 11 1.1.2 Effects of silvicultural practices on biodiversity 15 Mechanical site preparation 16 Thinning 16 Clear-cut 17 Removal of residual biomass 17 Short rotation 17 1.1.3 Use of exotic trees: the case-study of the eucalypt 18 1.2. Mediterranean basin 20 1.2.1 Biodiversity 20 1.2.2 Montados 21 Threats 22 1.2.3 Eucalypt plantations in the Mediterranean region 24 1.3. Focal species 25 1.3.1 Amphibians 26 1.3.2 Bats 28 1.3.3 Carnivores 29 1.4. The thesis 31 1.4.1 Study aims 31 1.4.2 Thesis structure 31 References 32 CHapter 2 .................................................................................................................. 51 3 Exotic fish in exotic plantations: a multi-scale approach to understand amphibian occurrence in the Mediterranean region 51 Preface 51 References 52 Abstract 53 Introduction 54 Materials and Methods 57 Study Area 57 Field sampling 58 Local scale 60 Intermediate scale 60 Broad scale 60 Model building and model selection 60 Results 63 Scale analysis 63 Pleurodeles waltl 65 Salamandra salamandra 71 Lissotriton boscai 71 Triturus marmoratus 73 Pelobates cultripes 74 Hyla arborea/meridionalis 74 Species richness 74 Discussion 75 References 80 Supporting Information 89 CHAPTER 3 ............................................................................................................. 95 Effects of exotic eucalypt plantations on native bats in a Mediterranean landscape 95 Preface 95 References 96 ABSTRACT 98 1. Introduction 99 2. Materials and methods 100 2.1. Study area 100 4 2.2. Sampling methodology 102 2.3 Bat sampling 103 2.4 Habitat structure 104 2.5 Data analyses 104 3. Results 106 4. Discussion 115 Acknowledgements 118 References 118 Supplementary Material 125 CHAPTER 4 ........................................................................................................... 134 Influence of exotic forest plantations on occupancy and co-occurrence patterns in a Mediterranean carnivore guild 134 Preface 134 References 135 Abstract 136 Keywords 137 Introduction 137 Materials and methods 141 Site description 141 Camera trapping 142 Explanatory variables 143 Single-species occupancy models 144 Two-species occupancy models 145 Temporal co-occurrence 146 Results 147 Single-species occupancy models 147 Species co-occurrence 150 Temporal partitioning 153 Discussion 155 Acknowledgements 158 References 158 Supplementary Information 165 CHAPTER 5 ........................................................................................................... 167 DISCUSSION 167 5 5.1 Summary 167 5.2 Eucalypt plantations: impact on biodiversity 169 5.3 Forest management practices to promote biodiversity 169 Ponds and fish exclusion 170 Promotion of understorey vegetation 170 Promotion of diverse age stand plantations 170 Promotion of patchy landscape 171 5.4 Eucalypt plantations, biodiversity and silvicultural practices – needs for future research 172 References 173 6 LIST OF TABLES Table Page number Chapter 1 Table 1 Impacts of forest plantations on the ecosystem 12 Chapter 2 Table 1 Species occurrence and species richness 64 Table 2 Coefficient estimates of the model averaged (top- ranked models) for each of the response variables 69 Table S1 Model selection results for analysis of the species occurrence and species richness 89 Chapter 3 Table 1 Summary of bat activity and species richness in eucalypt plantations and montados 108 Table 2 Model averaged coefficients for the variables of the top-ranked models 109 Table S1 Variables description 125 Table S2 Variables mean, standard deviation and Kruskal- Wallis results 129 Table S3 Summary of models showing Akaike information criteria corrected for small samples 130 Chapter 4 Table 1 Data for the four camera trap surveys 143 Table 2 Comparison of models exploring the land cover and landscape metrics on occupancy 149 Table 3 Comparison of co-occurrence models 152 Table S1 Variables description 176 7 LIST OF FIGURES Figure Page number Chapter 1 Figure 1 Distribution of the cultivated eucalypt plantations worldwide 19 Figure 2 Examples of montados in the study area 22 Figure 3 Eucalypt plantations in the study area 25 Chapter 2 Figure 1 The location of the study area 59 Figure 2 Flowchart describing the statistical analysis used 62 Figure 3 Fitted values predicted by the averaged models for each of the response variables 72 Chapter 3 Figure 1 Map of the study area 101 Figure 2 Fitted values predicted by the averaged models for each of the response variables 113 Chapter 4 Figure 1 Diagram with the hypothesis tested 140 Figure 2 Study area and the location of the camera traps 142 Figure 3 Mean and standard error for the probability of occupancy and detection 147 Figure 4 Estimated probability of detection as a function of eucalypt cover 148 Figure 5 Estimated probability of site occupancy 150 Figure 6 Probabilities of detection (±SE) estimated from two- species co-occurrence models 151 Figure 7 Coefficient of overlapping of daily activity patterns 154 8 ACKNOWLEDGEMENTS First and foremost, I would like to thank Piran White, Miguel Carretero and Hugo Rebelo for their guidance throughout my PhD. I was very lucky to have three excellent supervisors who were so dedicated. They provided knowledge, support and encouragement every time I needed. I gratefully acknowledge Fundação para a Ciência e a Tecnologia for funding my PhD. I thank the private landowners for allowing me access to their montados. I would also like to thank pulp mill company ALTRI, SGPS, S.A., especially Henk Feith, Luis Ferreira, Pedro Serafim and Mr. Arlindo, for granting me access to their properties, let me use Galisteu cottages, and help with GIS shapefiles. Their help was essential. I am indebted to every staff member that help me out in my data analysis and brainstorms, especially Colin McClean, Bryce Beukers-Stewart, Andrew Marshall and Dave Raffaelli. Also thanks to Phil Platts and Howard Peters who helped me out so much. Thank you to all my new friends that made me feel so welcomed in the Environment Department. You made this PhD a fun journey. Finally, a special thank you to Pedro for all his support throughout my PhD. He invested considerable amount of his time, night and day, to help me on my fieldwork, data analysis, and holding the fort so I could do this. He looked after our cats and dogs and managed to stay sane. Pedro, without you, this thesis would not have been possible. 9 AUTHOR’S DECLARATION The sampling survey was jointly designed by Dr. Miguel A. Carretero (Chapter 2), Dr. Hugo Rebelo (Chapter 3) and Dr. Pedro Sarmento (Chapter 4). The fieldwork for Chapter 2, Chapter 3 and Chapter 4 was carried out with the collaboration of Dr. Pedro Sarmento who also