UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL ACTIVITY, DISTRIBUTION AND MICROHABITAT USE BY THE IMPERILLED MIRA CHUB SQUALIUS TORGALENSIS Joana Maria Sofio Martelo Callapez Martins DOUTORAMENTO EM BIOLOGIA (Especialidade Ecologia) 2014 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL ACTIVITY, DISTRIBUTION AND MICROHABITAT USE BY THE IMPERILLED MIRA CHUB SQUALIUS TORGALENSIS Joana Maria Sofio Martelo Callapez Martins Tese orientada pela Professora Maria Filomena Magalhães e pelo Professor Gary Grossman, especialmente elaborada para a obtenção do grau de doutor em Biologia, especialidade Ecologia 2014 This dissertation should be cited as follows: Martelo, J. (2014) Activity, distribution and microhabitat use by the imperilled Mira chub Squalius torgalensis. PhD Thesis, Universidade de Lisboa, Portugal. Preliminary notes According with the Article 41 no 1 of the Post-Graduate Studies Regulation of the University of Lisbon (Diário da República II série nº 209 de 30 de Outubro de 2006), the current dissertation includes papers published or in preparation in co-authorship. As doctoral candidate presenting this dissertation, I was responsible for the study designs, data collection, statistical analyses and writing. The advisors of the thesis were deeply involved in the research conceptual framework and in all stages of the studies, being co-authors of the papers. This thesis was supported by the Portuguese Science and Technology Foundation (SFRH / BD / 35942 / 2007). Ao António e à estrelinha Index Acknowledgments/Agradecimentos .............................................................................................. i Resumo ......................................................................................................................................... iii Abstract ........................................................................................................................................ vii Chapter 1. General introduction .............................................................................................. 2 1.1. Setting the scene ................................................................................................................ 3 1.2. Spatial distribution and microhabitat use of stream fishes................................................. 4 1.3. Mechanistic approaches to microhabitat use of stream fishes .......................................... 5 1.4. Activity patterns of stream fishes ....................................................................................... 7 1.5. Fishes microhabitat use and activity in the context of Mediterranean streams ................ 9 1.6. Study objectives and approach ......................................................................................... 11 1.7. Thesis organization ........................................................................................................... 13 1.8. References ........................................................................................................................ 15 Chapter 2. Extrinsic and intrinsic factors influence daily activity of a Mediterranean cyprinid ..................................................................................................................................................... 25 2.1. Abstract ............................................................................................................................ 27 2.2. Introduction ...................................................................................................................... 28 2.3. Methods ............................................................................................................................ 30 Study site .................................................................................................................................. 30 Environmental data and daily activity patterns ............................................................................ 31 Statistical analyses ..................................................................................................................... 33 2.4. Results .............................................................................................................................. 37 Daily activity patterns................................................................................................................. 37 Extrinsic and intrinsic influences on behaviour ............................................................................. 38 2.5. Discussion ......................................................................................................................... 42 2.6. References ........................................................................................................................ 46 2.7. Corrigendum .................................................................................................................... 52 Chapter 3. Habitat patchiness affects distribution and microhabitat use of endangered Mira chub Squalius torgalensis ............................................................................................................... 53 3.1. Abstract ............................................................................................................................ 55 3.2. Introduction ...................................................................................................................... 56 3.4. Methods ............................................................................................................................ 58 Study species ............................................................................................................................. 58 Study reaches ............................................................................................................................ 58 Sampling regime ........................................................................................................................ 60 Fish and habitat sampling .......................................................................................................... 60 3.5. Data analysis ..................................................................................................................... 62 Variation in habitat characteristics .............................................................................................. 63 Spatial patterns in chub abundance ............................................................................................ 64 Microhabitat use by chub ........................................................................................................... 65 3.6. Results .............................................................................................................................. 67 Variation in habitat characteristics .............................................................................................. 67 Spatial patterns in chub abundance ............................................................................................ 69 Microhabitat use by chub ........................................................................................................... 75 3.7. Discussion ......................................................................................................................... 80 3.8. References ........................................................................................................................ 85 3.9. Supplementary material .................................................................................................... 90 Chapter 4. Linking microhabitat use with models of foraging success in the endangered Mira chub Squalius torgalensis ............................................................................................................... 94 4.1. Abstract ............................................................................................................................ 95 4.2. Introduction ...................................................................................................................... 96 4.3. Methods ............................................................................................................................ 98 Study reaches and species .......................................................................................................... 98 Microhabitat availability and use .............................................................................................. 100 Foraging success experiments ................................................................................................... 101 4.4. Data analyses .................................................................................................................. 104 4.4.1. Microhabitat availability and use .................................................................................. 104 4.4.2. Foraging success .......................................................................................................... 105 Proportion of fish capturing prey ............................................................................................... 105 Capture success and reactive distance ...................................................................................... 106 4.4.3. Model selection and averaging....................................................................................