UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL SKATES AND RAYS DIVERSITY, EXPLORATION AND CONSERVATION – CASE-STUDY OF THE THORNBACK RAY, RAJA CLAVATA Bárbara Marques Serra Pereira Doutoramento em Ciências do Mar 2010 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL SKATES AND RAYS DIVERSITY, EXPLORATION AND CONSERVATION – CASE-STUDY OF THE THORNBACK RAY, RAJA CLAVATA Bárbara Marques Serra Pereira Tese orientada por Professor Auxiliar com Agregação Leonel Serrano Gordo e Investigadora Auxiliar Ivone Figueiredo Doutoramento em Ciências do Mar 2010 The research reported in this thesis was carried out at the Instituto de Investigação das Pescas e do Mar (IPIMAR - INRB), Unidade de Recursos Marinhos e Sustentabilidade. This research was funded by Fundação para a Ciência e a Tecnologia (FCT) through a PhD grant (SFRH/BD/23777/2005) and the research project EU Data Collection/DCR (PNAB). Skates and rays diversity, exploration and conservation | Table of Contents Table of Contents List of Figures ............................................................................................................................. i List of Tables ............................................................................................................................. v List of Abbreviations ............................................................................................................. viii Agradecimentos ......................................................................................................................... x Abstract .................................................................................................................................. xiii Resumo ................................................................................................................................... xiv List of Publications .............................................................................................................. xviii 1. GENERAL INTRODUCTION .......................................................................................... 3 1.1. Objectives ....................................................................................................................... 9 1.2. Outline of the thesis ...................................................................................................... 10 2. SKATE FISHERIES ........................................................................................................ 15 2.1. Abstract ......................................................................................................................... 15 2.2. Introduction ................................................................................................................... 15 2.3. Material and Methods ................................................................................................... 17 2.3.1. Landing port selection .................................................................................... 17 2.3.2. Skates landings ............................................................................................... 18 2.3.3. Characterization of Fishing Strategies ........................................................... 19 2.4. Results ........................................................................................................................... 19 2.4.1. Landing port selection .................................................................................... 20 2.4.2. Skates landings ............................................................................................... 20 2.4.3. Characterization of Fishing Strategies ........................................................... 23 2.4.4. Description of fishing strategies ..................................................................... 23 2.5. Discussion ..................................................................................................................... 27 3. SKATE BIODIVERSITY ................................................................................................ 33 3.1. PHYLOGENY ............................................................................................................. 33 3.1.1. Abstract .......................................................................................................... 33 3.1.2. Introduction .................................................................................................... 34 3.1.3. Material and Methods ..................................................................................... 36 3.1.3.1. Sampling .................................................................................................. 36 3.1.3.2. DNA extraction, amplification ad sequencing ........................................ 36 3.1.3.3. Data analysis ............................................................................................ 37 3.1.4. Results ............................................................................................................ 39 Table of Contents | Skates and rays diversity, exploration and conservation 3.1.4.1. Intra-specific variability .......................................................................... 39 3.1.4.2. Phylogenetic analysis .............................................................................. 39 3.1.5. Discussion ...................................................................................................... 44 3.2. MORPHOMETRY ...................................................................................................... 47 3.2.1. Abstract .......................................................................................................... 47 3.2.2. Introduction .................................................................................................... 48 3.2.3. Material and Methods ..................................................................................... 50 3.2.3.1. Data analysis ............................................................................................ 51 3.2.4. Results ............................................................................................................ 52 3.2.4.1. Morphometric variation within species ................................................... 53 3.2.4.2. Species discrimination using morphometric analysis .............................. 56 3.2.5. Discussion ...................................................................................................... 58 3.3. FEEDING ECOLOGY ................................................................................................ 59 3.3.1. Abstract .......................................................................................................... 59 3.3.2. Introduction .................................................................................................... 60 3.3.3. Material and Methods ..................................................................................... 61 3.3.3.1. Sampling .................................................................................................. 61 3.3.3.2. Data analysis ............................................................................................ 62 3.3.3.2.1. Overall diet ....................................................................................... 62 3.3.3.2.2. Prey importance and feeding strategy .............................................. 62 3.3.4. Results ............................................................................................................ 63 3.3.4.1. Overall diet .............................................................................................. 63 3.3.4.2. Prey importance and feeding strategy ..................................................... 66 3.3.5. Discussion ...................................................................................................... 71 4. SKATE LIFE-HISTORY - case-study of the thornback ray, Raja clavata ..................... 77 4.1. AGE AND GROWTH ................................................................................................. 77 4.1.1. Abstract .......................................................................................................... 77 4.1.2. Introduction .................................................................................................... 78 4.1.3. Material and Methods ..................................................................................... 80 4.1.3.1. Sampling .................................................................................................. 80 4.1.3.2. Processing techniques .............................................................................. 80 4.1.3.3. Age and growth ....................................................................................... 81 4.1.4. Results ............................................................................................................ 83 4.1.4.1. Processing techniques .............................................................................. 83 4.1.4.2. Types of thorn and their suitability for age determination ...................... 83 4.1.4.3. Age and growth ....................................................................................... 86 4.1.5. Discussion ...................................................................................................... 89 4.2. REPRODUCTION .......................................................................................................