UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS Evaluation of thermal stress in tropical marine organisms in the context of climate warming Doutoramento em Biologia Especialidade em Biologia Marinha e Aquacultura Sara Carolina Gusmão Coito Madeira Tese orientada por: Doutora Catarina Vinagre Professor Doutor Mário Diniz Professor Doutor Henrique Cabral Documento especialmente elaborado para a obtenção do grau de doutor 2018 2018 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS Evaluation of thermal stress in tropical marine organisms in the context of climate warming Doutoramento em Biologia Especialidade em Biologia Marinha e Aquacultura Sara Carolina Gusmão Coito Madeira Tese orientada por: Doutora Catarina Vinagre Professor Doutor Mário Diniz Professor Doutor Henrique Cabral Documento especialmente elaborado para a obtenção do grau de doutor 2018 2018 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS Evaluation of thermal stress in tropical marine organisms in the context of climate warming Doutoramento em Biologia Especialidade em Biologia Marinha e Aquacultura Sara Carolina Gusmão Coito Madeira Tese orientada por: Doutora Catarina Vinagre Professor Doutor Mário Diniz Professor Doutor Henrique Cabral Júri: Presidente: ● Doutora Maria Manuela Gomes Coelho de Noronha Trancoso, Professora Catedrática e Membro do Conselho Científico, Faculdade de Ciências da Universidade de Lisboa Vogais: ● Doutor Luís Miguel dos Santos Russo Vieira, Investigador Auxiliar, Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR) da Universidade do Porto ● Doutora Maria Helena Ferrão Ribeiro da Costa, Professora Catedrática, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa ● Doutora Ana Margarida da Silva Faria, Investigadora, Centro de Ciências do Mar e do Ambiente (MARE) no ISPA – Instituto Universitário de Ciências Psicológicas, Sociais e da Vida ● Doutor José Pavão Mendes de Paula, Professor Associado com Agregação, Faculdade de Ciências da Universidade de Lisboa ● Doutora Catarina Maria Batista Vinagre, Investigadora FCT “nível inicial”, equiparação a Investigador Auxiliar da carreira de investigação científica, Faculdade de Ciências da Universidade de Lisboa Documento especialmente elaborado para a obtenção do grau de doutor Fundação para a Ciência e Tecnologia (FCT) 2018 2018 This study was funded by Fundação para a Ciência e Tecnologia, through a PhD scholarship SFRH/BD/92975/2013 and the research project WarmingWebs (PTDC/MAR-EST/2141/2012). Additional funding was provided by the strategic projects UID/MAR/04292/2013 granted to MARE and UID/Multi/04378/2013 granted to UCIBIO. i ii Nota prévia A presente tese apresenta artigos científicos já publicados ou submetidos para publicação (capítulos 2 a 8), de acordo com o previsto no n˚2 do artigo 25˚ do Regulamento de Estudos de Pós Graduação da Universidade de Lisboa, publicado em Diário da República 2ª série – N˚57 – 23 de Março de 2015. Uma vez que estes trabalhos foram realizados em colaboração, a candidata esclarece que participou integralmente na concepção dos trabalhos, obtenção de dados, análise e discussão dos resultados, bem como na redacção dos manuscritos. Lisboa, Março de 2018 Carolina Madeira iii iv “I like the scientific spirit — the holding off, the being sure but not too sure, the willingness to surrender ideas when the evidence is against them: this is ultimately fine — it always keeps the way beyond open — always gives life, thought, affection, the whole man, a chance to try over again after a mistake — after a wrong guess.” Walt Whitman Walt Whitman's Camden Conversations v vi Acknowledgements Someone once said “many times a day I realize how much my own outer and inner life is built upon the labors of my fellow people, both living and dead, both known and unknown and how I earnestly must exert myself in order to give in return as much as I have received”. I believe these words fully express the extent of my gratitude towards all the people that walked with me through the PhD journey, guiding, advising and supporting me in the ups and downs. If nothing else, this PhD pursuit has taught me that we are here for the sake of each other, human beings connected with the purpose of helping each other grow, and, in that way – helping us all evolve as a species. I will try - hoping words will not fail me, to express how thankful I am to each and everyone that made this work possible. Firstly, I thank Fundação para a Ciência e Tecnologia for giving me a PhD grant that made my dream of pursuing a career in Science come true. Then, I would like to thank my wonderful supervisors: Catarina Vinagre, Mário Diniz and Henrique Cabral. Your vision, hard work and ethics in science have been an inspiration to me and I’ll always admire you. You have given me all the tools I needed to accomplish this academic achievement, but, in fact, you have given me more: your time, your patience, your knowledge and life experience and your friendship. You have given me a piece of yourselves, of your lives, and for that, I cherish you. You helped me to be confident and believe in myself, knowing I had “all it takes” to get the job done. With the trust and freedom you gave me, I grew to be an autonomous researcher, yet unafraid to ask for help and guidance when I need it. That is something I will always be thankful for. Catarina, I am so grateful you proposed me this PhD, allowing me to follow my passion for tropical marine ecology. This PhD brought me amazing opportunities, not only to work with charismatic species, but also to travel to some incredible places during fieldwork and just feel amazed every day I stepped outside and into some beautiful tropical beach! You made me reach my life goal of living in shorts and flip-flops (and we both know I am a warm-adapted organism)!! Check √ You were tireless in your efforts to provide me with everything I needed. I am proud to have been your apprentice, and your perseverance in the difficult academia world has taught me immensely. Mário, you were a solid pillar during my lab work. Your guidance allowed me to refine my practice in molecular ecology and your scientific curiosity was a source of creativity in our vii scientific discussions. You taught me almost everything I know about biochemistry and metabolism. You are one of the most understanding and patient scientists I’ve ever met, and I knew I could always count on your wise words when the lack of motivation sometimes kicked in. I am also very thankful that you always encouraged me to go to scientific meetings and presentations, providing me with financial resources to do it. I can’t thank you enough for everything you did for me, since whenever something went wrong during work you were the first one to come up with all kinds of solutions to help me. You were always available and present during these 4 years. Prof. Henrique, we first met probably a decade ago (already?!) when I was doing my bachelor in Marine Biology at FCUL. Since then I’ve always considered you one of my main and most impressive references in the marine scientific community. I’ve always looked up to you and I’ve always felt inspired not only by your academic and professional achievements, but also because you always had a kind word of encouragement to your students. So, having you as my supervisor is more than what I could’ve asked for! Your care and interest in helping me to get through the different stages of my PhD (from the doctoral program to practical work, to article writing and thesis writing) have been essential to smooth the path. Your advice during statistical analyses was essential for the progress of this work. I am deeply grateful for always making yourself available for meetings and scientific discussions. I cannot emphasize enough how much I have learned from you during my entire professional life. Thank you. I also thank Guca Flores for the collaboration with Cebimar. You provided everything that was needed for fieldwork and experiments in Brazil and I can’t thank you enough for that, it absolutely saved my work at a time when things were going wrong. It was amazing to meet you and everyone at Cebimar! Thank you for a wonderful experience and for your valuable inputs and suggestions to my work. My colleague Miguel Costa Leal, who always challenged, helped and encouraged me even at a distance. I thank you for always thinking of me when you have new ideas – I always know something productive will come out of our chats and meetings (usually one or several scientific papers in pretty good IF peer-reviewed journals)!! You gave me the incredible opportunity of having an internship at Eawag, where I learned new methods and lab techniques, which very much enriched my PhD work. I thank you for everything you taught me about statistical analyses and scientific writing, and just general biology and ecology from our scientific discussions! viii I thank Alexandra Elbakyan and the Sci-Hub team for their revolutionary project of making all scientific articles available to the public. Your project is serving the best interests of society and it should be recognized as such. You saved me on so many occasions. I don’t even know you in person, but I can honestly say you made an incredible contribution to the work of this thesis. I would now like to thank my awesome colleagues from ECCOWEBS research group (MARE – FCUL): Vanessa Mendonça, Rui Cereja, Marta Dias, Sheila Alexandre and Pedro Fernandes. You were amazing friends and we had so many joyful moments together! I keep you all very close to my heart! Oh the fun