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Landscape Genetics of a Seagrass Species in a Tidal Mudflat Lagoon

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Landscape Genetics of a Seagrass Species in a Tidal Mudflat Lagoon Landscape genetics of a seagrass species in a tidal mudflat lagoon Buga Berković Tese para a obtenção do grau de doutor Doutoramento em Ciências do Mar, da Terra e do Ambiente Ramo Ciências do Mar Especialidade de Ecologia Marinha Orientadores Prof. a Dr. a Ester Serrão Prof. Dr. Filipe Alberto Faro 2015 Landscape genetics of a seagrass species in a tidal mudflat lagoon Buga Berković This dissertation is submitted to the University of Algarve, for the degree of Doctor of Philosophy in Sciences of Sea, Earth and Environment, area Marine Sciences, specialization Marine Ecology Supervisors: Prof. Dr. Ester Serrão Prof. Dr. Filipe Alberto Faro 2015 Declaração de autoria de trabalho Tese: Landscape genetics of seagrass species in a tidal mudflat lagoon Declaro ser a autora deste trabalho, que é original e inédito. Autores e trabalhos consultados estão devidamente citados no texto e constam da listagem de referências incluídas. © Copyright: Buga Berković A Universidade do Algarve tem o direito, perpétuo e sem limites geográficos, de arquivar e publicitar este trabalho através de exemplares impressos reproduzidos em papel ou de forma digital, ou por qualquer outro meio conhecido ou que venha a ser inventado, de o divulgar através de repositórios científicos e de admitir a sua cópia e distribuição com objetivos educacionais ou de investigação, não comerciais, desde que seja dado crédito ao autor e editor. 1 Apoio A presente tese teve o apoio da Fundação para a Ciência e Tecnologia (FCT), através da bolsa SFRH/BD/68570/2010 e do projecto RiaScapeGen PTDC/MAR/099887/2008 (PI Filipe Alberto). A secção de trabalho mostrada no capítulo dois foi financiada pela infraestrutura europeia ASSEMBLE (acordo de subvenção n. 227799) concedidos para o projecto DISPERSE. O trabalho foi realizado no laboratório do grupo MAREE no Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal. 2 Support This thesis was funded by Portuguese Science Foundation (FCT) through the doctoral grant SFRH/BD/68570/2010 and the project RiaScapeGen PTDC/MAR/099887/2008 (PI Filipe Alberto). Section of work shown in chapter two was funded by EU FP7 research infrastructure initiative Assemble (grant agreement no. 227799) awarded for the project DISPERSE. Work was carried out in the laboratory of MAREE group in the Centre of Marine Sciences CCMAR, University of Algarve, Campus Gambelas, Faro, Portugal. 3 Acknowledgments While working on this thesis, I have been very fortunate and immensely grateful for the love and support of colleagues, friends and family. First, I wish to thank my supervisors Filipe Alberto and Ester Serrão for this fantastic opportunity and experience. Regardless of the distance, time of the day or other duties they had, they were there for me and I’ve learnt so much from them. Filipe, thank you for the countless hours of Skype, for the cosy space to experience the cold Milwaukee winter and all the patience and care you put into me and this work. Ester, thank you for being there any time I needed you, for constant support, all the ideas and advice you gave me. I’d like to also extend my gratitude to Susana Cabaço, an unofficial supervisor, for giving up much of her time to share her knowledge of science, seagrasses and life with me. I wish to thank the MAREE lab group in CCMAR where an essential part of this work was carried out. Most importantly I’d like to acknowledge Nelson and Licínia. You know what you did, and you know what it means for this thesis and me. You are both incredible and I wouldn’t hesitate a moment to work again with you. Fieldwork in the mudflats of the Ria Formosa was unique but dirty work and luckily there is a long list of people to thank! Firstly, Diogo and Sue, who ventured into the deepest mud with me. And everyone who lent a hand, Francisco, Carmen, Licínia, Nelson, Maria, Juan, Filipe, Onno and my skippers - Bruno C. and Bruno F. I thank you all from the bottom of my heart. For every breaking dawn, every hot midday sun, every low tide that exposed the wonderful world of mud and seagrasses. For all the mud, sweat, the car rides, kilometres in kayaks, skipper services, and the best company I could ever wished for. It was the experience of a lifetime and I would gladly repeat it with all of you! I also wish to thank the other researchers and colleagues with whom I collaborated for a number of different tasks that made this thesis possible. They are Pedro Duarte, Fernando Canovas, Rui Santos, Per Jonsson, João Reis, Oscar Ferreira and Andre Pacheco. Thanks go also to my two students, who helped me with my work but also helped me to learn how to teach, collaborate and mentor, Sue and Federica, thank you. Next, to my friends and family. I am lucky to have met so many amazing people throughout this journey. These friends have literally become a family to me, my Faro family, 4 became a part of me. They have helped me to come where I am and were present at every step along the way. This was more than I could have ever asked for. I thank you for living with me, letting me in your homes, fighting through the bureaucracy with me, being my personal translators, drivers, drinking buddies, tourist guides, hiking buddies, cooking partners and most of all friends. In more or less chronological order: Catarina C., Maria, Carlos, Ana C., Ana L., Joana B., Nelson, Diogo, Gonçalo, Tania A., Tania P., Xana, Dinarte, Joana M., Licínia, André, Patricia, Carlos S., Carla, Ruben and Rita, thank you! And a special thank you to my Croatians in Portugal, Martina and Marin, thanks for endless great days of feeling like home! Lara, Anja, Bruna, Miguel and Juan … few words can suffice. You made the difference. You are with me, no matter how scattered around the world we are. Because of you distance doesn’t matter, time zones are just a thing to keep us awake until weird hours and home is all over the world. I love you guys! Finally and most importantly – mama, tata i buraz, volim vas najviše na svijetu i hvala za sve što ste istrpili i sve što činite za mene. Ne bih bila ovo što jesam bez vas! 5 Abstract In this thesis I looked at different components of dispersal in the seagrass Zostera noltii , from the dispersal potential of both sexual and asexual propagules to indirect genetic estimation and landscape genetics analysis. Methodological approaches The first part of the work focused on understanding the dispersal biology of the species, previously undescribed. Dispersal is defined by three phases: propagule separation, transport and settlement. Initial phases of dispersal were studied in the experimental study aiming to define the dispersal potential of the propagules. In the following study I evaluated success of post-dispersal settlement of the fragments – propagules shown to have the highest dispersal potential. To evaluate dispersal potential of sexual and asexual propagules of Z. noltii I quantified spatial and temporal scales of possible dispersal in still water and under different currents. I estimated sinking rates of seeds and changes over time in shoot buoyancy, shoot viability, fragment breakage, shoot growth rate and spathe release rate of floating fragments. To determine the fate of fragments after the dispersal, I quantified survival, rooting and development of vegetative fragments following dispersal and settlement. In case of successful establishment I analysed parameters which might depict the future of the established fragment, i.e. state of the apical shoot, branching and biomass. I tested the effect of two independent factors - the initial fragment size and the dispersal regime, i.e. different ratios of period of floating and settlement in sediment within 10 weeks of experiment. The second part of this thesis aimed to estimate the spatial genetic structure across the whole population of Z. noltii in the Ria Formosa lagoon (about 84 km 2), using an individual-based sampling design where four ramets were sampled in each of 803 sampling plots randomly distributed over this seagrass habitat. Sampled ramets were processed utilizing nine polymorphic microsatellite markers to identify their multi locus genotypes (MLGs). Then I looked at the frequency of sampling particular MLGs (clonal frequency) and the spatial distribution of MLGs sampled multiple times. Due to the wide spatial distribution of clones observed, I applied a commonly used clonal age estimation method which excludes the possibility of long distance dispersal of vegetative fragments (LDD), but iteratively corrected the age estimates in each step by combining sampling locations with spatially 6 explicit sea-level data for the time the clone would have been initiated. Finally, I looked at the association between disturbance, i.e. sediment dynamics associated with the barrier islands, and clonal richness at the landscape scale. The final chapter of this thesis presents the results of high resolution landscape genetics analyses carried out on the same data set as the clonal structure analysis. I used the digital terrain model to extract spatial variables (elevation, slope, aspect, curvature of the terrain), while the dynamic parameters (current velocity, direction and flow) were obtained from the hydrodynamic model EcoDynamo. Identification of clusters or groups was done using different clustering methods implemented in STRUCUTRE software, Geneland package and Discriminant Analysis of Principal Components. Spatial autocorrelation analysis was used to test the hypothesis of random spatial distribution of MLGs. Linear models served to test the association between landscape-derived pairwise distances and the pairwise genetic distances (Loiselle kinship coefficient). The dependent variables were Euclidian distance and four additional measures of connectivity across the landscape (cost distance, hydrographical distance and two tide-dependent resistance distances).
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