FACULTY OF SCIENCE Food resources of Lake Tanganyika sardines Metabarcoding of the stomach content of Limnothrissa miodon and Stolothrissa tanganicae Charlotte HUYGHE Supervisor: Prof. F. Volckaert Thesis presented in Laboratory of Biodiversity and Evolutionary Genomics fulfillment of the requirements Mentor: E. De Keyzer for the degree of Master of Science Laboratory of Biodiversity and Evolutionary in Biology Genomics Academic year 2018-2019 © Copyright by KU Leuven Without written permission of the promotors and the authors it is forbidden to reproduce or adapt in any form or by any means any part of this publication. Requests for obtaining the right to reproduce or utilize parts of this publication should be addressed to KU Leuven, Faculteit Wetenschappen, Geel Huis, Kasteelpark Arenberg 11 bus 2100, 3001 Leuven (Heverlee), Telephone +32 16 32 14 01. A written permission of the promotor is also required to use the methods, products, schematics and programs described in this work for industrial or commercial use, and for submitting this publication in scientific contests. i ii Acknowledgments First of all, I would like to thank my promotor Filip for giving me this opportunity and guiding me through the thesis. A very special thanks to my supervisor Els for helping and guiding me during every aspect of my thesis, from the sampling nights in the middle of Lake Tanganyika to the last review of my master thesis. Also a special thanks to Franz who helped me during the lab work and statistics but also guided me throughout the thesis. I am very grateful for all your help and advice during the past year. I would also like to thank all the people from the LBEG lab, including the other master students, especially Dorien, for giving ideas and advice. I want to thank VLIR-UOS and KU Leuven for giving me the opportunity to travel abroad for my master thesis. During my sampling trip to Uvira in Congo I met a lot of wonderful people who put a lot of effort in their work. A great thanks to the people from the hydrobiological research centre CRH in Uvira, especially Pascal, Mulimbwa, Fidel, Kaps, Kambale, Eugène, Innocent, Papy, Deo and all the other wonderful people. They helped me with sampling, dissections and zooplankton identification, and gave me a lot of advice and information that I used in my master thesis. I also want to thank the Belgian people that joined me in Congo including Leona, Maarten, Maarten and Joost who inspired me with their research. I learned a lot about Congo and the fauna of Lake Tanganyika. A special thanks to my family who always supported me while I chased my dream of becoming a biologist. I couldn’t have done it without you. I want to thank my close friends who supported me at all times and who gave me amazing memories of my student time. But I would also like to thank all my friends and the wonderful people that I met over the years, both from Belgium and other places. Many of you inspired me with your passion and endurance. At last, I would like to thank all the sardines and zooplankton that gave their life for this thesis. iii Table of contents Acknowledgements ................................................................................................................... iii Table of contents ....................................................................................................................... iv Abbreviations ............................................................................................................................ vi Summary .................................................................................................................................. vii Samenvatting ........................................................................................................................... viii Introduction ................................................................................................................................ 1 1.1 Understanding Ecosystem-Based Fisheries Management ........................................... 1 1.2 Lake Tanganyika ......................................................................................................... 3 1.2.1 Geology and geography ....................................................................................... 3 1.2.2 Limnology and seasonality ................................................................................... 4 1.2.3 Biodiversity .......................................................................................................... 5 1.2.4 The pelagic ecosystem ......................................................................................... 5 1.3 The clupeid species ...................................................................................................... 8 1.3.1 Stolothrissa tanganicae ........................................................................................ 9 1.3.1.1 Ecology of Stolothrissa tanganicae ..................................................................... 9 1.3.1.2 Food sources of Stolothrissa tanganicae ........................................................... 10 1.3.2 Limnothrissa miodon .......................................................................................... 11 1.3.2.1 Ecology of Limnothrissa miodon ....................................................................... 11 1.3.2.2 Food sources of Limnothrissa miodon ............................................................... 13 1.4 Fisheries: opportunities and threats ........................................................................... 13 1.4.1 Fisheries ............................................................................................................. 13 1.4.2 Pollution ............................................................................................................. 16 1.4.3 Global warming .................................................................................................. 17 2 Aim ................................................................................................................................... 19 3 Material and Methods ....................................................................................................... 20 3.1 Sampling .................................................................................................................... 20 3.2 Dissection .................................................................................................................. 21 3.3 Metabarcoding stomach content ................................................................................ 23 3.4 Species identification ................................................................................................. 25 3.5 COI sequencing of zooplankton species .................................................................... 26 3.6 Data filtering and statistical analysis ......................................................................... 28 iv 4 Results ............................................................................................................................... 30 4.1 Sardine species identification .................................................................................... 30 4.2 Stomach content ........................................................................................................ 30 5 Discussion ......................................................................................................................... 36 5.1 Experimental design .................................................................................................. 36 5.2 The effect of species, location, season and body size ............................................... 38 5.3 Prey composition ....................................................................................................... 39 5.4 Implications for trophic relationships ........................................................................ 43 5.5 Potential trophic cascades .......................................................................................... 44 6 Conclusion and future perspectives .................................................................................. 47 7 References ......................................................................................................................... 48 Addendum .............................................................................................................................. A.1 A Risk assessment ....................................................................................................... A.1 B Tables and Figures ................................................................................................... A.3 C Previous presentations ........................................................................................... A.11 v Abbreviations COI – cytochrome c oxidase subunit 1 gene EBFM – Ecosystem-Based Fisheries Management ITCZ – Intertropical convergence zone LM – Limnothrissa miodon LT – Lake Tanganyika Mya – million years ago N – nitrogen P – phosphor PCR – polymerase chain reaction PCoA – principal coordinate analysis SDG – Sustainable Development Goals SL – standard length ST – Stolothrissa tanganicae vi Summary The sardines from Lake Tanganyika in Africa are an important food source for millions of people living around the lake. Stocks of Stolothrissa tanganicae and Limnothrissa miodon have been declining over the years due to overfishing, climate change and other anthropogenic