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Open Research Online Oro.Open.Ac.Uk Open Research Online The Open University’s repository of research publications and other research outputs Phylogenetics and Phylogeography in the Planktonic Diatom Genus Chaetoceros Thesis How to cite: De Luca, Daniele (2019). Phylogenetics and Phylogeography in the Planktonic Diatom Genus Chaetoceros. PhD thesis The Open University. For guidance on citations see FAQs. c 2019 The Author https://creativecommons.org/licenses/by-nc-nd/4.0/ Version: Version of Record Link(s) to article on publisher’s website: http://dx.doi.org/doi:10.21954/ou.ro.00010bf4 Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online’s data policy on reuse of materials please consult the policies page. oro.open.ac.uk THE OPEN UNIVERSITY, MILTON KEYNES (UK) STAZIONE ZOOLOGICA ANTON DOHRN, NAPLES (IT) School of Life, Health and Chemical Sciences Doctor of Philosophy (Ph.D.) Phylogenetics and Phylogeography in the Planktonic Diatom Genus Chaetoceros Daniele De Luca (M.Sc.) Personal ID: F3576948 Director of Studies External Supervisor Dr. Wiebe H.C.F. Kooistra Prof. Dr. Christine A. Maggs Stazione Zoologica Anton Dohrn, IT Bournemouth University, UK Internal Supervisor Dr. Diana Sarno Stazione Zoologica Anton Dohrn, IT September 2019 II Abstract The initial aims of this thesis were to assess the systematics of the planktonic diatom genus Chaetoceros and the phylogeographic patterns of selected species in this genus across spatial and temporal scales. As expected in every experiment, some initial ideas have been pursued as they were; others have taken a different route and led to different questions. Consequently, the systematics of Chaetoceros has become a multigene phylogeny and a revision of the classical taxonomic scheme for the family Chaetocerotaceae (Chapter II). Then, the phylogeographic approach, initially meant as a Sanger sequencing of a few genes from specimens collected around the world, turned into the analysis of the C. curvisetus cryptic species complex by using an approach which combines haplotype networks and metabarcoding data (Chapter IV). The mapping of this complex against a temporal metabarcoding dataset (MareChiara, Gulf of Naples, IT) has become a story of concerted evolution and has been extended to different Chaetoceros species and supported by a single strain 18S-V4 high throughput sequencing (Chapter V). Amid these experiments, the potential of metabarcoding data for biological recording was explored and tested in the whole genus Chaetoceros to assess diversity and distribution (Chapter III). Such data were integrated with classical ones from public repositories and literature and used to produce, among the other results, distribution maps of Chaetoceros species. III IV To my Mom, For having taken on so many burdens, allowing me to fully dedicate myself to this thesis For having endured me during my rainy days For having surrendered to the constant entry of books in the house: one day all these books will drive us away. V VI Acknowledgements It is almost impossible to thank all the people who made my time at the SZN an unforgettable and great experience. Most of them contributed with a simple “buongiorno”, a smile, or a chat on the terrace, and to them goes my gratitude. Others occupy a more special place in my heart. Therefore, my “special” thanks go… …To my Director of Studies, Dr. Wiebe Kooistra, who gave me the opportunity to carry out my Ph.D. research and the freedom to develop my ideas, showing me the way, provide guidance and alternative routes, and not dictating the rules. This is the best gift I could have ever received. … To my internal supervisor, Dr. Diana Sarno, for the taxonomic knowledge she shared with me, and her passion for diatoms, which she transmitted to me and which inspired me to immerse myself fully into the diversity of diatoms and, in particular, Chaetoceros. … To my external supervisor, Prof. Dr. Christine A. Maggs, for the time spent together during her visits at the SZN, talking about my project, science in general and ordinary life. Her suggestions and enthusiasm were pure positive energy that prompted me to do better and better. …To Dr. Roberta Piredda, for the invaluable time she invested in me teaching, discussing, listening and for her friendship. Thanks to her, I have domesticated the untamed beasts of “Linux”, “batching”, “server” and “big data”, I was introduced to the –omics world, and looked with new eyes to the ecology of communities. I own her everything I know about metabarcoding and much more about evolutionary methods for the study of biodiversity. Someone said: “together you are war machines”. Nothing more true. … To Carmen Minucci, for the training in the lab and the constant help in carrying it on. VII … To Dr. Grazia Quero, for being my friend and the best office partner I could ever have desired. Thank you for introducing me to the metagenomics world and for the constant help every time the machine took control over the man. … To Dr. Isabella D’Ambra, for the morning chats and the courage with which she faces life every day. You are an example of success. … To the old and new people of the Procaccini lab, my first house at the SZN: Gabriele, Miriam, Chiara, Emanuela, Domenico, Gaetano, Lazaro, Marlene, Lucia, Roberto, Jessica... Among you are head of departments, researchers, post-docs, but there is no “Dr” because you will be always my second family first, and then the brilliant scientists and lovely persons I have ever met. I am proud to have been a Procaccinidae. … To Dr. Graziano Fiorito, my first “official” mentor at SZN for the esteem and affection he has always shown to me. I was proud to be “his compulsive student”. … To Pamela, Elena, Giovanna, Ruth, Caitlin, Paola and Andrea of the “OctoLab” for being my friends and all the lunches and “mozzarella days” we had together. Pam, we started this adventure almost together several years ago and I am proud of how far you went. The spirit of my “Pam!” along the corridors will accompany your for many years to come. … To the people of the SBM: the big boss, Dr. Elio Biffali, who made me a better molecular biologist with his original way of teaching; Dr. Pasquale De Luca, for adopting me as “cousin” and witnessing all my feats; Elvira Mauriello and Raimondo Pannone, for all the support in molecular biology techniques and the chats and laughs together. I own you thousands of DNA sequences! … To Gabriella Grossi and Daniela Consiglio for the support in the life as Ph.D. student and student’s representative the first, and as reference student for the invited speakers the latter. Thanks for the passion you have for your work and the kindness showed. VIII Table of Contents Chapter I - Introduction 1.1. Diversity, the hallmark of living organisms 3 1.1.1. Diatom diversity and evolution 5 1.2. The species problem 8 1.2.1. Species concepts in diatoms 11 1.3. Do species really exist? 14 1.4. The need for classification 16 1.5. DNA barcoding 18 1.6. From barcodes to metabarcodes 20 1.6.1. DNA barcoding and metabarcoding in diatoms 21 1.7. Case study: the planktonic diatom family Chaetocerotaceae, with emphasis on the genus Chaetoceros 24 1.7.1. Fossil record of Chaetoceros 27 1.7.2. The ecological and evolutionary importance of Chaetoceros 28 1.7.3. Aim of Ph.D. thesis 30 References 31 Chapter II - Inferring the evolutionary history of Chaetocerotaceae 2.1. Introduction 55 2.1.1. Systematics of Chaetocerotaceae 55 2.2. Materials and methods 58 2.2.1. Taxon sampling, outgroups selection and DNA extraction 58 2.2.2. Selection of genes, amplification and sequencing 59 2.2.3. Sequence editing and alignment 61 2.2.4. Nucleotide composition and substitution saturation analyses 62 IX 2.2.5. Model selection and phylogenetic inference 62 2.2.6. Morphological sections and species assignment 63 2.3. Results 64 2.3.1. Dataset characteristics 64 2.3.2. Assignment of species to sections 67 2.3.3. Nuclear, plastid and mitochondrial phylogenies 67 2.3.4. Concatenated phylogenies 68 2.3.5. Comparison between morphological sections and molecular clades 70 2.4. Discussion 73 2.4.1. General comments to the dataset 73 2.4.2. Phylogenetic position of the genera Bacteriastrum and Chaetoceros 75 2.4.3. Subgeneric division 75 2.4.4. The sectional division 77 2.4.5. Future directions 83 References 84 Appendix II 95 Chapter III - Assessing diversity and distribution in Chaetoceros: integration of classical and novel strategies 3.1. Introduction 129 3.1.1. Primary Biodiversity Data: recording the occurrence of species 129 3.1.2. Primary Biodiversity Data for planktonic species 130 3.1.3. Aim of this work 133 3.2. Materials and methods 134 X 3.2.1. Data collected from available public repositories, literature and checklists 134 3.2.2. Data generated from molecular sources 136 3.3. Results 138 3.3.1. Data collected from available public repositories, literature and checklists 138 3.3.2. Data generated from molecular sources 142 3.4. Discussion 146 3.4.1. Global distribution of Chaetoceros 146 3.4.2. Abundance of Chaetoceros at global scale 148 3.4.3. Integration of literature and metabarcoding data: three study cases in Chaetoceros 149 3.4.4. Assessing species distribution in Chaetoceros 151 3.4.5. Future directions 151 References 152 Appendix III 163 Chapter IV - Resolving the Chaetoceros curvisetus cryptic species complex 4.1. Introduction 177 4.1.1. Cryptic species complexes: origin, distribution and methodology of study 177 4.1.2.
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