This thesis examines the biodiversity and evolutionary ecology of Lumnitzera mangroves in the Indonesian Archipelago. Using a combination of genomics and metabolomics, the study arrived at several key findings: (1) Investigation into 14 populations of L. littorea and 21 populations of L. racemosa revealed low genetic variation, with significant barriers like Sulawesi and the Java Sea influencing genetic differentiation. (2) Specifically for L. littorea, Wallace's line was identified as a key biogeographical separator, marking divergent evolutionary pathways and separating phylogroups, whereas L. racemosa showed a mixing population in the Wallacea region. (3) Uniquely, the research discovered a diversity in sulfated constituents, including previously unknown compounds like Lumnitzeralactone. (4) Further emphasizing the mangroves' medicinal importance, antibacterial potential was uncovered in the species. (5) The study innovatively linked phylogenetic data with chemical analyses, offering a comprehensive view of mangrove evolution and ecology. (6) Finally, the findings highlighted the need for specific conservation strategies, considering the genetic differentiation within populations, to protect the mangroves' ecological significance and medicinal value across Indonesia.:Preface 4 Summary 5 Zusammenfassung 10 1. Introduction 15 1.1. Characteristics, significance, and threat of mangroves 15 1.1.1. Characteristics of mangroves 15 1.1.2. Significance of Indonesian mangroves 16 1.1.3. Threats to mangroves 18 1.2. Evolutionary processes and diversity of mangroves 19 1.2.1. Evolution of mangroves 19 1.2.2. Sea surface currents in Indonesia shape genetic structure 20 1.2.3. The relevance of Wallace’s line to mangrove evolution 22 1.2.4. Isolation by geographical distance 24 1.2.5. Genetic diversity and population structure 25 1.3. Diversity of bioactive compounds of mangrove genus Lumnitzera 27 1.3.1. Sulfur-containing metabolites 27 1.3.2. Phylogenetics 28 1.3.3. Anti-infective potential 29 1.4. Study species 30 1.5. Aim of the thesis 33 2. Material and Methods 37 2.1. Sampling and sample design 37 2.2. Laboratory procedures and genetic analysis 38 2.2.1. DNA isolation 38 2.2.2. ddRADseq sequencing, and bioinformatics 38 2.2.3. Genetic diversity, population structure and differentiation 40 2.2.4. Identifying barriers and areas of connectivity 41 2.2.5. Isolation by distance and sea surface current connectivity 42 2.2.6. Polymerase Chain Reaction (PCR), and phylogenetic analyses 43 2.3. Laboratory procedures and phytochemical analysis 44 2.3.1. Root sample extraction 44 2.3.2. TLC, Low-resolution ESI-MS spectra, HPLC, and NMR 45 2.3.3. UHPLC-ESI-QqTOF-MS and MS/MS 46 2.3.4. RP-UHPLC-ESI-LIT-Orbitrap-MS 47 2.3.5. Extraction and isolation of compounds 47 2.3.6. Anti-infective bioassays 51 3. Results 52 3.1. Genetic diversity and population structure 52 3.1.1. Genetic diversity 52 3.1.2. Population structure and genetic differentiation 54 3.1.3. Effective migration 58 3.1.4. Isolation by distance and sea surface current connectivity 59 3.2. Unusual-sulfated constituent and anti-infective properties 61 3.2.1. Phytochemical screening 61 3.2.2. Phylogenetic tree of Lumnitzera 69 3.2.3. Evaluation of anti-infective properties 70 4. Discussion 74 4.1. Population genomics of Lumnitzera mangroves in Indonesia 74 4.1.1. The genetic diversity paradox in mangroves 74 4.1.2. Phylogroups and the Sunda-Wallacea biogeographical pattern 76 4.1.3. Limited mixture among phylogroups and populations by sea surface currents 78 4.1.4. Restricted gene flow by geographical distance 80 4.1.5. Evolutionary ecology of Lumnitzera inferred by genetics and chemodiversity 81 4.2. Bioactive compounds and anti-infective potential of Lumnitzera 82 4.2.1. Diversity of bioactive compounds 82 4.2.2. Sulfated and nonsulfated ellagic acid supported by phylogenetic pattern 83 4.2.3. Anti-infective properties and their restriction to particular locations 86 5. Conclusion and future perspective 89 6. References 94 7. Appendix 111 Curriculum vitae 119 Declaration of independent work 122 Acknowledgments 123 Author contributions statement 125 Authors’s Addendum / Diese Arbeit untersucht die biologische Vielfalt und evolutionäre Ökologie der Lumnitzera-Mangroven im indonesischen Archipel. Unter Verwendung einer Kombination aus Genomik und Metabolomik gelangte die Studie zu mehreren wichtigen Ergebnissen: (1) Die Untersuchung von 14 Populationen von L. littorea und 21 Populationen von L. racemosa ergab eine geringe genetische Variation, wobei signifikante Barrieren wie Sulawesi und die Javasee die genetische Differenzierung beeinflussen. (2) Speziell für L. littorea wurde die Wallace-Linie als wichtige biogeografische Trennlinie identifiziert, die divergierende Evolutionspfade markiert und Phylogruppen trennt, während L. racemosa eine Mischpopulation in der Wallacea-Region aufweist. (3) Einzigartig war die Entdeckung einer Vielfalt an sulfatierten Bestandteilen, darunter bisher unbekannte Verbindungen wie Lumnitzeralacton. (4) Ein weiterer Beleg für die medizinische Bedeutung der Mangroven ist das antibakterielle Potenzial, das in der Art entdeckt wurde. (5) Die Studie verknüpfte auf innovative Weise phylogenetische Daten mit chemischen Analysen und bot so einen umfassenden Einblick in die Evolution und Ökologie der Mangroven. (6) Schließlich verdeutlichten die Ergebnisse die Notwendigkeit spezifischer Erhaltungsstrategien, die die genetische Differenzierung innerhalb der Populationen berücksichtigen, um die ökologische Bedeutung und den medizinischen Wert der Mangroven in ganz Indonesien zu schützen.:Preface 4 Summary 5 Zusammenfassung 10 1. Introduction 15 1.1. Characteristics, significance, and threat of mangroves 15 1.1.1. Characteristics of mangroves 15 1.1.2. Significance of Indonesian mangroves 16 1.1.3. Threats to mangroves 18 1.2. Evolutionary processes and diversity of mangroves 19 1.2.1. Evolution of mangroves 19 1.2.2. Sea surface currents in Indonesia shape genetic structure 20 1.2.3. The relevance of Wallace’s line to mangrove evolution 22 1.2.4. Isolation by geographical distance 24 1.2.5. Genetic diversity and population structure 25 1.3. Diversity of bioactive compounds of mangrove genus Lumnitzera 27 1.3.1. Sulfur-containing metabolites 27 1.3.2. Phylogenetics 28 1.3.3. Anti-infective potential 29 1.4. Study species 30 1.5. Aim of the thesis 33 2. Material and Methods 37 2.1. Sampling and sample design 37 2.2. Laboratory procedures and genetic analysis 38 2.2.1. DNA isolation 38 2.2.2. ddRADseq sequencing, and bioinformatics 38 2.2.3. Genetic diversity, population structure and differentiation 40 2.2.4. Identifying barriers and areas of connectivity 41 2.2.5. Isolation by distance and sea surface current connectivity 42 2.2.6. Polymerase Chain Reaction (PCR), and phylogenetic analyses 43 2.3. Laboratory procedures and phytochemical analysis 44 2.3.1. Root sample extraction 44 2.3.2. TLC, Low-resolution ESI-MS spectra, HPLC, and NMR 45 2.3.3. UHPLC-ESI-QqTOF-MS and MS/MS 46 2.3.4. RP-UHPLC-ESI-LIT-Orbitrap-MS 47 2.3.5. Extraction and isolation of compounds 47 2.3.6. Anti-infective bioassays 51 3. Results 52 3.1. Genetic diversity and population structure 52 3.1.1. Genetic diversity 52 3.1.2. Population structure and genetic differentiation 54 3.1.3. Effective migration 58 3.1.4. Isolation by distance and sea surface current connectivity 59 3.2. Unusual-sulfated constituent and anti-infective properties 61 3.2.1. Phytochemical screening 61 3.2.2. Phylogenetic tree of Lumnitzera 69 3.2.3. Evaluation of anti-infective properties 70 4. Discussion 74 4.1. Population genomics of Lumnitzera mangroves in Indonesia 74 4.1.1. The genetic diversity paradox in mangroves 74 4.1.2. Phylogroups and the Sunda-Wallacea biogeographical pattern 76 4.1.3. Limited mixture among phylogroups and populations by sea surface currents 78 4.1.4. Restricted gene flow by geographical distance 80 4.1.5. Evolutionary ecology of Lumnitzera inferred by genetics and chemodiversity 81 4.2. Bioactive compounds and anti-infective potential of Lumnitzera 82 4.2.1. Diversity of bioactive compounds 82 4.2.2. Sulfated and nonsulfated ellagic acid supported by phylogenetic pattern 83 4.2.3. Anti-infective properties and their restriction to particular locations 86 5. Conclusion and future perspective 89 6. References 94 7. Appendix 111 Curriculum vitae 119 Declaration of independent work 122 Acknowledgments 123 Author contributions statement 125 Authors’s Addendum

Mangrove ecosystems are found in tropical coastal areas and play vital roles in shoreline protection, habitat support, and medicinal value. These ecosystems are under threat from human activities and climate change. This thesis explored the biodiversity and evolutionary ecology of mangroves in the Indonesian Archipelago, home to the world’s richest composition of mangrove species. Indonesia's geography, including over 17,500 islands and the intersection of Laurasian and Gondwanan flora, makes it an ideal location for studying mangrove evolution. Sea level changes and the presence of land and oceanic barriers have shaped the distribution and evolution of mangroves, with the Indonesian Throughflow (ITF) playing an essential role in genetic exchange. The study analyzed 14 populations of Lumnitzera littorea and 21 populations of L. racemosa, utilizing DNA sequencing to assess genetic diversity, structure, and dispersal in relation to geographical distance and sea surface currents. Both species showed low genetic variation, and significant effects of distance and sea current connectivity were observed. Sulawesi acted as a barrier in genetic differentiation, while other barriers were discovered affecting population structure. Divergent evolutionary trajectories were noted between L. littorea and L. racemosa. The study also investigated the relationship between phylogeny and the chemophenetic patterns of their natural products, given their anti-microbial, antioxidant, and other properties. Techniques such as chromatographic separation and high-resolution ESI-MS were used to link molecular phylogeny with phytochemical characterizations. Root samples were collected for chemical analysis, revealing an unusual diversity in sulfated constituents, with some compounds found for the first time in mangroves. Specific geographical areas showed antibacterial potential, and a previously unknown compound, Lumnitzeralactone, was identified. The conclusion highlights this study as the first to reveal molecular evidence of intraspecific phylogroups in Lumnitzera mangroves, with distinctions defined by geographical lines such as Wallace's line. Additionally, the study found promising sources for anti-bacterial agents and potential therapeutic benefits to human health. The observed genetic differentiation emphasizes the need for conservation strategies at the population level, and the potential for new medicines underscores the importance of mangrove conservation in their natural habitats across Indonesia.:Preface 4 Summary 5 Zusammenfassung 10 1. Introduction 15 1.1. Characteristics, significance, and threat of mangroves 15 1.1.1. Characteristics of mangroves 15 1.1.2. Significance of Indonesian mangroves 16 1.1.3. Threats to mangroves 18 1.2. Evolutionary processes and diversity of mangroves 19 1.2.1. Evolution of mangroves 19 1.2.2. Sea surface currents in Indonesia shape genetic structure 20 1.2.3. The relevance of Wallace’s line to mangrove evolution 22 1.2.4. Isolation by geographical distance 24 1.2.5. Genetic diversity and population structure 25 1.3. Diversity of bioactive compounds of mangrove genus Lumnitzera 27 1.3.1. Sulfur-containing metabolites 27 1.3.2. Phylogenetics 28 1.3.3. Anti-infective potential 29 1.4. Study species 30 1.5. Aim of the thesis 33 2. Material and Methods 37 2.1. Sampling and sample design 37 2.2. Laboratory procedures and genetic analysis 38 2.2.1. DNA isolation 38 2.2.2. ddRADseq sequencing, and bioinformatics 38 2.2.3. Genetic diversity, population structure and differentiation 40 2.2.4. Identifying barriers and areas of connectivity 41 2.2.5. Isolation by distance and sea surface current connectivity 42 2.2.6. Polymerase Chain Reaction (PCR), and phylogenetic analyses 43 2.3. Laboratory procedures and phytochemical analysis 44 2.3.1. Root sample extraction 44 2.3.2. TLC, Low-resolution ESI-MS spectra, HPLC, and NMR 45 2.3.3. UHPLC-ESI-QqTOF-MS and MS/MS 46 2.3.4. RP-UHPLC-ESI-LIT-Orbitrap-MS 47 2.3.5. Extraction and isolation of compounds 47 2.3.6. Anti-infective bioassays 51 3. Results 52 3.1. Genetic diversity and population structure 52 3.1.1. Genetic diversity 52 3.1.2. Population structure and genetic differentiation 54 3.1.3. Effective migration 58 3.1.4. Isolation by distance and sea surface current connectivity 59 3.2. Unusual-sulfated constituent and anti-infective properties 61 3.2.1. Phytochemical screening 61 3.2.2. Phylogenetic tree of Lumnitzera 69 3.2.3. Evaluation of anti-infective properties 70 4. Discussion 74 4.1. Population genomics of Lumnitzera mangroves in Indonesia 74 4.1.1. The genetic diversity paradox in mangroves 74 4.1.2. Phylogroups and the Sunda-Wallacea biogeographical pattern 76 4.1.3. Limited mixture among phylogroups and populations by sea surface currents 78 4.1.4. Restricted gene flow by geographical distance 80 4.1.5. Evolutionary ecology of Lumnitzera inferred by genetics and chemodiversity 81 4.2. Bioactive compounds and anti-infective potential of Lumnitzera 82 4.2.1. Diversity of bioactive compounds 82 4.2.2. Sulfated and nonsulfated ellagic acid supported by phylogenetic pattern 83 4.2.3. Anti-infective properties and their restriction to particular locations 86 5. Conclusion and future perspective 89 6. References 94 7. Appendix 111 Curriculum vitae 119 Declaration of independent work 122 Acknowledgments 123 Author contributions statement 125 / Viele Mangrovenarten haben neben Holz- und Nichtholzprodukten auch einen medizinischen Wert und werden traditionell genutzt. Doch durch menschliche Aktivitäten und den Anstieg des Meeresspiegels durch den Klimawandel verschwinden sie rasch. Diese Arbeit erforscht die biologische Vielfalt der Mangroven im indonesischen Archipel, insbesondere die Arten Lumnitzera littorea und Lumnitzera racemosa. Der indonesische Archipel hat die weltweit reichste Mangrovenzusammensetzung und dient als Übergangsregion für verschiedene Pflanzenlinien. Der Meeresspiegelanstieg und dessen mögliche Auswirkungen auf Mangroven wurden genau untersucht. Mangroven besitzen schwimmfähige Fortpflanzungsorgane, und die Meeresströmungen des Indonesian Throughflow (ITF) könnten den genetischen Austausch zwischen verschiedenen Populationen ermöglichen. In der Studie wurden 14 Populationen von L. littorea und 21 von L. racemosa genotypisiert. Die Ergebnisse zeigten eine geringe genetische Variation auf Populationsebene und eine signifikante genetische Differenzierung, beeinflusst von Entfernung und Meeresströmung. Es wurden auch divergierende Entwicklungsverläufe und zwei Phylogruppen bei beiden Arten beobachtet. Die Studie untersuchte auch die phylogenetischen Beziehungen und die Chemophenetik der beiden Arten. Mangrovenböden weisen einen hohen Sulfatgehalt auf, und medizinisch wirksame Verbindungen werden oft von Mikroorganismen wie endophytischen Pilzen produziert. Schwefelverbindungen in Mangroven wurden bisher vernachlässigt. Durch Kombination von phylogenetischen Daten mit chemischen Analysen wurde die Entwicklung der Mangrovenarten und die Vielfalt der Wurzelmetaboliten untersucht. Es wurden chromatographische und tandemmassenspektrometrische Techniken eingesetzt, um eine molekulare Phylogenie mit phytochemischen Charakterisierungen zu verbinden. Die Untersuchung ergab eine ungewöhnliche Vielfalt an sulfatierten Bestandteilen und antibakterielles Potenzial. Zusammenfassend liefert die Studie molekulare Beweise für intraspezifische Phylogruppen in Lumnitzera-Mangroven, definiert durch die biogeografische Trennung von Sunda und Wallacea. Beide Arten stellen eine vielversprechende Quelle für antibakterielle Wirkstoffe dar, einschließlich sulfatierter Ellagsäurederivate. Die populationsgenomischen Ergebnisse liefern Informationen über die Erhaltungsstrategie von Lumnitzera-Arten, und die metabolomischen Ergebnisse berichten über potenzielle neue Arzneimittel, was die Bedeutung der Erhaltung von Mangroven in ihren natürlichen Lebensräumen im gesamten indonesischen Archipel unterstreicht.:Preface 4 Summary 5 Zusammenfassung 10 1. Introduction 15 1.1. Characteristics, significance, and threat of mangroves 15 1.1.1. Characteristics of mangroves 15 1.1.2. Significance of Indonesian mangroves 16 1.1.3. Threats to mangroves 18 1.2. Evolutionary processes and diversity of mangroves 19 1.2.1. Evolution of mangroves 19 1.2.2. Sea surface currents in Indonesia shape genetic structure 20 1.2.3. The relevance of Wallace’s line to mangrove evolution 22 1.2.4. Isolation by geographical distance 24 1.2.5. Genetic diversity and population structure 25 1.3. Diversity of bioactive compounds of mangrove genus Lumnitzera 27 1.3.1. Sulfur-containing metabolites 27 1.3.2. Phylogenetics 28 1.3.3. Anti-infective potential 29 1.4. Study species 30 1.5. Aim of the thesis 33 2. Material and Methods 37 2.1. Sampling and sample design 37 2.2. Laboratory procedures and genetic analysis 38 2.2.1. DNA isolation 38 2.2.2. ddRADseq sequencing, and bioinformatics 38 2.2.3. Genetic diversity, population structure and differentiation 40 2.2.4. Identifying barriers and areas of connectivity 41 2.2.5. Isolation by distance and sea surface current connectivity 42 2.2.6. Polymerase Chain Reaction (PCR), and phylogenetic analyses 43 2.3. Laboratory procedures and phytochemical analysis 44 2.3.1. Root sample extraction 44 2.3.2. TLC, Low-resolution ESI-MS spectra, HPLC, and NMR 45 2.3.3. UHPLC-ESI-QqTOF-MS and MS/MS 46 2.3.4. RP-UHPLC-ESI-LIT-Orbitrap-MS 47 2.3.5. Extraction and isolation of compounds 47 2.3.6. Anti-infective bioassays 51 3. Results 52 3.1. Genetic diversity and population structure 52 3.1.1. Genetic diversity 52 3.1.2. Population structure and genetic differentiation 54 3.1.3. Effective migration 58 3.1.4. Isolation by distance and sea surface current connectivity 59 3.2. Unusual-sulfated constituent and anti-infective properties 61 3.2.1. Phytochemical screening 61 3.2.2. Phylogenetic tree of Lumnitzera 69 3.2.3. Evaluation of anti-infective properties 70 4. Discussion 74 4.1. Population genomics of Lumnitzera mangroves in Indonesia 74 4.1.1. The genetic diversity paradox in mangroves 74 4.1.2. Phylogroups and the Sunda-Wallacea biogeographical pattern 76 4.1.3. Limited mixture among phylogroups and populations by sea surface currents 78 4.1.4. Restricted gene flow by geographical distance 80 4.1.5. Evolutionary ecology of Lumnitzera inferred by genetics and chemodiversity 81 4.2. Bioactive compounds and anti-infective potential of Lumnitzera 82 4.2.1. Diversity of bioactive compounds 82 4.2.2. Sulfated and nonsulfated ellagic acid supported by phylogenetic pattern 83 4.2.3. Anti-infective properties and their restriction to particular locations 86 5. Conclusion and future perspective 89 6. References 94 7. Appendix 111 Curriculum vitae 119 Declaration of independent work 122 Acknowledgments 123 Author contributions statement 125

Lumnitzera littorea and Lumnitzera racemosa are mangrove species distributed widely along the Indonesian coasts. Besides their ecological importance, both are of interest owing to their wealth of natural products, some of which constitute potential sources for medicinal applications. We aimed to discover and characterize new anti-infective compounds, based on population-level sampling of both species from across the Indonesian Archipelago. Root metabolites were investigated by TLC, hyphenated LC-MS/MS and isolation, the internal transcribed spacer (ITS) region of rDNA was used for genetic characterization. Phytochemical characterization of both species revealed an unusual diversity in sulfated constituents with 3,3’,4’-tri-O-methyl-ellagic acid 4-sulfate representing the major compound in most samples. None of these compounds was previously reported for mangroves. Chemophenetic comparison of L. racemosa populations from different localities provided evolutionary information, as supported by molecular phylogenetic evidence. Samples of both species from particular locations exhibited anti-bacterial potential (Southern Nias Island and East Java against Gram-negative bacteria, Halmahera and Ternate Island against Gram-positive bacteria). In conclusion, Lumnitzera roots from natural mangrove stands represent a promising source for sulfated ellagic acid derivatives and further sulfur containing plant metabolites with potential human health benefits.