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

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Le transfert trans-générationnel d’immunité (TTGI) est défini comme étant une élévation de l’immunocompétence de la descendance suite à la rencontre des femelles avec un organisme pathogène. Le TTGI est un phénomène bien connu chez les vertébrés, chez lesquels il se réalise par le transfert d’anticorps de la mère au jeune. Il n’a été décrit que récemment chez les invertébrés, chez lesquels le support de sa transmission est encore inconnu. Le TTGI apporte un bénéfice aux descendants lorsqu’ils rencontrent l’infection vécue par la mère, dans quel cas l’élévation de leur immunocompétence a un effet protecteur. Cependant, au-delà de ce bénéfice, plusieurs indices suggèrent que le TTGI est un phénomène coûteux pour les organismes. L’évolution du TTGI ne sera permise chez une espèce que lorsque les bénéfices qu’il représente en termes de protection des descendants surpasseront les coûts qu’il représente pour eux en termes de fitness. Ainsi, l’étude de ses coûts et de ses bénéfices nous renseigne sur les pressions de sélection qui ont conduit à son évolution chez les invertébrés. Au cours de cette thèse, j’ai associé l’expression du TTGI chez un insecte avec un certain nombre de coûts, tant pour les femelles qui le réalisent que pour les descendants qui l’expriment. Pour ce faire, j’ai utilisé comme organisme modèle le ver de farine, Tenebrio molitor. Dans le premier chapitre, nous avons stimulé le système immunitaire des femelles adultes de T. molitor avec un immunogène non pathogène, et étudié divers aspects de la transmission d’activité antibactérienne aux œufs qui en résultait. Cela nous a permis de voir que la transmission d’activité antibactérienne interne aux œufs commençait deux jours après la stimulation du système immunitaire des femelles et cessait après dix jours. Enfin, nous avons pu mettre en évidence un coût pour les femelles à la protection de leurs œufs, en termes de fécondité. Dans le second chapitre, nous stimulé le système immunitaire avec trois microorganismes différents tués par la chaleur, et exposé leurs jeunes larves à des microorganismes vivants. Nous n’avons pas réussi à mettre en évidence d’effet protecteur du TTGI sur les jeunes larves de T. molitor. Il s’avère cependant que l’exposition des jeunes larves à un champignon entomopathogène réduit le délai avant leur seconde mue larvaire. Dans le troisième chapitre, nous avons stimulé soit le système immunitaire des femelles, soit celui des mâles de T. molitor avec un immunogène non pathogène, et observé différents paramètres de l’immunité de leurs descendants adultes. Cela nous a permis de mettre en évidence que le TTGI d’origine maternelle et paternelle n’affecte pas les mêmes effecteurs immunitaires chez les descendants, et que le TTGI d’origine maternelle comportait un coût pour eux en termes de temps de développement. Ces coûts au TTGI suggèrent qu’il n’est pas seulement une conséquence de la stimulation du système immunitaire des femelles de la génération parentale, mais qu’il est bien un mécanisme qui a été sélectionné du fait des bénéfices qu’il représente pour les organismes dans certaines conditions écologiques / Trans-generational immune priming (TGIP) is defined as the plastic enhancement of offspring's immunocompetence following an immune challenge of the females of the parental generation. In vertebrates, this phenomenon is well described, and is achieved by the maternal transfer of antibodies. In invertebrates however, it has only recently been described. Since invertebrates do not possess antibodies, the mechanism of this transmission remains unknown. If the offspring is exposed to the maternal infection, an elevated immunocompetence can help it cope better with it. Nonetheless, apart from this benefit, several cues indicate that the TGIP bears some fitness costs for individuals. The evolution of TGIP will be favoured when its benefits outweigh its fitness costs. Thus, studying its costs and benefits can lead us to a better understanding of the selection pressures that lead to its evolution in invertebrates. During my thesis, I associated the occurrence of TGIP in an insect, the mealworm beetle Tenebrio molitor, to several fitness costs for the females transmitting it as well as for the offspring receiving it.In the first chapter, we stimulated the adult female's immune system with a non pathogenic immunogene, and studied several aspects of the subsequent transfer of antibacterial activity to the eggs. We saw that the transmission of antibacterial activity inside the eggs started two days after the immune challenge, and stopped at ten. Then, we highlighted a cost for the females on their fecundity to this transmission.In the second chapter, we stimulated the immune system of the females with three different heat-killed microorganisms, and exposed their larval progeny to living microorganisms. We did not see any benefit of the TGIP on the young larvae of T. molitor. However, we saw that the exposure of young larvae to an entomopathogenic fungus decreased the time-lap between the two first larval moults.In the third chapter, we stimulated the immune system of either the adult females or the males of T. molitor, and we observed several immune parameters in their adult offspring. This allowed us to see that maternally and paternally-derived TGIP affected different immune effectors in the adult offspring, and that maternally-derived TGIP bear a cost on the developmental time of the offspring.These fitness costs to the TGIP suggest that it is not just a side-effect of the immune reaction of the females, but rather an investment that has been selected because of the benefits it represents for the offspring in certain ecological conditions

Die Bedeutung ökologischer Faktoren bei der Entstehung phänotypischer sowie genetischer Vielfalt durch natürliche Selektion, besonders bei sympatrischer Artbildung, ist derzeit ein Fokus der Evolutionsforschung. Gemeinsam vorkommende und nah verwandte Arten werden daher als Modellorganismen verwendet, um die Ursachen und Mechanismen ökologischer und evolutionärer Diversifizierung zu untersuchen. Ein sympatrisches Fisch-Artenpaar, für das eine sympatrische Artbildung auf Basis genetischer Analysen vermutet wird, existiert im norddeutschen Stechlinsee. Die zwei Maränenarten sind morphologisch kaum zu unterscheiden, zeigen eine ähnliche Nahrungszusammensetzung und kommen gemeinsam im Freiwasser, allerdings in leicht unterschiedlichen Wassertiefen, vor. Die Hypothese meiner Arbeit war, dass sich die Physiologie bzw. das Verhalten der Arten in Bezug auf die wichtigsten Umweltfaktoren ihres Lebensraumes, Futterdichte, Lichtintensität und Wassertemperatur unterscheiden. Daher haben wir Fraßeffizienz, Stoffwechselraten und Temperaturpräferenzen in Abhängigkeit dieser Faktoren bei beiden Arten untersucht, nachdem diese zuvor unter identischen Laborbedingungen herangezogen wurden. Wir fanden keinen Unterschied in der Fraßeffizienz, allerdings zeigten beide Arten je nach Temperatur unterschiedliche Stoffwechselraten sowie entsprechende Unterschiede in der Temperaturpräferenz. Die Ergebnisse legen nahe, dass temperaturbedingte physiologische Anpassungen sowie die Nutzung unterschiedlicher thermischer Mikrohabitate die zwischenartliche Konkurrenz verringern und eine gemeinsame Existenz ermöglichen. Um die mögliche Bedeutung einer solchen öko-physiologischen Spezialisierung für die Artbildung innerhalb des Sees einschätzen zu können, haben wir basierend auf den Freiland- und Labordaten ein mathematisches Evolutionsmodell entwickelt. Demnach ist ein Aufspalten einer Ausgangspopulation in zwei Populationen mit unterschiedlichen Temperaturoptima wahrscheinlich. Eine ökologische und evolutionäre Diversifizierung entlang des Temperaturgradienten ist somit ein empirisch und theoretisch plausibles Szenario für die sympatrische Artbildung der Stechlinsee-Maränen. / Abstract The role of ecological factors in generating phenotypic and genetic diversity through natural selection has received increasing attention in evolutionary biology during the last decade, especially with respect to diversification in sympatry. Sympatrically occurring and closely related species are used as model systems to study the causes and mechanisms of ecological and evolutionary diversification. A sympatric species pair of coregonid fish, for which a speciation in sympatry has been suggested based on genetic analyses, coexists in the German Lake Stechlin. The two species are morphologically similar planktivores with weak divergence in diet composition that co-occur within the pelagic area of the lake at slightly different water depths. Accordingly, it was hypothesized that the species would differ in physiology and behaviour with respect to the most important environmental factors of their natural habitat, food density, light intensity and water temperature. We studied the feeding efficiencies, metabolic rates, and temperature preferences of both species previously hatched and raised under identical laboratory conditions. We found no divergence in feeding efficiency, but significant differences in temperature-related metabolic costs as well as a corresponding difference in thermal preference. These results suggest that temperature-related physiological adaptations and the associated use of slightly different thermal microhabitats reduces exploitative competition between the species and facilitates their coexistence. To evaluate a potential role of this eco-physiological specialization for a speciation in sympatry, we developed a mathematical evolutionary model, based on our field observations and laboratory experiments. The model showed that an evolutionary splitting of an ancestral into two coexisting populations with different temperature optima is likely in this system. In conclusion, an eco-physiological and evolutionary diversification along the temperature-depth gradient of the lake is an empirically and theoretically plausible scenario for the sympatric speciation of the coregonids.

Unraveling soil microbial ecology is essential for improving sustainable agricultural productivity. Community-based studies revolutionized this field in the last decades, but much is yet to be disclosed. This thesis proposed an approach to increase the resolution of such studies by combining 16S rDNA high-throughput sequencing and population genomics, aiming to further explore the differences pointed by community analyses, as well as to overcome the limitations of using operational taxonomic units (OTUs) as ecological entities, and to introduce the evolutionary thinking in microbial ecology. Our main goal was to understand the features that make bacteria able to colonize sugarcane rhizosphere or live saprophytically in bulk soil. Rhizosphere and bulk soil are contrasting habitats for microbial life as they are highly distinct in its physical, chemical and consequently biological characteristics. Our results indicated that sugarcane shapes the rhizosphere microbiome and metabolism of D-galacturonic acid is a key function for colonizing this niche. Among the taxa prevailing in the rhizosphere, Pseudomonas genus was targeted for a more detailed study considering its known attributes for plant growth promotion. Seventy-six fluorescent Pseudomonas spp. were isolated and submitted to whole genome sequencing (WGS). A comparative genomic analysis was performed between populations from rhizosphere and bulk soil. Phylogenetic analyses classified the isolates in the P. fluorescens (57) or P. putida (19) groups. Twelve putative new species and two new proposed P. fluorescens subgroups were found in the prospected tropical soil. Comparative genomics revealed that phosphatases or xylose-utilization genes were significantly enriched in the rhizosphere and bulk soil populations of the P. fluorescens group, respectively. D-galactonate catabolism was higher in the rhizosphere population of the P. putida group based on both genotypic and phenotypic results. Growth in D-xylose was further explored using genetic modified strains and confirmed that this sugar is more used by members of the bulk soil than the rhizosphere population of the P. fluorescens group, a pattern also observed in the bulk soil microbiome. In summary, these findings constitute a step forward in understanding the ecology of rhizosphere and bulk soil bacteria, by overcoming some limitations of community-based analyses and showing genomic differences between bacterial populations of these habitats. / Desvendar a ecologia microbiana do solo é essencial para aumentar a produtividade agrícola sustentável. Estudos baseados em comunidades revolucionaram esse campo nas últimas décadas, mas ainda há muito a ser revelado. Esta tese propôs uma abordagem para aumentar a resolução desses estudos, combinando sequenciamento em larga escala de rDNA 16S e genômica populacional, com o objetivo de explorar mais a fundo as diferenças apontadas por análises de comunidades, assim como superar as limitações do uso de unidades taxonômicas operacionais (UTOs) como entidades ecológicas e introduzir o pensamento evolutivo na ecologia microbiana. Nossa principal meta foi entender as características que tornam as bactérias hábeis em colonizar a rizosfera de cana-de-açúcar ou viver no solo saprofiticamente. Rizosfera e solo são hábitats contrastantes para a vida microbiana, já que são altamente distintos em suas características físicas, químicas e, consequentemente, biológicas. Nossos resultados indicaram que a cana-de-açúcar modifica o microbioma da rizosfera e o metabolismo do ácido D-galacturônico é uma função chave para colonizar este nicho. Dentre os táxons que prevalecem na rizosfera, o gênero Pseudomonas foi escolhido para um estudo mais detalhado, considerando os seus atributos de promoção de crescimento de plantas. Setenta e seis Pseudomonas spp. fluorescentes foram isoladas e submetidas ao sequenciamento do genoma. Uma análise de genômica comparativa foi realizada entre as populações obtidas do solo e rizosfera. As análises filogenéticas classificaram os isolados nos grupos P. fluorescens (57) ou P. putida (19). Doze prováveis novas espécies e dois novos subgrupos propostos de P. fluorescens foram encontrados no solo tropical prospectado. A genômica comparativa revelou que genes de fosfatases e de uso de xilose foram significativamente enriquecidos nas populações da rizosfera e solo do grupo P. fluorescens, respectivamente. O catabolismo do ácido D-galactônico foi maior na população da rizosfera do grupo P. putida, baseado tanto em resultados genotípicos quanto fenotípicos. O crescimento em D-xilose foi mais explorado usando linhagens geneticamente modificadas e confirmou que este açúcar é mais utilizado por membros da população do solo do que da rizosfera no grupo P. fluorescens, um padrão também observado no microbioma do solo. Em resumo, essas descobertas constituem um passo adiante no entendimento da ecologia bacteriana do solo e rizosfera, por superar algumas limitações de análises de comunidades e mostrar diferenças genômicas entre populações bacterianas destes hábitats.

Unraveling soil microbial ecology is essential for improving sustainable agricultural productivity. Community-based studies revolutionized this field in the last decades, but much is yet to be disclosed. This thesis proposed an approach to increase the resolution of such studies by combining 16S rDNA high-throughput sequencing and population genomics, aiming to further explore the differences pointed by community analyses, as well as to overcome the limitations of using operational taxonomic units (OTUs) as ecological entities, and to introduce the evolutionary thinking in microbial ecology. Our main goal was to understand the features that make bacteria able to colonize sugarcane rhizosphere or live saprophytically in bulk soil. Rhizosphere and bulk soil are contrasting habitats for microbial life as they are highly distinct in its physical, chemical and consequently biological characteristics. Our results indicated that sugarcane shapes the rhizosphere microbiome and metabolism of D-galacturonic acid is a key function for colonizing this niche. Among the taxa prevailing in the rhizosphere, Pseudomonas genus was targeted for a more detailed study considering its known attributes for plant growth promotion. Seventy-six fluorescent Pseudomonas spp. were isolated and submitted to whole genome sequencing (WGS). A comparative genomic analysis was performed between populations from rhizosphere and bulk soil. Phylogenetic analyses classified the isolates in the P. fluorescens (57) or P. putida (19) groups. Twelve putative new species and two new proposed P. fluorescens subgroups were found in the prospected tropical soil. Comparative genomics revealed that phosphatases or xylose-utilization genes were significantly enriched in the rhizosphere and bulk soil populations of the P. fluorescens group, respectively. D-galactonate catabolism was higher in the rhizosphere population of the P. putida group based on both genotypic and phenotypic results. Growth in D-xylose was further explored using genetic modified strains and confirmed that this sugar is more used by members of the bulk soil than the rhizosphere population of the P. fluorescens group, a pattern also observed in the bulk soil microbiome. In summary, these findings constitute a step forward in understanding the ecology of rhizosphere and bulk soil bacteria, by overcoming some limitations of community-based analyses and showing genomic differences between bacterial populations of these habitats. / Desvendar a ecologia microbiana do solo é essencial para aumentar a produtividade agrícola sustentável. Estudos baseados em comunidades revolucionaram esse campo nas últimas décadas, mas ainda há muito a ser revelado. Esta tese propôs uma abordagem para aumentar a resolução desses estudos, combinando sequenciamento em larga escala de rDNA 16S e genômica populacional, com o objetivo de explorar mais a fundo as diferenças apontadas por análises de comunidades, assim como superar as limitações do uso de unidades taxonômicas operacionais (UTOs) como entidades ecológicas e introduzir o pensamento evolutivo na ecologia microbiana. Nossa principal meta foi entender as características que tornam as bactérias hábeis em colonizar a rizosfera de cana-de-açúcar ou viver no solo saprofiticamente. Rizosfera e solo são hábitats contrastantes para a vida microbiana, já que são altamente distintos em suas características físicas, químicas e, consequentemente, biológicas. Nossos resultados indicaram que a cana-de-açúcar modifica o microbioma da rizosfera e o metabolismo do ácido D-galacturônico é uma função chave para colonizar este nicho. Dentre os táxons que prevalecem na rizosfera, o gênero Pseudomonas foi escolhido para um estudo mais detalhado, considerando os seus atributos de promoção de crescimento de plantas. Setenta e seis Pseudomonas spp. fluorescentes foram isoladas e submetidas ao sequenciamento do genoma. Uma análise de genômica comparativa foi realizada entre as populações obtidas do solo e rizosfera. As análises filogenéticas classificaram os isolados nos grupos P. fluorescens (57) ou P. putida (19). Doze prováveis novas espécies e dois novos subgrupos propostos de P. fluorescens foram encontrados no solo tropical prospectado. A genômica comparativa revelou que genes de fosfatases e de uso de xilose foram significativamente enriquecidos nas populações da rizosfera e solo do grupo P. fluorescens, respectivamente. O catabolismo do ácido D-galactônico foi maior na população da rizosfera do grupo P. putida, baseado tanto em resultados genotípicos quanto fenotípicos. O crescimento em D-xilose foi mais explorado usando linhagens geneticamente modificadas e confirmou que este açúcar é mais utilizado por membros da população do solo do que da rizosfera no grupo P. fluorescens, um padrão também observado no microbioma do solo. Em resumo, essas descobertas constituem um passo adiante no entendimento da ecologia bacteriana do solo e rizosfera, por superar algumas limitações de análises de comunidades e mostrar diferenças genômicas entre populações bacterianas destes hábitats.

A tribo Hydropsini compreende três gêneros de serpentes. Dados alimentares são escassos, mas indicam que as espécies consomem principalmente peixes e secundariamente anfíbios anuros. Os Hydropsini são ovíparos ou vivíparos e o polimorfismo é sugerido para algumas espécies. Entretanto, outros aspectos reprodutivos são desconhecidos para a maioria dessas serpentes. Por outro lado, as relações filogenéticas entre os Hydropsini estão estabelecidas. Este trabalho teve como objetivo caracterizar a reprodução e alimentação de doze espécies dos três gêneros, mapear a evolução e analisar possíveis relações entre a evolução de caracteres morfológicos, reprodutivos e alimentares, utilizando a filogenia disponível. Dados foram obtidos de indivíduos preservados (N = 2.871) de espécies amazônicas (Hydrops spp., Pseudoeryx spp., Helicops hagmanni, H trivittatus, H angulatus, H polylepis), do sudoeste (H leopardinus) e sudeste do Brasil (H carinicaudus, H modestus, H infrataeniatus, H gomesi). Os Hydropsini são especialistas em peixes, porém algumas Helicops (exceto H hagmanni) podem consumir anfíbios e lagartos. Hydrops triangularis e P. plicatilis são especialistas em peixes alongados (Synbranchiformes), Peixes Gymnotiformes, Siluriformes e Perciformes foram dominantes nas dietas de Hy. martii, H polylepis e H hagmanni, respectivamente. Nenhum tipo de presa teve dominância importante nas dietas das demais espécies, porém Perciformes foram consumidos com maior freqüência pela maioria. Esses dados indicam que as espécies diferem quanto ao local de forrageio. Aparentemente, o ancestral da tribo possuía cabeça pequena e dieta composta por Synbranchiformes. A dieta se toma mais ampla e o tamanho da cabeça parece ter aumento no ancestral de Helicops. As presas consumidas por muitas Helicops possuem corpos relativamente mais altos e são mais robustas o que pode explicar alterações no crânio de determinadas espécies. Fêmeas atingem a maturidade com tamanho, relativo ao tamanho médio dos adultos, similar em comparação aos machos. Fêmeas são maiores, possuem maior cabeça, circunferência e cauda mais curta que machos. O menor tamanho dos machos indica que o ritual de combate não deve ocorrer na tribo. Os Hydropsini são ovíparos ou vivíparos e o polimorfismo foi confirmado para H angulatus. A reprodução da maioria das espécies deve ser bienal, já que menos de 50% das fêmeas estavam reprodutivas. Os ciclos das fêmeas são sazonais, exceto para H angulatus. A reprodução das espécies amazônicas ocorre ao longo da estação seca e parte da chuvosa. Ciclos reprodutivos restritos às chuvas ocorrem para as espécies do sudeste e sudoeste. Diferenças nos ciclos das fêmeas podem estar associadas à variação no clima dessas regiões. A espermatogênese pode ser contínua ou sazonal. Os duetos deferentes de muitas espécies estão maiores na seca, sugerindo a ocorrência de cópula nesta estação. A fecundidade e o tamanho dos filhotes, relativos ao tamanho das fêmeas, não diferiu entre serpentes ovíparas e vivíparas. A oviparidade é característica plesiomórfica e a viviparidade pode ter surgido três vezes entre as Helicops. A fecundidade parece aumentar no ancestral do clado (Pseudoeryx, Helicops), o qual é composto por serpentes mais robustas em comparação a Hydrops e a muitos Xenodontinae. Porém, o tamanho dos filhotes tende a diminuir nessas serpentes. / The tribe Hydropsini comprises three genera of snakes. Information on food habits is scarce. However previous data indicate that species feed mainly upon fishes but also eat anurans. The Hydropsini are oviparous or viviparous and the polymorphism is suggested for some species. Other reproductive traits are unknown for most species. On the other hand, the phylogenetic relationships of Hydropsini are established. This study aimed to characterize the reproduction and the feeding habits of twelve species of three genera, hypothesise the evolution of morphological, reproductive and diet characters, as well as probable relationships among these traits. Data were obtained from preserved individuals (N = 2.871) of species from northern (Hydrops sp., Pseudoeryx sp., Helicops hagmanni, H. trivittatus, H. angulatus, H. polylepis), southwestern (H. leopardinus) and southeastern Brazil (H. carinicaudus, H. modestus, H. infrataeniatus, H. gomesi). The Hydropsini feed on fishes, but most Helicops eat also frogs and eventually lizards. Hydrops triangularis and P. plicatilis are specialized on Synbranchiformes fishes. Siluriformes, Perciformes and Gymnotiformes were the dominant item in of H. polylepis, H. hagmanni and Hy. martii, respectively. Other species eat several fishes, but Perciformes were consumed more frequently by most. These data here obtained suggest that the species differ in foraging microhabitat. The ancestor of the tribe probably had small head and diet composed predominantly by Synbranchiformes. The diet became widespread and the size of the head increase in the ancestor of Helicops. The preys consumed by most Helicops are stouter and have higher bodies, which may explain changes in the skull of some species. Females and males attain sexual maturity at similar body size, but adult females are larger. Moreover females have larger head and body circumference, and shorter tail than males. The smaller size of males indicates that the combat behavior should not occur in the tribe. The Hydropsini are oviparous or viviparous and the polymorphism was confirmed to H. angulatus. The reproduction of most species may be biennial, since less than 50% of females were reproductive. The cycles of females are seasonal. At the least H. angulatus, has continuous cycle. The reproduction of the Amazonian species occurs throughout the dry season and part of the rainy season. Cycles restricted mainly to the rainy season occur for species in southeastern and southwestern. Differences in the females cycles may be related to distinct climate in the occurrence areas of the species. The spermatogenesis are continuous or seasonal (restricted to the dry or rainy season). The diameter of deferent ducts of most species are larger in the dry season, suggesting that mating is restricted to this season. The fecundity and size of newborns, relative to the body size of female, was similar among species and did not differ between oviparous and viviparous snakes. The oviparity is plesiomorphic and the viviparity may have arisen at the least three times among Helicops. The fecundity increases in the ancestor of the clade (Pseudoeryx, Helicops), which is stouter than Hydrops and many Xenodontinae. However, the size of newborns tends to decrease in these snakes.

In nature, environments are often variable and heterogeneous influencing ecological and evolutionary processes. This thesis focus on how animals interact with their environment and how that affects the reproductive decisions they make. Using empirical data collected from wild collared flycatcher populations, experiments and molecular approaches I try to unveil some of these relationships and the evolutionary, ecological and conservation implications of these findings are discussed. Firstly, collared flycatchers were shown to use breeding densities of their own and other species using similar resources when assessing costs and benefits associated to breeding in specific habitats. However, species will vary in how informative they are, and the worst competitor – with whom you overlap most in resources needs – also provides the best source of information. Collared flycatcher parents will also benefit differentially from investments in sons and daughters due to habitat characteristics and dispersal differences between the sexes. Here, I show that they will produce more of the sex that will give the highest expected fitness return given the environment they are in. These results also provide a reciprocal scenario to Clark's (1978) classical study of sex ratio adjustment in relation to local resource competition (LRC), as more of the natal philopatric sex is produced when LRC is low. Secondly, the effect of elaborated ornaments on paternity in the socially monogamous collared flycatcher was shown to be of more importance in areas where the intensity of intra- and intersexual conflicts are expected to be elevated. Hence, ornamentation by environmental interactions determines paternity, illustrating that sexual selection through extra-pair paternity is context dependent. Finally, even though the collared flycatcher populations that this thesis is based on have been studied on their breeding grounds for more then 25 years, we know little of where they are when they are not breeding. Here, stable isotope signatures in winter-grown feathers suggests that they may spend their winter with their breeding ground neighbours and do so repeatedly over years. Differences between breeding populations at this small scale should have many impactions for evolutionary and ecological processes as it will, for example, determine with whom individuals interact throughout their life.

Malgré leur importance reconnue pour la santé publique et la conservation, les études sur l’écologie et l’évolution des maladies infectieuses dans les populations sauvages souffrent de contraintes sur la disponibilité de données permettant l’identification des processus impliqués dans les systèmes considérés. Les méthodes sérologiques (i.e., détection d’anticorps dans des échantillons biologiques) permettent de retracer l’exposition à des agents infectieux spécifiques mais leur interprétation est complexe. Par exemple, la prévalence d’individus séropositifs dans une population résulte d’une combinaison de dynamiques épidémiologiques (ex. : l’incidence de la maladie) et démographiques (ex. le taux de renouvellement de la population). Dans ce contexte, l’objectif de cette thèse est de montrer comment les processus sous-jacents à la circulation d’agents infectieux en populations sauvages peuvent être inférés à partir de données sérologiques. Tout d’abord, j’illustre comment les études transversales focalisée sur une espèce sentinelle à l’interface entre populations sauvages et humaines peuvent permettre d’efficacement décrire informer sur les patterns d’exposition à une hiérarchie d’échelles spatiales. Ensuite, je compare les avantages et inconvénients de ce type d’approches transversales à ceux d’approches longitudinales basées sur les suivis d’individus marqués et je propose une solution pour intégrer ensemble ces deux types de données pour quantifier les dynamiques éco-épidémiologiques. Finalement, en utilisant une population menacée d’oiseaux longévifs régulièrement touchée par des épizooties de choléra aviaire comme cas d’étude, j’illustre les bénéfices de combiner la sérologie avec d’autres approches. Ce travail souligne la valeur des études à long-terme de l’exposition d’hôtes à des agents infectieux en milieu naturel, où les processus écologiques et évolutifs sont clés pour comprendre les dynamiques éco-épidémiologiques et peuvent avoir d’importantes implications pour la conservation de la biodiversité. / Despite their increasingly recognized interest for public health and biodiversity conservation, investigations on the ecology and evolution of infectious diseases in wildlife have been hampered by the difficulty of collecting data allowing efficient inference of underlying processes. Serology (i.e., detection of antibodies in biological samples) is a useful tool to detect past exposure to specific infectious agents. Still, interpreting serological data is not straightforward. For instance, the prevalence of seropositive individuals in a population is driven by a combination of epidemiological (e.g., disease incidence) and demographic (e.g., population turnover) dynamics. In this context, the objective of this thesis is to show how processes underlying infectious agent circulation in wild populations can be inferred from serological data. First, I illustrate how cross-sectional studies focusing on a sentinel species at the wildlife-human interface can efficiently inform on patterns at a hierarchy of scales. Then, I compare the pros and cons of such cross-sectional approaches to longitudinal sampling designs involving marked individuals when attempting to quantify the dynamics of infectious agents and I propose a way to integrate those two approaches in future studies. Finally, using avian cholera epizootics in a threatened long-lived seabird on an isolated island as a case study, I illustrate the benefits of combining serology with other approaches. This work notably highlights the value of detailed long-term studies of host exposure to infectious agents in the wild, where ecological and evolutionary processes are likely critical drivers of disease dynamics and can have important implications for biodiversity conservation.

Tous les hôtes ne contribuent pas également à la transmission de parasites. Certains individus ou espèces peuvent par exemple être davantage infectés que d'autres, une observation qui a mené à la proposition de la règle des `20/80', selon laquelle 20 % des individus seraient responsables de 80 % de la transmission. Cependant, les études qui se sont intéressées à l'hétérogénéité de la transmission se sont principalement focalisées sur les sources d'hétérogénéité intrinsèques à l'espèce ou à l'individu, telles que la susceptibilité ou l’infectivité, tandis que les facteurs extrinsèques, comme la connectivité entre espèces au sein de la communauté d'hôtes et le rôle de différents types de mouvements des hôtes ont été relativement négligés. Dans ce contexte, cette thèse aborde le rôle des causes extrinsèques de l'hétérogénéité de transmission sur la propagation d'infections dans les systèmes multi-hôtes, en utilisant notamment les systèmes tiques-oiseaux marins-microparasites comme support empirique à des approches de modélisation théorique. Quatre principales sources d'hétérogénéité dans les systèmes à transmission vectorielles ont ainsi été considérées : (i) l'hétérogénéité de l'abondance des vecteurs, de leur distribution, et l'estimation des paramètres de la dynamique de leurs populations, (ii) l'hétérogénéité de contact entre espèces de communautés multi-hôtes et multi-vecteurs, (iii) l'hétérogénéité de la propagation d'infections en raison de différents types de comportements des hôtes (avec en particulier, l'importance de considérer les mouvements de prospection entre groupes d'hôtes chez les espèces sociales) et (iv) l'hétérogénéité dans les capacités de dispersion et de transmission d'infections entre vecteurs à traits d'histoire de vie contrastés (dispersion en fonction du stade de vie). Nous soulignons d'abord l'importance potentielle d'une estimation fiable des abondances d'ectoparasites, à l'aide d'approches hiérarchiques susceptibles de prendre en compte à la fois l'hétérogénéité de leur probabilité de détection et leur distribution agrégée. Ensuite, nous utilisons une approche permettant d'étudier l'impact des caractéristiques du réseau d'interactions au sein de la communauté d'hôtes sur la transmission et le maintien d'infections. Nos résultats indiquent que la structure de la communauté mais aussi les propriétés locales des espèces modèlent l'émergence d'espèces qui contribuent disproportionnellement à la transmission de l'infection (`superspreader') et d'espèces qui contribuent disproportionnellement au maintien de l'infection (`keystone') dans les communautés d'infections multi-hôtes, multi-vecteurs. Nous avons également exploré le rôle de la contribution de différents comportement de déplacement des hôtes et des traits d'histoire de vie des vecteurs sur la propagation d'agents infectieux. Une revue de la littérature nous a permis de souligner l'importance potentielle, relativement aux autres comportements de déplacement plus communément considérés, des mouvements de prospection entre groupes d'hôtes sur le rôle dans la transmission d'infections. Les résultats d'un travail théorique nous on également permis de montrer l'importance des caractéristiques des traits d'histoire de vie des vecteurs (notamment la durée de repas sanguins) et des contraintes démographiques (effet Allee) sur le potentiel de colonisation des tiques. Cette différence de dispersion en fonction du stade est ainsi susceptible d'avoir une incidence sur la propagation d'infections à transmission vectorielle et la structure génétique des populations de tiques. Dans l'ensemble, les travaux menés ont permis de mettre en évidence l'importance de l'étudie des déterminants des hétérogénéités de transmission et leurs conséquences dans les systèmes à transmission vectorielles, pour une meilleure compréhension de l’écologie et l’évolution des interactions entre hôtes et parasites, avec des implications potentielles pour le contrôle des maladies. / Different hosts may not contribute equally to parasite transmission. For instance, some individuals or species may be more heavily infected than others, an observation that lead to the `20/80' rule, stating that in many cases 20% of individuals are responsible for 80% of the transmission. However, studies on heterogeneity in transmission have primarily focused on intrinsic factors of transmission, such as susceptibility and infectivity, while the impact of extrinsic factors, such as connectivity network among individuals or species of the host community and the role of various host movements has been relatively neglected. This thesis investigates the role of extrinsic transmission heterogeneities on the spread of infectious disease in multi-host systems, using tick-seabird-microparasite system as empirical models for theoretical investigations. Four main causes of heterogeneity in transmission of vector-borne diseases were considered : (i) heterogeneity in vector abundance, distribution, and estimation thereof (ii) heterogeneity in contact among species in a multi-host, multi-vector community, (iii) heterogeneity in infection spread caused by different host mouvement behaviors (notably the potential role of ‘prospecting’ by host individual among host groups), and (iv) heterogeneity in dispersal ability and transmission competence among vectors with different life-history traits (stage-dependent dispersal). First, we highlight the need to accurately estimate ectoparasite abundances with hierarchical modeling approaches that can take into account both heterogeneity in their detection probability and their aggregated distribution among hosts. Next, using network theory to examine the impact of community context on disease transmission and maintenance, we found that network structure (modularity, nestedness) and node-based measures (e.g., centrality) both shape the emergence of ‘super-spreader’ species (i.e., species that contribute disproportionally to disease transmission) and keystone species (i.e., species that contribute disproportionally to disease maintenance) in multi-host, multi-vector pathogens communities. Finally, we explored the contribution of host behavior and vector life-history traits to the spread of infectious agents. By reviewing the recent literature, we highlight the fact that prospecting, relative to various other types of host movement, may be of key importance to disease transmission among host groups, notably in social species. We also show how vector life history characteristics (e.g. length of bloodmeals) and demographic constraints (Allee effects) affect their colonization potential. Soft ticks, which take a single, long bloodmeal at only the larval stage, should have much lower colonization rates than hard ticks, which take a single, long bloodmeal at every life stage. These stage-dependent dispersal discrepancies may have direct consequences for the genetic structure of their populations and the spread of vector-borne infectious agents. Overall, these findings highlight the importance of studying the causes and consequences of transmission heterogeneity in multi-host, multi-vector systems. A series of potentially important sources of heterogeneity in parasite transmission are outlined, together with perspectives of empirical and theoretical studies to further explore their implications for understanding ecology and evolution of host-parasite interactions and for disease management purposes.