Dokument: Inference and Evolutionary Impact of Horizontal Gene Transfer in Bacteria: Quality Over Quantity on the Road to New Environments

Titel:	Inference and Evolutionary Impact of Horizontal Gene Transfer in Bacteria: Quality Over Quantity on the Road to New Environments
URL für Lesezeichen:	https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=71472
URN (NBN):	urn:nbn:de:hbz:061-20251127-111302-9
Kollektion:	Dissertationen
Sprache:	Englisch
Dokumententyp:	Wissenschaftliche Abschlussarbeiten » Dissertation
Medientyp:	Text
Autor:	Mishra, Swastik [Autor]
Dateien:	[Dateien anzeigen] Adobe PDF [Details] 17,89 MB in einer Datei [ZIP-Datei erzeugen] Dateien vom 21.11.2025 / geändert 21.11.2025
Beitragende:	Prof. Dr. Lercher, Martin [Betreuer/Doktorvater] Prof. Dr. Martin, William F. [Gutachter]
Dewey Dezimal-Klassifikation:	000 Informatik, Informationswissenschaft, allgemeine Werke » 004 Datenverarbeitung; Informatik
Beschreibung:	Regarded as a cornerstone of prokaryotic innovation, the process of horizontal gene transfer (HGT) drives genetic exchange between organisms and, in doing so, is widely believed to significantly enhance the adaptability and evolutionary success of prokaryotes. HGT is associated with bacterial colonization of diverse environments, from antibiotic-resistant pathogens in clinical settings to extremophiles in harsh ecological niches. However, large-scale empirical studies of HGT's role in environmental adaptation remain limited, constrained by significant methodological challenges in accurately detecting and validating transfer events. This cumulative thesis addresses both methodological issues and the evolutionary significance of horizontal gene transfer. Manuscript 1 systematically evaluates the performance of diverse HGT inference methods. By testing whether HGT events inferred from real genomic data follow expected patterns, such as neighboring genes being co-transferred on the same DNA fragment, we identify best practices for recovering biologically realistic HGT events. Contrary to prevailing assumptions, our results demonstrate that implicit phylogenetic approaches using gene presence-absence matrices outperform gene tree-based and parametric sequence composition-based methods, yielding fewer false positives and thus more meaningful biological inferences. Based on these methodological insights, Manuscript 2 applies the best-performing HGT inference technique to probe the relationship between HGT and environmental transitions at scale. By integrating gene and ecosystem presence-absence data across a wide array of bacterial lineages, we reveal that bacteria colonizing new ecosystems generally possess smaller genomes and undergo lower rates of HGT – with both observations contradicting a priori expectations. The reduced HGT frequency is entirely explained by genome size, with no independent effect of environmental change, challenging prevailing ideas that genomic flexibility via increased HGT rates is essential. In Manuscript 3, we investigate the evolutionary fate of transferred genes, uncovering a two-phase process: rapid loss of most long-distance HGTs shortly after transfer, followed by persistence in the remaining cases. Remarkably, a minority of bacterial genomes harbor the majority of inter-phylum transfers. The retention of these genes is gene function-dependent, illustrating the swift and selective nature of bacterial genome streamlining following HGT. The final chapter, Chapter 5, synthesizes the main findings and explores their broader implications for prokaryotic genome evolution. It discusses how the methodological and conceptual advances developed in this thesis can inform future research, and proposes new directions for advancing our understanding of horizontal gene transfer and genome dynamics in prokaryotes. In sum, this dissertation demonstrates that the evolutionary success of bacteria hinges on the discerning retention of functionally relevant genes and the efficient purging of superfluous ones – embodying a "quality over quantity'' principle at the genomic level. This same philosophy of "quality over quantity'' applies to the inference of horizontal gene transfer: methods grounded in limited but high-quality information yield more precise and meaningful evolutionary insights than approaches that merely maximize the information used for inferences. By developing and applying robust strategies for both HGT detection and interpretation, this work provides essential conceptual and methodological advances for the broader study of prokaryotic genome evolution.
Lizenz:	Dieses Werk ist lizenziert unter einer Creative Commons Namensnennung 4.0 International Lizenz
Fachbereich / Einrichtung:	Mathematisch- Naturwissenschaftliche Fakultät » WE Informatik » Bioinformatik
Dokument erstellt am:	27.11.2025
Dateien geändert am:	27.11.2025
Promotionsantrag am:	20.08.2025
Datum der Promotion:	06.11.2025