Elucidating the (re )emergence of human pathogens with Bayesian phylogenetics The (re )emergence of an infectious disease is a complex phenomenon that requires the interplay of multiple factors involving the pathogen (e.g. virulence transmissibility immune scape capacity) host species (e.g. population size mobility immunity level) and the environment (e.g. climatic conditions hygiene conditions). In the manuscripts included in this thesis I employed Bayesian phylogenetic models to elucidate the (re )emergence of three human pathogens that occurred under different conditions and at distinct time points. At the start of the timeline represented by the analyzed datasets I investigated in manuscript C the emergence of human adapted Salmonella enterica enterica serovars and its connection to animal domestication by performing a molecular dating analysis using modern samples and ancient genomes up to 5500 years old. Moving forward in the timeline in Manuscript A I studied the migration dynamics of the bacterium Yersinia pestis in Madagascar to elucidate the factors that led to the re emergence of plague in the city of Mahajanga during the 1990s. Lastly in Manuscript B I performed a recombination aware phylogenetic analysis to clarify the role of genetic recombination in the emergence of SARS CoV 2 the latest human pathogen to cause a severe pandemic which started in 2019. Altogether the three manuscripts provide new knowledge about the (re )emergence of viral and bacterial pathogens that have left an indelible mark on human history. Furthermore I showed that Bayesian phylogenetic models can be applied to perform molecular dating analyses of datasets with very different time windows and to disentangle the role of pathogens mobility and recombination on disease (re ) emergence.