Studies of mammalian genomes and their associated microorganisms can provide unique insights into the evolutionary processes that shape species diversity, drive local adaptation and promote co-diversification (and possibly co-evolution) of hosts and their microbiomes. We are working on a set of projects that range from speciation genomics to population genomics to metagenomics. First, we look at the effects of (ancient) gene flow on generating remarkable species diversity in a group of African monkeys, known as guenons. To this end, we analyse whole genome sequences of almost all guenon species, reconstruct evolutionary relationships using markers of different inheritance modes (mitochondrial, autosomal and sex-linked genes) and analyse the frequency, prevalence and timing of gene flow across this radiation. We pay particular attention to introgressed genes that may promote adaptations and speculate that some species in the complex could be the result of hybrid speciation. Second, we attempt to understand how genomic architecture may promote or hinder gene flow. To this end, we generate genome assemblies of multiple guenon species that differ in their karyotypes but have experienced ancient (or present-day) hybridization. We localize the introgressed region on the chromosome models to understand which genome structures are conductive of introgression. Third, we investigate how adaptations to the simian immunodeficiency virus (SIV), a close relative of the human immunodeficiency virus (HIV) and a strong selective force in primates, affected the guenon evolution. Some guenon species are natural hosts to SIV and live with the virus without developing AIDS. The prevalence of SIV among guenons differs, however, and may have led to host-virus co-evolution. Fourth, we try to decipher the factors shaping the oral microbiome, using a metagenomic approach on dental calculus – a calcified form of the microbial biofilm. Using 29 different species with different ecologies and habitats, we attempt to understand if host phylogeny or ecology are the main drivers of oral microbiome evolution. Finally, we infer how human use of antibiotics may have impacted the prevalence and diversity of antibiotic resistance genes that reside in the oral microbiome of wild animals around the globe.