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. 1) 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 analyze whole genome sequences of almost all guenon species, reconstruct evolutionary relationships and analyze the frequency, prevalence and timing of gene flow across this radiation. We pay particular attention to introgressed genes that may promote adaptations. 2) 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 explore the patterns of introgression near to the chromosomal breakpoints, investigating if presence of particular genomic features (e.g., repeats) can explain chromosomal instability. 3) 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. 4) 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 >30 different mammalian host species with different ecologies and diets, we attempt to understand if host phylogeny or ecology are the main drivers of oral microbiome evolution. 5) 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. 6) We study the connection between population declines and microbiomes, hypothesizing that changes in host genetic diversity triggered by population decline will have an impact on the associated microbial communities, possibly driving them towards a pathogenic state. 7) We investigate the evolutionary processes behind different color patterns of strawberry poison dart frogs, inferring both the action of natural and sexual selection. To this end we assemble the frog genome and use both DNA sequencing and transcriptomic data to identify changes in population size and differentially expressed genes.