Evolution of prokaryotes (bacteria and archaea) and viruses is fueled by intense gene exchange and shaped by the incessant arms race between parasites (bacteriophages and archaeal viruses) and hosts. Both processes account for microbes’ diversity and ability to quickly adapt to and exploit changing environments through the acquisition of new genes and antiviral defense systems. In this talk, I will focus on three fundamental questions concerning microbial and viral evolution: How beneficial (or burdensome) are different classes of genes for the organisms that harbor them? How can slightly beneficial genes and genetic parasites persist in spite of rampant gene loss? And finally, can we develop a conceptual framework to study deep evolutionary relationships among viruses in the absence of a viral Tree of Life?
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