Benjamin Toups, Jeremy M. Brown

DNA sequences have become ubiquitous across the biological sciences and are even embedded in the public psyche, perhaps most famously in the context of forensic science. A human being’s DNA changes very little over his or her lifetime, and this inherent stability lends itself well to positively identifying individuals using DNA samples. However, not all genomes are so stable, even over short timespans. One particularly dramatic example is human immunodeficiency virus (HIV-1). Unlike the human genome, the HIV-1 genome has an extraordinarily high mutation rate. This, in combination with recombination, rapid proliferation, and strong selection exerted by host immune systems, leads to exceptionally fast rates of evolution. The result of these interacting processes is a population of diverse and dynamically evolving HIV-1 genomes in the host, which is one reason why the virus is so difficult to eradicate. HIV-1’s rapid rate of evolution also prevents the use of standard DNA fingerprinting techniques that rely on stable, unchanging genomes to connect the infections in different individuals, but such rapid evolution does lend itself particularly well to phylogenetic analysis.