Catch a Killer
Perhaps the most widely circulated (and most tabloid-worthy) example of phylogenetics in action is the case of the State of Louisiana versus Richard J. Schmidt (Vogel 1996). As summarized by Wiley (2010), in 1995, Schmidt (a medical doctor) was accused of injecting his former mistress (Janet Allen, a nurse) with HIV-positive blood from one of his patients. Allen and Schmidt had been romantically involved for a decade, and Schmidt had been giving her regular vitamin injections. After threatening to break off the affair, Allen found that she was HIV positive and accused Schmidt of substituting tainted blood for one of her injections.
Did the doctor do it? If Schmidt were accused of retaliating against Allen with a simple poison, the investigation would have taken a very different course. But unlike a poison, HIV has genetic material (RNA) and makes copies of itself, meaning that it can evolve. In fact, because of its high mutation rate and rapid replication rate, HIV evolves remarkably quickly. While the process of speciation may take tens or hundreds of thousands of years in animals like fruit flies, HIV can diversify into many different strains within a single individual in less than a year (Fig. 1). As HIV evolves, it accumulates mutations in its genome—some beneficial to the virus (and likely, bad for human hosts!), some slightly deleterious to the virus, and most with no notable effect at all. Whatever their impact, those mutations record events in the lineage’s history, turning the genome into something of a marked-up road map—a spotty, but informative, account of where the lineage has been at different points in its evolutionary past. This makes it possible for scientists to use the virus’s RNA sequence to reconstruct the family relationships among different strains (i.e., to build a phylogeny).
Biologists compared samples of HIV strains from the victim to samples from the doctor’s HIV-positive patient and to viral strains from other HIV-positive people living in the local area (Metzker et al. 2002). The biologists sequenced different regions of the viral RNA and used these data to build phylogenies. Figure 2 shows the phylogeny they built using part of the HIV reverse transcriptase gene. Every HIV strain sequence is different, but the phylogeny shows how they are related. The victim’s sequences are most closely related to those of the doctor’s HIV-positive patient and are much more distantly related to other HIV strains. Even more convincingly, the victim’s sequences are nested within the clade formed by the patient’s sequences; they are a subset of the patient’s sequences. This is exactly what we would expect to observe if the patient was infected with HIV, the virus evolved into many different strains within him, and then the victim was infected with one of the patient’s strains, and the virus continued to evolve within her. Based partly on the strength of phylogenetic evidence such as this, the doctor was convicted of attempted murder in 1998 (Vogel 1996).