Seeing Phylogenetic Trees in Action

As this chapter shows, it's possible to reconstruct the history of evolution through phylogenetic trees. Now the question is how scientists can use these trees. The answer is that they can use trees for all sorts of purposes, like these:

1 Reconstructing the history of human migration patterns 1 Quantifying the process of co-evolution il Tracing the spread of the human immunodeficiency virus (HIV) epidemic I Designing a better flu vaccine

The following paragraphs offer several examples that involve the HIV virus. The other items are covered in detail in other chapters.

Example 1: The Florida dentist

In the early 1990s, a large number of patients of a particular Florida dentist contracted HIV. The research question at the time was whether they could have contracted the HIV virus from the dentist. Specifically, given that many strains of the HIV virus were circulating in the community, was it possible to connect the HIV strains found in the infected patients with the virus found in their dentist?

By constructing a phylogenetic tree that included the dentist's HIV strain, the six patients' HIV strains, and a selection of HIV strains from the broader community, investigators showed that the patient strains had a recent common ancestor with the dentist's strain, not with the strains sampled from the community.

The take-home message is that even though researchers don't know exactly how these viruses got from the dentist to the patients, they know that the patients did indeed contract HIV from the dentist.

Example 2: General exposure to HIV

In this example, the question is how did the human species become exposed to HIV? Phylogenetic analysis can address this question by reconstructing an evolutionary tree of not just HIV, but of other species' immunodeficiency viruses as well.

The two major types of human immunodeficiency virus are HIV-1 and HIV-2. Reconstructing the tree of immunodeficiency viruses reveals that HIV-1 strains are most closely related to the simian immunodeficiency virus found in chimpanzees, whereas HIV-2 strains are more closely related to the simian immunodeficiency virus found in sooty mangabeys.

The fact that each human virus is related to a different simian virus indicates that the human viruses are the result of two separate events in which a simian immunodeficiency virus jumped to a human host. The phylogenetic analysis that produced this information also directs researchers' attention to the specific simian viruses that are implicated as the parent of the human infection.

You can read more about the origins of HIV in Chapter 18.

Example 3: Legal cases

The science of phylogenetics has made its way into the legal world, where it has been used to prove both guilt and innocence. In the first case, a doctor was convicted of attempted murder after infecting his former girlfriend with an HIV strain from one of his patients. This case was the first instance in which phylogenetic evidence was admitted in a U.S. court. Phylogenetic analysis of HIV sequences from the infected woman and the patient, as well as analysis of additional sequences from the community, revealed that the infected woman's HIV strain was most closely related to the strain from the patient. Her strain even had resistance genes against the HIV medications with which the patient was being treated.

The second case involved six foreign health workers in Libya accused of intentionally spreading the HIV virus to hospital patients. An analysis of the HIV strains infecting those patients revealed such a diversity of strains that the parent strain from which the strains evolved would have to have been present in Libya before any of the foreign health workers arrived. Initially sentenced to death despite the scientific evidence supporting their innocence, the sentence was later commuted to life imprisonment. Jailed since 1999, the workers were finally able to leave Libya in the summer of 2007 following diplomatic negotiations.

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