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CSI evolution

HIV tree
Phylogenetics revealed that the accused could not have caused the infections in the Libyan outbreak of HIV because they were not working at the hospital when the infections began.
Beyond showing patterns of lineage splitting, evolutionary trees can help us determine when those splitting events happened. This can come in handy for understanding when a particular infection occurred. For example, in 1999 a group of foreign health workers in Libya were accused of deliberately infecting hospitalized children with HIV. However, other lines of evidence pointed to the poor hygiene practices at the hospital as the culprit. In an effort to defend the health workers and establish their innocence, an international team of researchers sequenced the infected children's HIV viruses and used them to build an evolutionary tree relating those viruses to other HIV viruses. The children's viruses clustered together in a clade, suggesting a single original source of the infection, but they had also evolved many differences from one another — so many that it seemed that their viruses had been diversifying for some time. When mathematical models were used to reconstruct the timing of events, it became clear that the viruses had begun infecting children at the hospital around 1995 or 1996.13 Since the foreign workers didn't even arrive at the hospital until 1998, they could not have been responsible. Instead, it seems that a patient who visited the hospital before 1997 was the unwitting source of the outbreak, which was propagated by practices like reusing dirty needles. After many articles about their innocence and much negotiation, the medics were released. Similar techniques have been used to study the evolutionary history of the most common strain of HIV. These efforts have pinpointed 1908 as the year that this virus made the leap from chimpanzees to humans.14 Using these techniques, scientists have been able to reconstruct the pattern of events that characterized the origin of the HIV epidemic, the 1918 Spanish flu epidemic,15 and other disease outbreaks, shedding light on the conditions that foster deadly cross-species disease swaps.

13 de Oliveira, T., O.G. Pybus, A. Rambaut, M. Salemi, S. Cassol, M. Ciccozzi, G. Rezza, G.C. Gattinara, R. D'Arrigo, M. Amicosante, L. Perrin, V. Colizzi, C.F. Perno, and Benghazi Study Group. 2006. HIV-1 and HCV sequences from Libyan outbreak. Nature 444:836-837.

14 Worobey, M., M. Gemmel, D.E. Teuwen, T. Haselkorn, K. Kunstman, M. Bunce, J. Muyembe, J.M. Kabongo, R.M. Kalengayi, E. Van Marck, M.T.P. Gilbert, and S.M. Wolinsky. 2008. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455:661-664.

15 Dos Reis, M., A.J. Hay, and R.A. Goldstein. 2009. Using non-homogeneous models of nucleotide substitution to identify host shift events: Application to the origin of the 1918 'Spanish' influenza pandemic virus. Journal of Molecular Evolution 10.1007/s00239-009-9282-x

Trees matter
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Evo examples
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