Phylogenetic trees can help solve practical problems.

The sequence of changes on a tree from its root to its tips documents evolutionary changes that have accumulated through time. Trees suggest which groups are older than others, and which traits came first and which followed later. Proper phylogenetic placement thus reveals a great deal about evolutionary history, and it can have practical consequences as well. For example, oomycetes, microorganisms responsible for potato blight and other important diseases of food crops, were long thought to be fungi because they look like some fungal species. The discovery, using molecular characters, that oomycetes belong to a very different group of eukaryotic organisms, has opened up new possibilities for understanding and controlling these plant pathogens. Similarly, in 2006, researchers used DNA sequences to identify the Malaysian parent population of a species of butterfly called lime swallowtails that had become an invasive species in the Dominican Republic, pinpointing the source populations from which natural enemies of this pest can be sought.

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Phylogenetics solved a famous case in which an HIV-positive dentist in Florida was accused of infecting his patients (Fig. 23.10). HIV nucleotide sequences evolve so rapidly that biologists can build phylogenetic trees that trace the spread of specific strains from one individual to the next. Phylogenetic study of HIV present in samples from several infected patients, the dentist, and other individuals provided evidence that the dentist had, indeed, infected his patients.

HOW DO WE KNOW?

FIG. 23.10

Did an HIV-positive dentist spread the AIDS virus to his patients?

BACKGROUND In the late 1980s, several patients of a Florida dentist contracted AIDS. Molecular analysis showed that the dentist was HIV-positive.

HYPOTHESIS It was hypothesized that the patients acquired HIV during dental procedures carried out by the infected dentist.

METHOD Researchers obtained two HIV samples each (denoted 1 and 2 in the figure) from several people, including the dentist (Dentist 1 and Dentist 2), several of his patients (Patients A through G), and other HIV-positive individuals chosen at random from the local population (LP). In addition, a strain of HIV from Africa (HIVELI) was included in the analysis.

RESULTS Biologists constructed a phylogeny based on the nucleotide sequence of a rapidly evolving gene in the genome of HIV. Because the gene evolves so quickly, its mutations preserve a record of evolutionary relatedness on a very fine scale. HIV in some of the infected patients—patients A, B, C, E, and G—were more similar to the dentist’s HIV than they were to samples from other infected individuals. Some patients’ sequences, however, did not cluster with the dentist’s, suggesting that these patients, D and F, had acquired their HIV infections from other sources.

CONCLUSION HIV phylogeny makes it highly likely that the dentist infected several of his patients. The details of how the patients were infected remain unknown, but rigidly observed safety practices make it unlikely that such a tragedy could occur again.

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FIG. 23.10

FOLLOW-UP WORK Phylogenies based on molecular sequence characters are now routinely used to study the origin and spread of infectious diseases, such as swine flu and Ebola.

SOURCE Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. “Application and Accuracy of Molecular Phylogenies.” Science 264: 671–677.

Similarly, phylogenetic studies of influenza virus strains show their origins and subsequent movements among geographic regions and individual patients. Today, there is a growing effort to use specific DNA sequences as a kind of fingerprint or barcode for tracking biological material. Such information could quickly identify samples of shipments of meat as being from endangered species, or track newly emerging pests. The Consortium for the Barcode of Life has already accumulated species-specific DNA barcodes for more than 100,000 species. Phylogenetic evidence provides a powerful tool for evolutionary analysis and is useful across timescales ranging from months to the entire history of life, from the rise of epidemics to the origins of metabolic diversity.

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