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Most practically for humans, a universal tree of life is important for placing pathogens in their evolutionary context. For example, people thought that organisms called microsporidia which cause wasting diarrhea in patients with AIDS were early diverging eukaryotes. But when you build evolutionary trees, you discover that microsporidia are actually fungi (that have gone crazy).
If patients are infected with this organism, youd certainly like to know who it is to determine how to treat the infection. Using a universal tree to understand the diversity of key ecosystem players - major oxygen producers or carbon cyclers, for example - is also really critical.