Here are three examples. 1) Pneumocystis, an opportunistic pathogen causing mortality in AIDS patients and immunocompromised individuals, is now known to be a fungus, indicating a different treatment regimen is needed. 2) Phytophtora, an organism causing potato blight, such as the one that caused the Irish famine in the 19th century, is now known not to be a fungus, which explains why fungicides are not effective treatments. 3) Plasmodium, the causative agent of malaria, is now known to share ancestry with photosynthetic organisms and has a vestigial chloroplast, called the apicoplast. This knowledge opens exciting possibilities for novel drug therapies.
The clusters are 1) the Opisthokonta, grouping the animals, fungi, choanoflagellates, and Mesomycetozoa; 2) the Amoebozoa, grouping most traditional amoebae, slime moulds, many testate amoebae, some amoebo-flagellates, and several species without mitochondria; 3) the Excavata, grouping oxymonads, parabasalids, diplomonads, jakobids, and several other genera of heterotrophic flagellates, and possibly including the Euglenozoa and Heterolobosea; 4) the Rhizaria, grouping the Foraminifera, most of the traditional Radiolaria, and the Cercozoa with filose pseudopodia, such as many amoebo-flagellates and some testate amoebae; 5) the Archaeplastida, grouping the Glaucophyta, red algae, green algae, and Plantae; 6) the Chromalveolata, grouping the Alveolata (including ciliates, the dinoflagellates, and the Apicomplexa), cryptophytes, haptophytes, and stramenopiles (including brown algae, the diatoms, many zoosporic fungi, opalinids, amongst others).
Finally, the authors noted that they "adopted a hierarchical system without formal rank designations, such as "class," "sub-class," "su per-order" or "order," The decision to do so has been primarily motivated by utility, to avoid the common problem of a single change causing a cascade of changes to the system. We believe this to be more utilitarian, and less problematic than traditional conventions, as it is not constrained by formally attributing a limited number of rank names."