In fact, find me one bebeficial mutation in Nature. Sickle-cell anemia is a genetic mutation. In Africa, malaria is a devastating disease that kills many people. There is a greater frequency of people with the sickle cell gene in Africa than in the rest of the world. This in fact is the definition of evolution - a change in gene frequencies of a population over time.
Taxonomy is a system used to make things easier for biologists.
This being said, nature never fits into the neat little categories that we as humans like to put things into. There are many, many exceptions to the species rule. Even amongst humans there are people with extremely different genetic makeups. For example people with Downs Syndrome have a whole extra chromosome. Ah, but the mutation is not beneficial to survival.