Over the decades, the protist kingdom was dismantled as sequence analysis revealed new genetic (and thus evolutionary) relationships among these eukaryotes.
Moreover, protists that share similar morphological features may have evolved similar structures due to similar selective pressures rather than due to a recent common ancestor. This phenomenon, called convergent evolution, is one of the reasons protists are so difficult to classify. The resulting taxonomy scheme groups the entire eukaryotic domain into six 'supergroups' that include all protists as well as animals, plants and fungi that evolved from a common ancestor. Supergroups are believed to be monophyletic. That is, because all organisms within each supergroup are thought to have evolved from a single common ancestor, all members are most closely related to each other than organisms outside that group.
Evidence for monophyly of some groups is still lacking.
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