The fields of biological classification and phylogenetics are in a state of upheaval. It was very natural for biologists to group plants, animals, and fungi into separate eukaryotic kingdoms, and to throw all the little eukaroytes that didn't seem to fit into the kingdom Protista. However, advancements in microscopy and comparative genetics have given biologists a much stronger understanding of the evolutionary tree. It is now clear that the kingdom Protista is not a true clade.
A clade is defined as a group of organisms that contains a most recent common ancestor and all of its descendants. The adjective used to label a group a clade is monophyletic. Animalia, Plantae, and Fungi are all monophyletic. Protista fails to meet both criteria for a clade. For example, biologists have agreed that the protist Microsporidia evolved from Fungi, but the protist Myxozoa evolved from Animalia. Furthermore, animals seem to have evolved from the protist Choanoflagellates. A group of organisms like the protists that meets neither criterion for a clade is termed polyphyletic.
Biologists aim for a comprehensive hierarchical classification system based on clades. It will take a while for phylogeneticists to sort through the evolutionary chain, but they are making progress. A new monophyletic kingdom Chromista has been agreed upon and more are to come. Some protists will be grouped into the new kingdoms and others will be grouped into Plantae, Metazoa (Animalia), or Fungi. In the meantime, the group Protista is a collection of tiny eukaryotic organisms that we don't know where to put.
"Phyla" of "kingdom" Protista
Not complete, and of course non-monophyletic.
References:
- http://tolweb.org/tree/
- http://www.ucmp.berkeley.edu/alllife/eukaryota.html