Sequence of evolutionary events

Exact orders of evolution are difficult to determine, because of morphological inconsistencies within groups. For instance, dinoflagellates have a number of less specialized features, but they also have more derived features including being biflagellate and having scales, characteristics that bring them close to the alveolata.

Even sequencing of nucleic acid to provide phylogenetic gene trees may not answer all the questions. For instance, sequencing the small subunit nuclear-encoded rRNA reveals that one can follow the evolution of an individual gene, but not necessarily the whole organism, as different regions of rRNA genes evolve at different rates. Phylogenetic pat- terns may also be confused because of transfer of genetic information between lineages as a consequence of endosymbiosis and other mechanisms. Parallel evolution within these organisms is also likely to occur, and superficial similarities within distinct lineages may arise because of loss of features, which is likely to be a significant factor within these apparently simple organisms.

Even the current proposal for five supergroups seems likely to change; recent analysis of opisthokonts and  amoebozoa shows that they  are  closely  related, and  possibly are  still a polyphyletic group. It seems probable that they are close to the root of the tree of life.