How many kingdoms of life are there? or What classification system do you use?
Evolutionary biology is a great help as a basis for thinking through many problems in biology. Unfortunately there isn’t broad awareness of the somewhat recent dramatic changes in understand of just how amazingly diverse life is on earth. The old plant animal fungi, or plant animal fungi protest monera systems don’t account for the vast majority of species. For that we have to take into account some revolutionary work done in the 70’s by Carl Woese and others, who demonstrated that there are three domains of life. These are the bacteria the achaea and the eukaryotes. Bacteria are single celled organisms with no nucleus. Archaea are superficially similar to bacteria but have diverged into different domain at a very early time in the history of life. Archaea were identified by measuring how similar some of their cellular machinery (rDNA sequences) was to other organism. These microorganisms were found to be more similar to the eukaryotes than bacteria. The eukaryotes then are the third domain of life consisting of cells that have a nucleus that compartmentalizes the DNA from the rest of the cell.
Current models of early life propose that early on archaea and bacteria diverged. Some archea began evolving into eukaryotes with the introduction of a nucleus. Later symbiotic associations with bacteria gave the organelles the mitochondria important for energy and metabolism, and the chloroplasts that allow plants to undergo photosynthesis.
Complicating this is the recent discovery of rampant later gene transfer between bacteria, between archaea, and even between plant species, with mechanisms differing between them. This creates a web of relationships more so than a tree.
Lastly It’s controversial as to where viruses fit in this scheme. It’s likely that they have ancient origin but exactly how is unknown. Classification of viruses themselves however can be accomplished by how they replicate, called the Baltimore system after David Baltimore.
Photo credit from:Wikipedia; and Barth F. Smets & Tamar Barkay, Nature Reviews Microbiology (2005)