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One of the principal modes of evolution is thought to involve gene duplication followed by divergence.
The original gene retains its vital function, while the copy can change and ultimately can encode a new function.
Eukaryotes must have arisen from prokaryotic ancestors.
Many aspects of this are still unknown, but there is persuasive evidence that the mitochondria and plastids (chloroplasts) of todays eukaryotes are derived from prokaryotes.
If these paralogous gene pairs can be identified by sequence similarity, then the original gene should be present in all organisms whereas the new version will be present only in the more recently derived organisms.
The root for the tree in the diagram above was determined by using paralogous genes for translation elongation factors involved in synthesis of protein chains on the ribosomes.
The gene most commonly used for this codes for the RNA in the small subunit (SSU) of the ribosome.
These domains seem to have diverged from one another a long time ago, presumably from an extinct or as yet undiscovered ancestral line.
The geological record shows that organisms resembling today's prokaryotes have existed on earth for probably 3,500 million years, whereas eukaryotes have existed for perhaps only 1,500-2,000 million years.
In recent years biologists have tended to recognise five Kingdoms of organisms: the Monera (bacteria and bacterium-like organisms) representing prokaryotes, and plants, animals, fungi and protists (mainly unicellular nucleate organisms) representing eukaryotes.
The Five Kingdom approach is attractive in its simplicity, but has significant problems.
One of these concerns the protists - a wide range of disparate organisms such as amoebae, slime moulds, ciliates, algae, etc.
This site was developed as a resource to support my teaching. Of all the cells that make up the normal, healthy human body, more than 99 per cent are the cells of microorganisms living on the skin or in the gut, etc.