1What counts as evidence of common ancestry

A shared feature is good evidence of common ancestry when three things are true.

• It is complex. Many parts must work together, so it would be unlikely to arise twice in the same form.
• It is arbitrary. Other designs would do the job as well, so similarity cannot be explained by function alone.
• It is shared in detail. Not just "both have a nucleus" but "both build the nucleus the same way, with the same kinds of proteins".

The three features in the CED meet all three tests. Compare that with the shape of a fish and a dolphin, which is similar because both swim fast, not because they inherited it from a shared ancestor. Similarity from function alone is not evidence of close ancestry (topic 7.10, convergent evolution).

A complex, detailed feature shared by every eukaryote is best explained by a single origin in a common ancestor, not by many separate inventions.

2Evidence 1: membrane-bound organelles

Every eukaryotic cell divides its interior into compartments bounded by membranes.

• A nucleus, enclosed by a double membrane (the nuclear envelope) perforated by nuclear pores, holds the chromosomes. Transcription happens inside, translation outside.
• An endomembrane system of endoplasmic reticulum, Golgi apparatus and vesicles makes, modifies and ships proteins and lipids.
• Mitochondria, with their own small circular DNA and their own ribosomes, carry out aerobic respiration. Nearly all eukaryotes have them, and the few that live without oxygen and lack typical mitochondria still carry small organelles derived from them.

The mitochondria are the strongest single clue. Their DNA and ribosomes resemble those of bacteria, which is the evidence that they began as bacteria living inside an ancestral cell. All eukaryotes having mitochondria, or traces of them, means that this engulfing event happened in the common ancestor of all eukaryotes, before the lineages that became animals, plants and fungi split apart. Chloroplasts, found only in plants and algae, came later, in one branch.

In prokaryotes the DNA lies in the cytoplasm, in a region with no membrane around it, and there is no endomembrane system and no mitochondria.

3Evidence 2: linear chromosomes

A typical prokaryote has one circular chromosome. Eukaryotes package their DNA as several to many linear chromosomes, each a single long DNA molecule with two ends.

Having ends creates a problem that circles do not have: the very tip of a linear DNA molecule cannot be fully copied in replication, so a little is lost each time. Eukaryotes deal with this in the same way: their chromosome tips carry telomeres, repeated non-coding sequences that act as buffers. So linear chromosomes come as a package with telomeres and with the machinery that maintains them, shared across eukaryotes.

Linear chromosomes also go with the eukaryotic way of dividing: mitosis and meiosis, with chromosomes condensed and separated on a spindle (Units 4 and 5). Prokaryotes divide by binary fission.

4Evidence 3: genes that contain introns

Most eukaryotic genes are split. The coding sequences, exons, are interrupted by non-coding sequences, introns. The whole gene is transcribed into pre-mRNA, and a large complex of proteins and RNA, the spliceosome, cuts out the introns and joins the exons before the mRNA leaves the nucleus.

• Introns are found in genes of animals, plants, fungi and protists.
• The spliceosome is built from similar parts and recognises similar signals at the edges of introns across eukaryotes.
• Prokaryotic genes generally have no introns of this kind, and prokaryotes have no spliceosome.

Splitting genes and then splicing them is not the only way to make a protein, as bacteria show every second. Its presence everywhere among eukaryotes, with the same machinery, points to one origin.

5Predicting the effect of a change

The CED pairs this topic with predicting the effects of a change to a biological system. Practise it on the shared features.

A eukaryotic gene in a bacterium. Insert a human gene, introns and all, into a bacterium. The bacterium transcribes the gene, but it has no spliceosome, so the introns stay in the mRNA. Ribosomes translate the intron sequences as if they were coding, so the protein contains wrong amino acids, or translation stops early at a stop codon inside an intron. The protein does not work. (This is why biotechnologists give bacteria a copy of the gene made from mature mRNA, with the introns already gone.)

A faulty spliceosome in a eukaryote. If a mutation damages a spliceosome protein, introns are not removed correctly from many pre-mRNAs at once. Many proteins are made wrongly, and the cell is likely to die. Splicing is shared and essential, which is why it has changed so little.

Removing the nuclear envelope. If ribosomes could reach the DNA, translation could begin on RNA before it had been spliced. The nucleus keeps splicing and translation apart, in space and time.

A newly discovered organism. Suppose a single-celled organism is found that has a nucleus, linear chromosomes with telomeres, and genes with introns removed by a spliceosome. Prediction: it is a eukaryote, and its spliceosome proteins and organelle structures will be more similar in sequence to those of other eukaryotes than to any prokaryote's.