Common Ancestry: Study Guide (Biology 7.7)

What “common ancestry” means

Two species share a common ancestor if, traced back far enough, both lineages lead to the same ancestral population. Mushrooms, oak trees, amoebae and humans look nothing alike. Yet inside their cells you find the same set of structures, built in the same way. This topic asks: what is that shared set, and why does it point to one ancestor of all eukaryotes?

A eukaryote is any organism whose cells have a nucleus. The group includes animals, plants, fungi and many single-celled protists. The other two domains of life, bacteria and archaea, are prokaryotes.

Background: unity across all of life

Before looking at eukaryotes, notice what every living cell shares. This is background linking to Topic 7.6 and Unit 6.

• DNA stores the genetic information, and RNA carries it to the ribosomes.
• The genetic code is almost the same in every organism: the same codon means the same amino acid.
• Ribosomes build proteins in every cell.
• Every cell has a plasma membrane built mainly from phospholipids and uses ATP to carry energy.

These features link all three domains. The features in the next section are different. They appear in eukaryotes, and are missing from most bacteria and archaea. So they mark a later common ancestor: the ancestor of all eukaryotes.

Three features every eukaryote shares

1. Membrane-bound organelles

Every eukaryotic cell divides its interior into compartments with membranes around them.

• The nucleus is wrapped in a double membrane, the nuclear envelope, with pores that control what passes in and out.
• The endomembrane system (endoplasmic reticulum, Golgi complex, vesicles, lysosomes or vacuoles) folds, sorts and ships proteins and lipids.
• Mitochondria are found in nearly all eukaryotes. A very few have lost them or kept only reduced remnants. Plants and algae also have chloroplasts.

Topic 2.10 showed that mitochondria and chloroplasts came from bacteria taken in by an ancestral cell (endosymbiosis). Mitochondria in fungi, plants and animals have the same double membrane, their own DNA (often a circular molecule, like a bacterial chromosome) and their own bacteria-like ribosomes. The simplest explanation is that the endosymbiosis happened once, in an ancestor of all of them, rather than separately in each group.

Bacteria and archaea have no nucleus and no membrane-bound organelles. Their DNA sits in a region of the cytoplasm called the nucleoid.

2. Linear chromosomes

A eukaryotic nucleus holds several linear chromosomes, each a long DNA molecule with two free ends. The ends are capped by telomeres: repeated DNA sequences that protect the ends and are kept in length by the enzyme telomerase in some cells. Linear chromosomes are copied, condensed and separated by the same process, mitosis, in every eukaryote.

Most bacteria and archaea have a single circular chromosome, with no ends, so they need no telomeres. (A few bacteria have linear chromosomes, but they protect the ends in other ways.)

3. Genes that contain introns

In animals and plants, most protein-coding genes are split genes, and nearly every eukaryote studied has at least some. Coding stretches (exons) are interrupted by non-coding stretches (introns). After transcription, a large RNA-and-protein machine called the spliceosome cuts out the introns and joins the exons (Topic 6.3).

The spliceosome is built from the same kinds of small RNAs and proteins in fungi, plants, animals and protists. Its parts are homologous: their sequences are clearly related. Introns are rare in bacteria and archaea, and the few they have are of other kinds, removed without a spliceosome. Prokaryotes have no spliceosome.

Why shared features point to one ancestor

Two kinds of similarity exist in biology.

• Homology: similarity because the feature was inherited from a common ancestor. The detailed build is the same, even when the use differs.
• Independent origin (convergence): similarity because two lineages met a similar problem in a similar way. The general function matches, but the detailed build differs.

Eukaryotic features pass the homology test in three ways.

1. They match in fine detail. The nuclear pores, the spliceosome and the proteins that move chromosomes in mitosis are made of related molecules in yeast, plants and humans. Separate origins would be very unlikely to produce the same molecules for the same jobs.
2. They occur together. The same organisms have all three features. Nothing about having a nucleus forces a cell to split its genes into exons and introns. A package of unrelated features shared by one group is best explained by inheritance from one ancestor that already had the package.
3. They fit with other evidence. DNA and protein sequence comparisons (Topic 7.6) group all eukaryotes together and place them separately from most bacteria.

Common ancestry is therefore an explanation that makes predictions. If all eukaryotes share one ancestor, then a newly discovered eukaryote should also have linear chromosomes and a spliceosome, and a drug that blocks a shared eukaryotic machine should work on very different eukaryotes. Worked example 2 tests that kind of prediction.

Comparing gene structure

If two species inherited a split gene from a common ancestor, some of their introns may sit at exactly the same place in the gene, even in species that look very different. Figure 2 shows a fictional example.

Worked example 1: reading gene structures as evidence

Question. Use Figure 2. (a) Which intron positions are shared by P and Q, and which by all three species? (b) Explain how shared positions support common ancestry. (c) Species R has only one intron. Does this weaken the conclusion?

(a) Reading the figure.

1. P has introns after codons 42, 118 and 230.
2. Q has introns after codons 42, 118, 230 and 301.
3. R has one intron, after codon 118.
4. Shared by P and Q: 42, 118 and 230. Shared by all three: 118 only.

(b) Explanation. An intron could in principle be inserted anywhere in a 360-codon gene. If introns had arisen separately in animals, plants and fungi, the chance that they would land after exactly the same codon is very small. Shared positions are best explained if the common ancestor of P, Q and R already had a split gene with introns at those places, and each lineage inherited them. The spliceosomes that remove these introns are also homologous, so the whole system was inherited.

(c) Caution. Introns can be lost (and occasionally gained) over evolutionary time. Some fungi, such as yeasts, have far fewer introns than animals or plants. So R’s single intron fits a lineage that lost introns after 42 and 230, while keeping the one after 118. The position R kept is one the others share, which still supports common ancestry. Q’s extra intron after 301 could have been gained in the plant lineage, or lost in the others. One gene is weak evidence on its own; biologists compare many genes and other data before drawing a firm conclusion.

Worked example 2: predicting the effect of blocking splicing

Question. A fictional drug, compound S, binds to a protein found in the spliceosome. Researchers grew five kinds of cell with and without compound S for 24 hours. For each kind of cell, the control and treated cultures started at the same density. Results (cell density, millions of cells per mL):

Cells	Control	With compound S
Yeast (fungus)	8.0	1.6
Green alga	5.0	1.2
Human cell line	2.4	0.30
E. coli (bacterium)	12.0	11.7
An archaeon	3.2	3.15

(a) Express growth with compound S as a percentage of the control for each kind of cell. (b) Explain the pattern using common ancestry. (c) Predict what happens inside a yeast cell exposed to compound S, at the level of RNA and protein.

(a) Calculation. Percentage of control = (treated ÷ control) × 100.

1. Yeast: 1.6 ÷ 8.0 × 100 = 20%.
2. Green alga: 1.2 ÷ 5.0 × 100 = 24%.
3. Human cell line: 0.30 ÷ 2.4 × 100 = 12.5%, about 13%.
4. E. coli: 11.7 ÷ 12.0 × 100 = 97.5%, about 98%.
5. Archaeon: 3.15 ÷ 3.2 × 100 = 98.4%, about 98%.

(b) Explanation. All three eukaryotes, from three very different groups, grew far less with compound S (13–24% of control). Both prokaryotes were almost unaffected. Compound S targets a spliceosome protein. Yeast, algae and human cells all have spliceosomes built from homologous parts, inherited from the common ancestor of eukaryotes, so the drug can bind in all three. Bacteria and archaea have no spliceosome, so the drug has nothing to act on. The shared response is evidence of a shared machine, and a shared machine is evidence of a shared ancestor.

(c) Prediction (cause and effect).

1. The spliceosome cannot remove introns properly, so pre-mRNA with introns builds up in the nucleus.
2. Fewer correctly spliced mRNAs leave the nucleus, so less of each protein encoded by an intron-containing gene is made. Any mRNA that keeps an intron may code for a faulty or shortened protein.
3. Proteins needed for growth and division run short, so the cells divide less. This matches the data.

Check. The control column matters. Without it, a low density could just mean that the cells grow slowly anyway. Comparing each cell type with its own control removes that difference.

Common misconceptions

• “Common ancestry means one living species evolved from another.” Living species share ancestors. Humans did not evolve from yeast; both descend from an ancient population.
• “Bacteria are the ancestors of eukaryotes, so modern bacteria will turn into eukaryotes.” Modern bacteria are modern species with their own long history. Eukaryotes arose once, long ago, from ancestors that were not like any single living species.
• “Any similarity shows common ancestry.” Only homologous features count. A plant cell wall (cellulose) and a bacterial cell wall (peptidoglycan) do a similar job but are built from different molecules.
• “Features shared by all life show that eukaryotes are related to each other.” They do, but they also link eukaryotes to bacteria. Only features limited to eukaryotes point to the common ancestor of eukaryotes.
• “Introns are useless, so they say nothing about evolution.” Whatever their function, their positions and the spliceosome that removes them are inherited, which makes them evidence.
• “Eukaryotes without mitochondria disprove common ancestry.” The few eukaryotes without full mitochondria have lost or reduced them. Losing a feature is a change within a lineage, not evidence of a separate origin.
• “Circular and linear chromosomes work the same way.” Linear chromosomes have free ends that need telomeres. Circular chromosomes have no ends.

Where this leads

Next, Topic 7.8 shows that evolution did not stop with the first eukaryotes: all species are still evolving. Go on to Continuing Evolution, and look back at Evidence of Evolution for the sequence data that support this topic. Test yourself with the practice questions, then use the revision notes and the checklist to consolidate.