High School Biology · Grades 10–12

24Diversification of Living Things

Bread wheat has 42 chromosomes, in six sets of seven: it is the sum of three wild grasses that crossed, twice, in the fields of the first farmers. A python has three hundred vertebrae and a mouse thirty, yet they build their backbones with the same genes. A lichen on a rock is two organisms, a fungus and an alga, that have lived as one for so long that neither can be found alone. And a young chimpanzee learns to crack nuts with a stone by watching its mother, in a forest where the chimpanzees a hundred kilometres away have never learnt. Mutation and the shuffle of the last chapter are not the only ways living things become different; this chapter surveys the others.

24.1 More than mutation

Proposition 24.1 (Sources of diversification)

Point mutations and the sexual shuffle create new alleles and new combinations of them. Beyond these, the diversity of living things has been produced by processes that change the genome on a larger scale — duplicating genes, importing genes from other species, adding whole sets of chromosomes — by changes in the way existing genes are used during development, by associations between species, and, in animals, by behaviour transmitted without any genes at all.

Proof. Admitted at this level. ∎

24.2 New genes from old

Proposition 24.2 (Gene duplication and divergence)

An unequal crossing-over (Chapter 23) or a copying error can leave a chromosome with two copies of a gene. One copy continues its original job; the other, freed of that constraint, accumulates mutations and may acquire a new function — or be lost. Repeated over evolutionary time, this produces gene families: sets of related genes descended from one ancestor, whose degrees of similarity record the order of the duplications.

Evidence. The three opsins and rhodopsin of Chapter 21 are one such family; the globins are another: the several genes for the chains of haemoglobin — one used in the embryo, one in the foetus, two in the adult — and the gene of myoglobin, the oxygen store of muscle, lie in clusters on two chromosomes, are 40% to 80% identical in sequence, and their tree matches the order in which the vertebrate groups appeared. Genomes carry hundreds of such families, and a sizeable fraction of every genome consists of duplicated segments. ∎

How a gene family grows. One gene is duplicated; the copies diverge by mutation until each does a different job; further duplications repeat the process. The globin family supplies different haemoglobin chains at different stages of life.

Proposition 24.3 (Horizontal gene transfer)

Genes can also enter a genome from another species. Bacteria exchange plasmids freely (Chapter 18); viruses carry fragments of their hosts’ DNA from one cell to another and leave copies of their own genes behind; and comparison of genomes shows that even animals and plants have acquired genes this way. About 8% of the human genome is of viral origin, and at least one of those genes, once a virus’s tool for fusing cells, now builds the placenta.

Proof. Admitted at this level. ∎

Proposition 24.4 (Hybridisation and polyploidy)

Two related species can sometimes cross; the hybrid carries one chromosome set from each and is usually sterile, since its chromosomes have no partners to pair with at meiosis. If, by an error of division, the hybrid doubles its chromosomes, every chromosome gains a partner, meiosis works, and a new fertile species — a polyploid — exists at once, isolated from both parents. Half of all flowering plant species have polyploidy in their history; bread wheat, cotton, tobacco and the potato are among them.

Evidence. Wheat: the wild einkorn has $2n = 14$ ; emmer, $2n = 28$ , contains the einkorn set and the set of another wild grass, chromosome by chromosome; bread wheat, $2n = 42$ , adds the set of a third. The three sets can be identified in the bread wheat karyotype and matched to the living wild species, and the crosses can be repeated in the laboratory. A cordgrass that appeared on the coast of Europe in the nineteenth century, fertile and vigorous, has the doubled chromosome set of a sterile hybrid of two species that had never met before ships brought one across the Atlantic. ∎

The origin of bread wheat: two hybridisations, each followed by a doubling of the chromosomes. Each letter is a set of seven chromosomes from one wild species; bread wheat carries six sets.

24.3 Same genes, different uses

Proposition 24.5 (Developmental genes and the timing of their expression)

The genes that lay out an animal’s body plan during development — which end is the head, where the limbs go, how many segments the trunk has — are shared, with little change in sequence, across the animals: the same family of developmental genes organises a fly, a mouse and a human. What differs between species is not so much these genes as where, when and how strongly they are switched on. A change in the regulation of a developmental gene can alter the shape of a body part or the number of repeated parts without changing any protein.

Evidence. The genes that define the regions of the trunk are expressed in the same order from head to tail in a mouse and a python; in the python the region that makes ribbed vertebrae extends along almost the whole body, and the region that would make limbs never receives the signal to do so: three hundred vertebrae and no legs, from the same genes expressed over different lengths. Among Darwin’s finches, the depth of the beak follows the level at which one growth signal is expressed in the embryonic beak: more signal, deeper beak. Raising that signal artificially in a chicken embryo produces a deep, finch-like beak. ∎

Same genes, different extents. The regional genes that pattern the trunk are the same in a mouse and a python; in the python the "ribbed trunk" state is expressed along almost the whole axis and the limb-forming signal is never given.

Example 24.6 (Beaks by the dose)

Thirteen species of finch on one group of islands have beaks from needle-thin to nutcracker-deep, and eat accordingly. Their beak genes are the same; the embryos of the deep-beaked species express one growth signal earlier and more strongly in the tissue that becomes the beak. A single change in the timing or amount of one signal, not a new gene, separates an insect-eater from a seed-crusher — which is why such differences can arise in a few thousand generations.

Four of Darwin’s finches, drawn by John Gould in 1845 from the specimens the Beagle brought back: the same bird in every other respect, with beaks from a nutcracker to a needle. One growth signal, dosed differently in the embryo, separates them. Engraving, public domain. — Four of Darwin’s finches, drawn by John Gould in 1845 from the specimens the *Beagle* brought back: the same bird in every other respect, with beaks from a nutcracker to a needle. One growth signal, dosed differently in the embryo, separates them. Engraving, public domain.

24.4 Living together: symbiosis

Definition 24.7 (Symbiosis)

A symbiosis is a lasting, close association of two species from which both benefit. A lichen is a fungus housing algal cells that feed it by photosynthesis while it shelters and waters them; a coral is an animal housing algae in its tissues; the roots of most plants are wrapped in fungi that supply minerals in exchange for sugar; the guts of animals hold bacteria that digest what the animal cannot. The association produces organisms, structures and ways of life that neither partner could achieve alone.

Lichens on a granite boulder. Each patch is a fungus and an alga grown into one body: a form of life, able to colonise bare rock, that neither partner can take alone.

Proposition 24.8 (The symbiosis inside every cell)

The mitochondria of every eukaryotic cell, and the chloroplasts of plant cells, descend from free-living bacteria that were engulfed by an ancestral cell some two billion years ago and stayed. The eukaryotic cell itself is the outcome of a symbiosis.

Evidence. Mitochondria and chloroplasts have their own DNA, a small circle like a bacterium’s, and their own ribosomes, of the bacterial kind, sensitive to the antibiotics that block bacterial but not eukaryotic ribosomes; they multiply by dividing in two, and cannot be made anew by the cell; they are wrapped in two membranes, the inner one resembling a bacterial membrane; and their genes are closest, in sequence, to those of specific groups of living bacteria — purple bacteria for mitochondria, cyanobacteria for chloroplasts. ∎

The origin of mitochondria. A bacterium engulfed by an ancestral cell was kept and multiplied inside it; its descendants are the mitochondria of every eukaryote, still carrying their own bacterial DNA and ribosomes. Chloroplasts arose the same way from a photosynthetic bacterium.

24.5 Diversity without genes: behaviour

Proposition 24.9 (Transmitted behaviour)

In many animals, part of what an individual does is learnt from others — by imitation, teaching or copying — and passed on in turn: a culture, transmitted without genes. Populations of the same species can therefore differ in behaviour as they differ in alleles, and a behaviour can spread through a population in a generation rather than over the many that a mutation would need.

Evidence. Chimpanzee communities in different forests use different tools — stones to crack nuts here, sticks to fish for termites there, leaves as sponges elsewhere — and the differences do not follow genetic relatedness or the availability of materials; a young chimpanzee acquires its community’s set by watching its elders. Songbirds raised in isolation sing a crude song; raised hearing adults, they sing the local dialect, which changes across a range like a human accent. A troop of macaques on an island learnt to wash sweet potatoes in the sea from one young female within a decade, and its descendants still do. ∎

A chimpanzee fishing for termites with a prepared stick. The technique is learnt by watching, and differs from one community to another: a tradition, transmitted without genes.

Method 24.10 (Naming the source of a difference)

Faced with a difference between two organisms or populations:

Is it in the sequence of a gene (mutation, allele)? In the number of copies of a gene (duplication)? In the presence of a gene from elsewhere (horizontal transfer)? In the number of chromosome sets (polyploidy)?
Is it in when, where or how much a shared gene is expressed during development (regulation)?
Is it the result of an association with another species (symbiosis)?
Is it learnt (behaviour transmitted by culture) — inherited, but not genetically?

More than one answer is often right; the questions are the inventory of this chapter.

Remark 24.11 (Diversification and selection)

Every process here produces variation; none of them decides what survives. A polyploid wheat, a python’s expression pattern, a lichen, a nut-cracking tradition each persisted because it worked where it arose. The sorting of variation — selection, and chance — is the subject of the next chapter; this one has laid out how much there is to sort, and how many ways there are of making it.

24.6 Exercises

Exercise 24.1 ★

List five sources of diversification besides point mutation.

Solution

Solution of Exercise 24.1.

Gene duplication and divergence; horizontal gene transfer; hybridisation with polyploidy; changes in the regulation of developmental genes; symbiosis; transmitted behaviour.

Exercise 24.2 ★

What is a gene family, and how does one arise?

Solution

Solution of Exercise 24.2.

A set of related genes descended from one ancestral gene by successive duplications, each copy then diverging by mutation to a distinct function (opsins, globins).

Exercise 24.3 ★

Why is a hybrid between two species usually sterile, and how can chromosome doubling make it fertile?

Solution

Solution of Exercise 24.3.

Its chromosomes, one set from each parent species, have no homologues to pair with at meiosis, so gametes are unbalanced. Doubling gives every chromosome an identical partner: pairing and meiosis become regular and the plant is fertile.

Exercise 24.4 ★

Give three lines of evidence that mitochondria descend from bacteria.

Solution

Solution of Exercise 24.4.

Their own circular DNA; bacterial-type ribosomes sensitive to antibacterial antibiotics; multiplication by division; a double membrane; sequences closest to a group of living bacteria.

Exercise 24.5 ★

What is meant by a culture in animals? Give an example.

Solution

Solution of Exercise 24.5.

A behaviour learnt from other members of the group and passed on without genes: nut-cracking with stones in some chimpanzee communities and not others.

Exercise 24.6 ★★

Emmer wheat has $2n = 28$ and einkorn $2n = 14$ . How many chromosomes has their hybrid, and how many pairs can form at its meiosis? Explain its sterility.

Solution

Solution of Exercise 24.6.

$14 + 7 = 21$ chromosomes: 7 A from einkorn, 7 A and 7 B from emmer. Seven pairs (A with A) can form; the 7 B chromosomes have no partner and are distributed at random, so the gametes are unbalanced: sterile.

Exercise 24.7 ★★

The $\alpha$ and $\beta$ globin genes are 50% identical; the $\beta$ and $\gamma$ genes 80%. Which duplication is older? Draw the tree.

Solution

Solution of Exercise 24.7.

The $\alpha$ – $\beta$ split (50% identical) is older than the $\beta$ – $\gamma$ split (80%): $\alpha$ branches first, then $\beta$ and $\gamma$ separate from each other.

Exercise 24.8 ★★

Explain how a python can have no legs although it carries the genes that build legs in a lizard.

Solution

Solution of Exercise 24.8.

The limb genes are present but the signal that switches them on in the embryo’s flank is not given, or is given and then stopped; the difference is in the regulation of expression, not in the genes.

Exercise 24.9 ★★

Two finch species differ in beak depth by a factor of two but have identical beak genes. Where does the difference lie, and why can it arise quickly?

Solution

Solution of Exercise 24.9.

In the amount and timing of a growth signal in the embryonic beak: a regulatory difference. A change in regulation needs only a small mutation in a control sequence, whereas a new protein would need many; it can arise and be selected within thousands of generations.

Exercise 24.10 ★★

A lichen grown from its fungus alone is a shapeless mould; from its alga alone, a green film. Explain in what sense the lichen is a new kind of organism.

Solution

Solution of Exercise 24.10.

Its form, its capacity to colonise bare rock, its resistance to drought and its slow growth belong to neither partner alone; they emerge from the association. The lichen is a compound organism with properties of its own.

Exercise 24.11 ★★

A population of chimpanzees cracks nuts; a neighbouring one, across a river, does not, although nuts and stones abound on both sides. Using Method 24.10, decide the source of the difference and justify.

Solution

Solution of Exercise 24.11.

Transmitted behaviour: materials are available on both sides, the populations are closely related, and the difference follows the river — a barrier to contact and hence to learning, not to genes or resources.

Exercise 24.12 ★★★

A gene of the human genome is nearly identical to a gene of a virus and to nothing in any other mammal except the primates. Propose its history, and say how you would test it.

Solution

Solution of Exercise 24.12.

A virus inserted its gene into the genome of a primate ancestor’s germ cell some tens of millions of years ago; the gene was inherited and kept. Test: the same gene should sit at the same chromosomal position in all primates and be absent from that position in other mammals; its sequence should be closest to the virus’s.

Exercise 24.13 ★★★

Antibiotics that block bacterial ribosomes have side effects on the patient’s mitochondria at high doses. Explain why, and what this says about the ancestry of mitochondria.

Solution

Solution of Exercise 24.13.

Mitochondrial ribosomes are of the bacterial type and bind the same antibiotics: at high doses the drug slows the mitochondria’s protein synthesis. The sensitivity is inherited from the mitochondria’s bacterial ancestor.

Exercise 24.14 ★★★

Explain why a new polyploid species is isolated from its parents from the first generation, while a new allele takes many generations to spread. What does this imply about the speed at which plant species can form?

Solution

Solution of Exercise 24.14.

The polyploid’s chromosome number no longer matches either parent’s, so crosses with them give sterile offspring: isolation is immediate. A new allele must spread through a population over many generations before it distinguishes a group. A plant species can therefore arise in a single generation.

Exercise 24.15 ★★★

"All diversity comes from mutation." Discuss in a paragraph: in what sense the statement is true at bottom, and in what senses the processes of this chapter go beyond it.

Solution

Solution of Exercise 24.15.

At bottom, every new sequence — a duplicated copy that diverges, a regulatory change, the genes of a transferred plasmid — began as a mutation somewhere. But duplication, transfer and polyploidy move and multiply whole genes and genomes at once; regulatory change produces new forms without new proteins; symbiosis combines genomes of different species; and culture transmits variation with no genes at all. Mutation supplies the letters; these processes rearrange whole pages and books.

24.7 Problem: Three Grasses in a Loaf

Problem 24.1

Weekend problem — the history of bread wheat reconstructed from chromosomes, a python’s genes read beside a mouse’s, and the bacterium inside every cell put on trial

Einkorn (AA), goat grass 1 (BB) and goat grass 2 (DD) each have $2n = 14$ . Emmer is AABB and bread wheat AABBDD.

Part I — The chromosomes of wheat.

Give the number of chromosomes in emmer and in bread wheat.
The hybrid of einkorn and goat grass 1 has 14 chromosomes, 7 of each kind. How many pairs of homologues form at its meiosis? What are its gametes like?
Explain why a doubling of its chromosomes restores fertility: count the pairs.
The hybrid of emmer and goat grass 2 has 21 chromosomes. Which of them can pair, and why is it sterile?
After doubling, bread wheat has 42. How many pairs form at its meiosis, and how many chromosomes does a pollen grain carry?

Part II — Reading the history.

Bread wheat carries three copies of most genes, one on each set. Explain why a mutation destroying one copy usually has no visible effect, and what this allows over time.
Emmer was cultivated 10 000 years ago and bread wheat appears in archaeological sites 8 000 years ago. Where and when did the second hybridisation probably occur? What had to be growing side by side?
Laboratory crosses of emmer with goat grass 2, followed by chemical doubling, give fertile plants resembling bread wheat. Which conclusion of this history does that confirm?
Bread wheat cannot cross with einkorn to give fertile offspring. Is it a separate species? Justify with the definition of Chapter 5.
A crop breeder wants to introduce a disease-resistance gene from goat grass 2 into bread wheat. Explain why this is easier than from an unrelated plant.

Part III — The python’s genes.

The regional genes of the trunk are 98% identical between mouse and python. What does that say about the source of the difference in their bodies?
In the mouse embryo the "ribbed trunk" gene is active over 13 segments; in the python over about 300. Name the kind of change involved.
The python embryo forms tiny buds where hindlimbs would be, which then stop growing. What does this suggest about the limb genes and the signal that would activate them?
Mice engineered to express the "ribbed trunk" gene over the lumbar region grow extra ribs there. What does this experiment add to the comparison?
Compare the two kinds of change: bread wheat’s and the python’s. Which changed the genome’s size, which its use?

Part IV — The bacterium inside.

List four features of mitochondria that fit a bacterial origin, and for each say what you would expect if mitochondria had instead been built by the cell from scratch.
Mitochondrial DNA carries only 37 genes, while the mitochondrion needs about 1500 proteins. Where are the other genes, and what happened to them over two billion years?
Every mitochondrion of a person comes from the egg, none from the sperm. What follows for the inheritance of mitochondrial genes, and for tracing maternal ancestry?
A lichen and a mitochondrion are both symbioses. In what way has the mitochondrion’s gone further?
State the result: the three species in a loaf and the number of chromosomes each contributed; the one word that names what differs between the python’s and the mouse’s use of their shared genes; and the organelle that is a former bacterium.

Solution

Solution of Problem 24.1.

1. Emmer 28, bread wheat 42.

2. None: the A and B chromosomes are not homologous. Gametes receive random assortments of the 14, almost never a complete set.

3. With 28 chromosomes, each A has an identical A partner and each B a B: 14 pairs, regular meiosis, balanced gametes of 14.

4. None can pair: 7 A, 7 B and 7 D chromosomes, each without a homologue. Sterile.

5. 21 pairs; a pollen grain carries 21.

6. The other two copies still supply the protein. Redundant copies are free to accumulate mutations and diverge — duplication on the scale of a whole genome.

7. In fields of the region where emmer was grown, between 10 000 and 8 000 years ago, with wild goat grass 2 growing as a weed among the crop.

8. That the two steps — hybridisation and doubling — are sufficient to produce bread wheat from its parents: the history can be re-run.

9. Yes: it cannot produce fertile offspring with einkorn, so by the definition it is a distinct species, although it descends from it.

10. Goat grass 2’s D chromosomes are homologous to the wheat’s D set and pair with them, so a cross followed by back-crosses can move the gene in; an unrelated plant’s chromosomes would not pair at all.

11. The genes themselves hardly differ; the difference in the bodies must lie in how the genes are used.

12. A change in the regulation of expression — the extent of the region along the axis where the gene is active.

13. The limb genes are present and begin to act; the signal that sustains limb growth is missing, so the buds stop. Again regulation, not the loss of the genes.

14. It shows that changing where the gene is expressed is sufficient to change the body region: the correlation between expression and form is causal.

15. Bread wheat’s change added whole sets to the genome (its size); the python’s changed where shared genes are used (their regulation).

16. Own circular DNA (expected: none, all genes nuclear); bacterial ribosomes (expected: eukaryotic ribosomes); multiplication by division (expected: assembly from parts); double membrane (expected: a single membrane like other organelles). And their genes resemble bacterial genes (expected: nuclear-type genes).

17. In the nucleus: over time most of the bacterium’s genes were transferred to the nuclear genome, and the organelle’s own genome shrank to a remnant.

18. Mitochondrial genes pass only from mother to child; a person’s mitochondrial DNA traces the unbroken maternal line.

19. The mitochondrion has given up most of its genes to its host and cannot exist outside the cell; the lichen’s partners keep their genomes and can, with difficulty, be separated.

20. Einkorn (14, A), goat grass 1 (14, B), goat grass 2 (14, D): 42 chromosomes; "regulation"; the mitochondrion.

Terms defined in this chapter

Symbiosis

See all 479 terms in the glossary