Questions on classification, phylogeny and molecular evidence

Question 1

A protein 200 amino acids long is compared between two primate species and found to differ at 3 positions. The same protein is compared between one of those species and a rodent, and differs at 46 positions. Calculate the percentage sequence identity in each comparison, and state what the two percentages suggest about which pair of species is more closely related.

Accepted Answer

M1 percentage identity = (number of positions unchanged ÷ total positions) × 100, using unchanged = total − differences A1 primate pair: (200 − 3) ÷ 200 × 100 = 98.5 per cent identical M1 rodent comparison: (200 − 46) ÷ 200 × 100 A1 77 per cent identical B1 the primates, with far higher sequence identity, are the more closely related pair, since fewer amino acid differences have accumulated since they last shared a common ancestor

Question 2

Explain why grouping organisms by how similar they look places a dolphin with a shark, and explain how homologous structures avoid that error.

Accepted Answer

B1 a phenetic classification counts observable resemblances without asking where the resemblance came from B1 unrelated lineages exposed to the same selective pressure end up with similar features, so a dolphin and a shark are both streamlined with fins because both hunt in open water; that is convergent evolution and the structures are analogous B1 a dolphin's flipper contains the pentadactyl limb: one upper arm bone, two forearm bones, wrist bones and five digits. That is the same plan as a bat's wing and a human hand, while a shark's fin has nothing of the kind B1 a shared underlying plan is homologous and can only be explained by inheritance from a common ancestor, so a phylogenetic classification uses homology as evidence of ancestry and discards analogy

Question 3

Two bird species are known from the fossil record to have diverged 12 million years ago, and a protein 150 amino acids long differs at 4 positions between them. The same protein differs at 7 positions between two other bird species. Calculate the rate of change and estimate when the second pair diverged. The counts are idealised.

Accepted Answer

M1 calibrate first: rate = number of amino acid differences divided by the time since divergence, using the pair whose date is known A1 4 ÷ 12 = 0.33 amino acid differences per million years M1 time since divergence = number of differences divided by that rate, kept unrounded: 7 ÷ (4 ÷ 12) A1 21 million years; accept 21.2 from a rate rounded to 0.33

Question 4

Compare the cell walls and the membrane lipids of Bacteria and Archaea, and compare how each domain responds to the antibiotic streptomycin.

Accepted Answer

B1 Bacteria have a cell wall containing peptidoglycan, whereas Archaea have no peptidoglycan in their walls, instead having wall material such as protein or pseudomurein B1 the membrane lipids of Bacteria are joined to glycerol by ester bonds and form unbranched chains, whereas those of Archaea are joined by ether bonds and form branched chains B1 growth of Bacteria is inhibited by streptomycin, whereas growth of Archaea is not inhibited by it B1 these differences show that although Bacteria and Archaea are both prokaryotes lacking a nucleus, they differ in fundamental aspects of cell chemistry, which is part of the evidence that they are not close relatives within a single group

Question 5

Describe how the immunological comparison technique is carried out to compare how closely two species are related, using an anti-human antiserum as an example, and describe what a smaller amount of precipitate formed indicates.

Accepted Answer

B1 a rabbit is injected with human blood serum, and the rabbit's immune system makes antibodies against the human proteins in it; that antiserum is then collected B1 the anti-human antiserum is added to serum taken from another species, and if that species' proteins are similar enough to the human proteins, the antibodies bind to them and a precipitate forms B1 the amount of precipitate formed is measured, for example as a percentage of the precipitate formed when the antiserum is tested against human serum itself B1 a smaller amount of precipitate indicates that the tested species' proteins are less similar to the human proteins, and so indicates a more distant evolutionary relationship to humans

Question 6

Explain why a group containing crocodiles and lizards but excluding birds is not a valid group in a phylogenetic classification.

Accepted Answer

B1 a phylogenetic classification requires each group it recognises to contain a common ancestor together with every one of that ancestor's descendants, and nothing else B1 the common ancestor of crocodiles and lizards is also the ancestor of birds, since birds branched from within that same lineage B1 a group made up of crocodiles and lizards but excluding birds therefore leaves out some of that ancestor's descendants, so it is not a complete section of the evolutionary tree B1 such a group is described as paraphyletic rather than as a valid, monophyletic, clade, which is why 'reptiles' defined that way is not used as a formal group in a phylogenetic classification

Question 7

A student says that humans evolved from chimpanzees. Discuss whether a cladogram showing humans and chimpanzees as the two closest living relatives on the tree supports this statement.

Accepted Answer

B1 what the cladogram does support: humans and chimpanzees share a more recent common ancestor with each other than either does with any other living species, so of all living species chimpanzees are humans' closest relatives B1 against: both humans and chimpanzees are tips on the tree, meaning both are living species rather than ancestors, and a cladogram never asserts that one tip is descended from another B1 against: the actual common ancestor of humans and chimpanzees sat at the fork where the two lineages split, some millions of years ago, and was itself neither a human nor a chimpanzee as either exists today B1 judgement: 'humans evolved from chimpanzees' misreads the tree; the accurate statement is that humans and chimpanzees evolved from a shared ancestral population, with each lineage changing over the same elapsed time since the split, rather than one being derived from the other

Question 8

A DNA base sequence comparison between two species finds more differences than an amino acid sequence comparison of the protein that DNA codes for. Suggest why the two methods can give different numbers of differences for what is ultimately the same gene.

Accepted Answer

B1 the genetic code is degenerate, so more than one triplet can specify the same amino acid B1 some of the base differences found between the two DNA sequences are therefore silent, changing the triplet but not the amino acid it specifies, so they leave the protein's amino acid sequence unaffected B1 the amino acid sequence comparison misses those silent differences, and so records fewer differences overall than a direct comparison of the DNA base sequence does B1 amino acid comparison is consequently the blunter of the two tools for measuring relatedness

Question 9

Describe the evidence from ribosomal RNA that led to the prokaryotes being separated into two domains.

Accepted Answer

B1 the base sequence of the RNA in the small subunit of the ribosome was compared across as many organisms as could be obtained B1 the prokaryotes fell into two groups whose sequences differed from each other about as much as either differed from those of eukaryotes B1 that supported a rank above kingdom, the domain, with Bacteria, Archaea and Eukarya, and with Archaea sharing a more recent common ancestor with Eukarya than with Bacteria

Question 10

Suggest why ribosomal RNA rather than haemoglobin was chosen as the molecule for comparing organisms drawn from all three domains.

Accepted Answer

B1 every organism that has been sequenced has ribosomes, so the same molecule can be compared right across life, whereas haemoglobin is present in only some animals B1 its job is the same in every organism, holding the ribosome together and positioning the tRNAs, so equivalent positions in the sequence can be lined up against one another B1 most of its sequence changes very slowly, because almost any change breaks a working ribosome, so a readable signal survives across billions of years, and it is long enough that the similarities are not coincidence

Question 11

Explain the role that a specific courtship behaviour plays in keeping two closely related animal species reproductively isolated from each other.

Accepted Answer

B1 many animal species have their own specific courtship behaviour, such as a display, a call, a scent or a dance, that differs from the courtship behaviour of even closely related species B1 that behaviour lets an individual recognise a potential mate as being of its own species, of the opposite sex, and in breeding condition, before mating is attempted B1 individuals of two different species are therefore much less likely to mate with each other in the first place, which keeps the two gene pools separate even where the two species' ranges overlap

Question 12

State the eight taxonomic ranks in order, beginning with the largest, and state the conventions for writing a binomial.

Accepted Answer

B1 domain, kingdom, phylum, class, order, family, genus, species B1 the genus takes a capital letter and the specific name does not, and both are printed in italics or underlined when written by hand

Question 13

Give two situations in which the biological species concept cannot be applied, and give the reason in each case.

Accepted Answer

B1 organisms that do not reproduce sexually, such as bacteria and archaea, never interbreed at all, so the test cannot be carried out and prokaryotes are grouped instead by how similar their genomes are B1 fossils cannot be bred, so the interbreeding test cannot be applied to them and the species are assigned from morphology instead

Question 14

State what is meant by describing the taxonomic hierarchy as nested, and state what is meant by saying it has no overlap at a rank.

Accepted Answer

B1 nested means every group at one rank sits inside exactly one group at the rank above, so every organism in a lower taxon belongs wholly to one higher taxon rather than partly to more than one B1 no overlap at a rank means no organism belongs to two different groups at the same rank, such as two different orders, at the same time

Question 15

Give two further situations, beyond asexual organisms and fossils, in which the biological species concept is difficult to apply, and give the reason in each case.

Accepted Answer

B1 a ring species: where a chain of populations runs around a geographical barrier and neighbouring populations along the chain can interbreed, but the two ends of the chain meet and cannot, so no single boundary can be drawn between one species and two B1 species that hybridise successfully in the wild, such as polar bears and brown bears or many flowering plants, since the concept assumes fertile offspring do not occur between different species