IB Biology A3.2: Classification and cladistics worked solutions

A shared order forces every higher rank to match, so both are in the same class (B). Family and genus are lower ranks than order, so sharing the order does not force them to match: the lion is a felid and the wolf a canid.

Parsimony prefers the hypothesis that needs the fewest changes, so tree 1 is the more probable (A). The other options reverse or ignore the principle.

Woese compared base sequences of 16S ribosomal RNA, which every cell has and which changes slowly enough to compare across all life (A). The other molecules are not universal markers used for the domains.

A clade is a common ancestor and all its descendants. The ancestor of P, Q and R has only these three descendants (B). Q and R omit P, R and S come from separate branches, and P, Q, R and S omit T.

S and T share their own node, while S meets R only at the root, so S is closer to T (A). R shares a more recent node with P than with S (B false), P shares a more recent node with Q than with S (C false) and Q shares a more recent node with R than with T (D false).

Corresponding sequences of the same gene can be aligned, and the differences are inherited, so they show relationships (A). Different genes cannot be compared position by position, and feather colour and egg number can arise by convergence or vary with environment.

Time = differences divided by rate = 6\div2=3 million years (B). The other values come from multiplying, adding or inverting the quantities.

Groups made of a common ancestor and all its descendants reflect real history (A). Members of a clade need not look alike, clades are unranked and the method uses sequence evidence.

Similar structures in groups with separate ancestors arise by convergent evolution under similar selection pressures (A). A recent common ancestor or a shared mutation would put the groups on one branch, and acquired characteristics are not inherited.

(a) Dolphin (1). (b) The baleen whale (1); it shares a more recent common ancestor with the dolphin than the hippopotamus does (1). (c) The claim is not supported (1): the sperm whale and the dolphin are both living tips that share a common ancestor, and neither is the ancestor of the other (1).

(a) W and Y differ at positions 4, 8 and 11: 3 differences (1). Y and Z differ at positions 1, 6, 9, 10 and 12: 5 differences (1). (b) W and X: they have the fewest differences (1), so they share the most recent common ancestor. (c) Z has the most differences from the others, so it diverged first (1); Y is next because it differs from X by 2 and from W by 3, and W and X separated most recently (1).

(a) Rate = differences divided by time =27\div15 (1) =1.8 differences per Myr (1). (b) Time = 63\div1.8 (1) =35 Myr (1). (c) Any two: the mutation rate depends on the generation time (1); it depends on the population size (1); it depends on the intensity of selection on the gene (1); the rate calibrated on one pair or one gene may not hold for another (1).

(a) The outgroup O branches first (1). The traits nest: S then R then the pair Q and P, so S branches, then R, then Q and P are sister species (1); trait 1 is marked on the branch to S, R, Q and P, trait 2 to R, Q and P, trait 3 to Q and P and trait 4 on P alone (1). In nested form: (O,(S,(R,(Q,P)))). (b) 4 changes: each trait arises once (1). (c) The outgroup shows the ancestral state, so traits it lacks are derived (1). (d) By parsimony the hypothesis needing the fewest changes is the most probable, and any other tree would need a trait to arise more than once (1).

(a) The branch leading to the common ancestor of C, D and E (1). (b) One origin on that branch explains the trait in all three species with one change (1); separate origins would need three changes, so by parsimony the single origin is more probable (1). (c) A and E are on separate branches, so trait Y most probably arose independently by convergent evolution and is not inherited from a recent common ancestor (1).

(a) More than 2 million species are known, so a shared system lets scientists and the public communicate about the same organism (1); it organises organisms so that relatives can be found and features of a new species predicted from its group (1). (b) Any four: every member of a group descends from one common ancestor, so groups reflect evolutionary history (1); sequence evidence is objective and separates species that look identical (1); it can show that a structural classification was wrong because of convergence, as in the figwort family (1); shared ancestry predicts inherited traits (1); unranked clades avoid arbitrary boundaries between ranks (1); a balanced answer notes that sequences are hard to obtain in the field, where structure is more practical (1).

(a) Species 4 (1.4 per cent) (1). (b) Species 3 differs from species 1 and 2 by 9.8 and 10.1 per cent (1) but from species 4 and 5 by only 1.4 and 1.6 per cent, so species 3 shares a more recent ancestor with 4 and 5 than with the rest of its family (1). (c) Convergent evolution: similar selection pressures produced similar leaves (1). (d) Species 3 should be reclassified with species 4 and 5 so that each group is a clade (1).

(a) The archaeon and the eukaryote (24 per cent) (1). (b) The archaeon differs from the bacterium by 31 per cent, almost as much as the eukaryote does (33 per cent) (1), and it is closer to the eukaryote (24 per cent) than to the bacterium, so archaea are as distinct from bacteria as eukaryotes are and are not part of the bacteria (1). (c) Domain (1). (d) Every cell has ribosomes, and the sequence changes slowly enough to align across all life (1).

(a) Gene X: 32.0\div40=0.80 per cent per Myr (1); gene Y: 8.0\div40=0.20 per cent per Myr (1). (b) Time =11.2\div0.80 (1) =14 Myr (1). (c) 14\times0.20=2.8 per cent (1). (d) Gene Y may code for a product whose structure is tightly constrained, so selection removes most changes (1); gene X may tolerate more neutral changes, which accumulate freely (1); because genes change at different rates each gene needs its own calibration, and the slower gene suits older divergences while the faster suits recent ones (1).

(a) Trait 5 is in C and E, which are not sister species on tree 1, so it needs 2 changes (1); this suggests it arose independently by convergent evolution (1). (b) Tree 1: traits 1, 2, 3, 4 and 6 need one change each and trait 5 needs two, so 5+2=7 (1). Tree 2: traits 1, 3, 5 and 6 need one change each and traits 2 and 4 need two each, so 4+4=8 (1). Working shown trait by trait (1). (c) Tree 1 (7 changes against 8) (1); parsimony: the hypothesis needing the fewest changes is the most probable (1). (d) C and E may face similar selection pressure, so a similar trait evolves separately (1); parsimony gives only the most probable tree, not a proof, and a trait with a high rate of change can mislead it (1).

(a) The same gene is sequenced in every species and the sequences are aligned (1); differences between species are compared, since each is inherited (1); species are grouped by shared changes into nested groups, choosing the tree that needs the fewest changes (1). (b) The family is not a clade: its members do not all descend from one common ancestor (1); the four groups have separate ancestors, each shared with species outside the family (1). (c) Similar selection, for example by the same type of pollinator, acted on each group (1), so the similar flowers arose independently by convergent evolution rather than by inheritance from one ancestor (1). (d) Split the family so that each of the four groups is placed with its closest relatives (1).

(a) 32 Myr (1). (b) A and C diverged 21 Myr ago, so rate =42\div21 (1) =2.0 per Myr (1). (c) A and B diverged 9 Myr ago: 9\times2.0=18 (1); A and O diverged 50 Myr ago: 50\times2.0=100 (1); the method is multiplication of the time at the shared node by the rate for the pair (1). (d) Any two: the lineage leading to O may have a longer generation time, so fewer mutations per Myr (1); more changes in that gene may have been removed by selection (1); the rate is not constant between lineages or over time (1).

(a) The family boundaries changed three times in 85 years as the evidence changed (1), which supports the claim that where the line is drawn is a human choice because variation is gradual (1); but the nested clades revealed by sequences stay the same whichever rank is named, so the groups themselves are not arbitrary (1). (b) The prokaryotes are Bacteria and Archaea (1). Their last common ancestor is the ancestor of all three domains, because Bacteria branch off first (1); Eukarya also descend from that ancestor but are not in the group, so it is not a clade (1).

(a) Homologous structures share an origin in a common ancestor even if their functions differ (1); analogous structures have similar functions but evolved separately (1). (b) The shape is an adaptation to moving fast in water, so it can arise by convergent evolution in separate lineages (1); similarity in structure is therefore not evidence of a recent common ancestor (1); sequences of the same gene, which are inherited, can be compared to find the true relationship (1). (c) Individuals vary in body shape (1); a streamlined shape lowers the cost of swimming, so those individuals survive and breed more (1); the allele frequencies for streamlining rise over generations in each group (1).

(a) Base differences: codon 1 (T to C), codon 2 (A to G), codon 3 (G to C), codon 4 (A to T) = 4 (1); amino acid difference: only codon 4 (Glu to Asp) = 1 (1). (b) The genetic code is degenerate: several codons code for the same amino acid (1), so the changes in codons 1, 2 and 3 are silent and leave the protein unchanged (1). (c) Silent base changes accumulate without changing the protein (1), so they record differences between close relatives that the amino acid sequences do not show (1). (d) Corresponding positions in the same gene can be aligned and compared one by one (1).

(a) LUCA, the last universal common ancestor (1). (b) A gene with the same function and recognisably similar sequence in every domain is most simply explained by inheritance from one ancestor (1), rather than by separate origins in each domain (1). (c) Archaea (1). (d) The molecule is part of the ribosome, which every cell needs to make proteins (1), so most changes harm function and are removed by natural selection, leaving a slow rate of change (1).