A3.2 Classification and cladistics HL only

1. The number of species is immense, and ordered groups make further study of them possible. — Classification is needed because of the immense diversity of species. After classification is completed, a broad range of further study is facilitated, from identifying organisms to predicting the characteristics of members of a group.
2. It gives each species a name, which is the only purpose it serves in science. — A student who sees classification as a naming and filing exercise picks this. Naming is part of it, but the reason classification is needed is the immense diversity of species, and its value is that it makes a broad range of further study possible.
3. It arranges organisms in order from the most primitive to the most advanced. — A student who pictures evolution as a ladder picks this. Classification groups organisms by shared characteristics and common ancestry; it does not rank living species as more or less advanced.
4. It records the natural rank that each organism already holds in nature. — A student who believes ranks such as family and order exist in nature picks this. Ranks are conventions imposed by taxonomists on a gradation of variation; classification is needed to cope with diversity, not to read off pre-existing ranks.

Syllabus statement A3.2.1 · Read this in Learn

1. One of the two taxonomists must be wrong, because the rank of a group is a fixed natural property. — A student who thinks ranks exist in nature picks this. There is no natural criterion that fixes whether a group is a family or a subfamily; the disagreement arises precisely because the rank is a convention, not a measurable property.
2. The ranks are arbitrary levels imposed on a continuous gradation of variation among organisms. — A fixed ranking of taxa is arbitrary because it does not reflect the gradation of variation. Two taxonomists can draw the family boundary at different levels with equal justification, which is one reason cladistics uses unranked clades.
3. The beetles cannot be a natural group, because a true clade fits exactly one rank. — A student who assumes traditional taxa and evolutionary groups always coincide picks this. Whether the beetles form a clade is a separate question from what rank to give them; a clade can be given any rank or none.
4. A cladogram of the beetles would settle the question by assigning the clade its correct rank. — A student who thinks cladistics is the ranked hierarchy drawn as a tree picks this. Cladistics uses unranked clades: a cladogram can show that the beetles form a clade, but it does not and cannot say whether that clade is a family.

Syllabus statement A3.2.2 · Read this in Learn

1. The groups show which of the organisms are the most advanced. — A student who sees evolutionary classification as a ranking from primitive to advanced picks this. Groups based on common ancestry make no claim that any living species is more advanced than another.
2. Every species is given a unique name made up of two parts. — A student who thinks classification is about naming picks this. Species are named whatever the basis of the classification; the advantage of following evolutionary relationships is predictive.
3. Organisms that look alike are placed together for identification. — A student who thinks classification is by resemblance picks this. Grouping by evolutionary relationships sometimes separates organisms that look alike and unites ones that look different; its advantage is that inherited characteristics can be predicted.
4. Characteristics of members of a group can be predicted. — When all the members of a taxonomic group have evolved from a common ancestor, characteristics of organisms within the group can be predicted because they are shared within the clade.

Syllabus statement A3.2.3 · Read this in Learn

1. The base sequence of a gene, or the amino acid sequence of a protein, that both species possess. — The most objective evidence for placing organisms in the same clade comes from base sequences of genes or amino acid sequences of proteins: differences can be counted position by position, with no judgement about which features to weight.
2. Morphological traits, because they can be measured directly rather than being inferred. — A student who finds visible features more trustworthy than sequences picks this. Morphological traits can be used to assign organisms to clades, but they are less objective: choosing and weighting them involves judgement, and similar structures can evolve independently.
3. A shared specialized structure, because such a structure could not have evolved twice. — A student who assumes a complex structure cannot evolve more than once picks this. Convergent evolution produces similar specialized structures in unrelated lineages, which is exactly why morphology misled the classification of the figwort family.
4. Membership of the same family or order in the traditional hierarchy of taxa. — A student who assumes traditional taxa are always natural groups picks this. The traditional hierarchy does not always correspond to patterns of divergence, so membership of a family is what cladistics tests, not evidence it can rely on.

Syllabus statement A3.2.4 · Read this in Learn

1. Differences between two sequences cannot be counted precisely enough to give a date. — A student who believes the rate is fixed, so that any error must be in the counting, picks this. Differences between sequences are counted exactly; the uncertainty lies in the rate at which they accumulated.
2. All the changes occurred in whichever lineage evolved faster, and that lineage cannot be identified. — A student who thinks the differences all belong to one lineage picks this. Both lineages accumulate changes after they diverge, and the clock estimates time from the differences per lineage; the uncertainty comes from variation in the rate, not from assigning changes to one side.
3. The ancestor at the node was a real fossil species, but its sequence has not been recovered. — A student who thinks a node is an identified fossil ancestor picks this. A node represents a hypothetical common ancestor inferred from the data (A3.2.7); the molecular clock compares the sequences of the two living species with each other, so no ancestral sequence is needed, and the uncertainty comes from variation in mutation rate (A3.2.5).
4. Mutation rates vary with generation time, population size and selective pressure. — The molecular clock can only give estimates because mutation rates are affected by the length of the generation time, the size of a population, the intensity of selective pressure and other factors, so the rate of accumulation of differences is not exactly constant across lineages or over time.

Syllabus statement A3.2.5 · Read this in Learn

1. One of the groups must have made an error, because a cladogram derived from sequences is a fact. — A student who treats a cladogram as a proven result picks this. A cladogram is a hypothesis about relationships, and two groups can each analyse their data correctly and still reach different hypotheses.
2. Different data can lead to different hypotheses; parsimony over all the sequences then selects the most probable. — Students should recognize that different criteria for judgement can lead to different hypotheses. Each cladogram is a hypothesis about relationships, not a fact; parsimony analysis, which favours the tree accounting for the observed variation in all the sequence data with the fewest changes, is used to select the most probable one.
3. The cladogram with fewer nodes should be accepted, because it is the simpler of the two hypotheses. — A student who equates parsimony with a simpler-looking diagram picks this. Parsimony compares the number of sequence changes each tree requires, not the number of nodes drawn.
4. Morphological evidence should now be used to decide the matter, because it is far more reliable than sequence data. — A student who trusts visible traits over sequences picks this. Sequence data are the most objective evidence available; the disagreement is resolved by applying a criterion such as parsimony to the sequences, not by falling back on morphology.

Syllabus statement A3.2.6 · Read this in Learn

1. A named living or fossil species from which the later lineages are descended. — A student who reads a cladogram like a family tree of named individuals picks this. The ancestor at a node is inferred from the data, not identified; living species appear only at the ends of terminal branches.
2. The point at which one lineage became more advanced than the other lineage. — A student who sees a cladogram as a ladder of progress picks this. A node is a branching point at which two lineages separate; neither lineage is more advanced than the other.
3. The hypothetical common ancestor of the lineages that branch from it. — A node represents a hypothetical common ancestor: the point at which the lineages arising from it diverged. All the organisms on the branches beyond a node form a clade.
4. The taxonomic rank, such as family, shared by lineages beyond it. — A student who thinks cladistics assigns Linnaean ranks picks this. Clades are unranked; a node marks a common ancestor and defines a clade, but it does not correspond to any rank.

Syllabus statement A3.2.7 · Read this in Learn

1. The floral similarities arose by convergent evolution, so the family was not a clade and its original classification has been falsified. — Similarities in morphology due to convergent evolution rather than common ancestry suggested a classification that cladistics has shown to be false. The sequence evidence shows that the family did not correspond to evolutionary relationships, illustrating that scientific knowledge claims may eventually be falsified.
2. The transferred genera must still share an ancestor with the figworts, because such similar flowers could not have evolved twice. — A student who assumes a specialized structure cannot evolve independently picks this. Convergent evolution can produce similar flowers in unrelated lineages, and the sequence evidence shows that this is what happened here.
3. Flower structure is directly observable and so more reliable than sequences, which makes the transfer premature. — A student who trusts morphology over molecular data picks this. Base sequences are the most objective evidence of common ancestry, and it was the morphological classification that proved misleading.
4. The original family should be retained, because an established classification is not overturned by later evidence. — A student who regards classifications as settled facts picks this. Classifications are scientific knowledge claims that may be falsified, and the reclassification is a direct example of that process.

Syllabus statement A3.2.8 · Read this in Learn

1. Visible differences in cell structure seen using the electron microscope. — A student who assumes every division of life is based on visible cell structure picks this. Archaea and bacteria are not distinguishable by cell structure alone; it was rRNA sequence comparison that revealed the split.
2. Comparison of the base sequences of ribosomal RNA across many different organisms. — The classification of all organisms into three domains was proposed in 1977 using evidence from rRNA base sequences, which showed that prokaryotes fall into two groups as different from each other as either is from eukaryotes.
3. Evidence that archaea are a subgroup of bacteria, so that all prokaryotes form one domain. — A student who takes archaea to be unusual bacteria picks this. The 1977 proposal rested on rRNA base sequences, which showed that Archaea and Bacteria are as different from each other as either is from Eukarya, so they were placed in separate domains (A3.2.9).
4. Overall similarity in the appearance and way of life of the organisms being classified. — A student who thinks classification rests on resemblance picks this. Overall similarity gives no basis for separating archaea from bacteria; the domains rest on rRNA sequence evidence.

Syllabus statement A3.2.9 · Read this in Learn

1. It draws the same ranked hierarchy of kingdom, phylum and class in a new, tree-shaped form. — A student who merges cladistics with the Linnaean hierarchy picks this. If cladistics only redrew the same ranks, it would be a change of presentation, not a paradigm shift; in fact it abandons fixed ranks altogether.
2. It replaces hypotheses with facts, because cladograms are built from DNA sequence data. — A student who takes cladograms to be proven facts picks this. A cladogram is a hypothesis selected by parsimony, and different criteria can lead to different hypotheses; the shift is in the framework, not from hypothesis to fact.
3. It replaces the assumption of fixed ranks with a different framework of nested clades. — A paradigm shift is a change in the underlying framework of a science. Cladistics discards the assumption that organisms fall into fixed ranks and instead groups them into unranked clades defined by common ancestry, which is a different way of thinking about classification rather than a refinement of the old one.
4. It provides a way of measuring the true rank of every group of organisms. — A student who believes ranks are real properties waiting to be measured picks this. Cladistics does not measure ranks; it does away with them, because a fixed ranking is arbitrary and does not reflect the gradation of variation.

Syllabus statement A3.2.2 · Read this in Learn

1. It will resemble the other members in appearance, because that is how the clade was defined. — A student who thinks classification is by appearance picks this. The clade was defined by common ancestry inferred from base sequences, not by appearance, and members of a clade can look very different from one another.
2. Nothing can be predicted until its morphology has been compared with that of the others. — A student who trusts morphology over sequence data picks this. Base sequences are the most objective evidence for clade membership, and once membership is established the shared characteristics of the clade can be predicted without a morphological comparison.
3. Only its DNA sequence is known to match the others; no other trait can be inferred. — A student who treats a clade as a loose group sharing only the trait used to define it picks this. A clade is a group descended from a common ancestor, so its members share many inherited characteristics beyond the sequence used to identify it.
4. It is likely to produce the alkaloid, a trait shared by descent within the clade. — This is the advantage of a classification that corresponds to evolutionary relationships: characteristics of organisms within a clade can be predicted because they are shared within the clade, having been inherited from the common ancestor. The prediction is probable rather than certain, since the trait could have been lost in one lineage.

Syllabus statement A3.2.3 · Read this in Learn

1. Reptilia is a clade, because all of its members share scales and a similar body plan, unlike birds. — A student who thinks any group with shared characteristics is a clade picks this. A clade must contain all the descendants of its common ancestor; shared scales do not make up for leaving out the birds.
2. Traditional Reptilia is not a clade, because it omits some descendants of its common ancestor. — The common ancestor of crocodiles and lizards is also an ancestor of birds, since birds and crocodiles share a more recent ancestor than either does with lizards. A clade includes all descendants of the common ancestor, so a Reptilia that excludes birds is not a clade.
3. Reptilia is a clade, because it is an established class in the traditional hierarchy. — A student who assumes every traditional taxon is a natural group picks this. The traditional hierarchy does not always correspond to patterns of divergence generated by evolution, and Reptilia is a standard example of the mismatch.
4. Birds cannot be grouped with crocodiles, because the two look so different from each other. — A student who classifies by appearance picks this. Clades are defined by common ancestry, not resemblance; feathers and flight are later modifications in the bird lineage and do not alter its shared ancestry with crocodiles.

Syllabus statement A3.2.4 · Read this in Learn

1. R has changed three times as much as P has since the two lineages separated from their common ancestor. — A student who attributes all the differences to one species picks this. The 18 differences between P and R accumulated in both lineages since their common ancestor, so under a molecular clock P and R have each changed by a similar amount.
2. R is the most primitive of the three species, because its lineage was the first to diverge. — A student who reads early branching on a cladogram as primitiveness picks this. All three species have been evolving for the same length of time since their common ancestor; R's lineage separated earlier, which says nothing about how advanced it is.
3. R's lineage separated from the lineage leading to P and Q before P and Q split from each other. — Sequence differences accumulate gradually with time, so the pair with the fewest differences, P and Q, diverged most recently, and R, which is equally distant from both, diverged from their shared lineage earlier. The clock gives only an estimate of the times, but the order is well supported.
4. No order of divergence can be inferred until the morphology of the three species has been compared. — A student who regards morphology as more reliable than sequence data picks this. Amino acid sequence differences are the most objective evidence of relationship, and the gradual accumulation of differences is the basis for estimating the order and timing of divergence.

Syllabus statement A3.2.5 · Read this in Learn

1. W with X and Y with Z, because that tree accounts for all the variation with only 7 base changes. — Positions 1, 2 and 3 each need one change if W is grouped with X and Y with Z, and positions 4 and 5 each need two changes, giving 7 in total (position 6 is invariant). Grouping W with Y and X with Z needs 8, and any other arrangement needs 10, so this is the most parsimonious hypothesis.
2. W with Y and X with Z, because W and Y share the same bases at positions 4 and 5. — A student who builds the tree from the first shared pattern noticed picks this. Positions 4 and 5 do favour this grouping, but positions 1, 2 and 3 then each need two changes instead of one, so the tree needs 8 changes overall against 7 for the alternative.
3. All four species branching from a single node, because that tree has the fewest nodes. — A student who takes parsimony to mean the simplest-looking diagram picks this. Parsimony counts sequence changes, not nodes: a tree in which all four species arise from one node needs two changes at each of the five variable positions, 10 in all.
4. No cladogram can be chosen until the morphological traits of the four species are compared. — A student who regards sequence data as insufficient without morphology picks this. Base sequences are the most objective basis for constructing cladograms, and parsimony analysis selects the most probable tree from the sequence data alone.

Syllabus statement A3.2.6 · Read this in Learn

1. Q is more closely related to R than to T, because Q and R branch at adjacent nodes. — A student who judges relatedness by adjacency picks this. Q's lineage separates at node 2 from the lineage leading to R, S and T together, so Q shares the same common ancestor with R as with T and is equally related to all three.
2. P is the most primitive of the five species, because it branches off nearest the root. — A student who reads early branching as primitiveness picks this. P's lineage separated first, but it has been evolving for as long as the others since the root; a cladogram shows branching order, not degree of advancement.
3. Q, R and S form a clade, and so do Q, R, S and T taken together as a group. — A student who treats any convenient grouping as a clade picks this. Q, R, S and T are all the descendants of the ancestor at node 2 and do form a clade, but Q, R and S without T omit a descendant of that ancestor, so they do not.
4. R shares a more recent common ancestor with S than it shares with Q. — R's lineage joins the S–T lineage at node 3, whereas it joins Q's lineage further back at node 2. The common ancestor at node 3 is more recent than the one at node 2, so R is more closely related to S than to Q.

Syllabus statement A3.2.7 · Read this in Learn

1. Archaea placed within the domain Bacteria, since both groups lack a nucleus. — A student who takes archaea to be unusual bacteria picks this. Lacking a nucleus is shared by both groups, but the rRNA evidence shows they are as far apart as either is from eukaryotes, which is inconsistent with one domain containing both.
2. Archaea as a sixth kingdom, the highest level of classification. — A student who thinks domain is just another name for kingdom picks this. The domains are an extra level above the kingdoms; the evidence places archaea at that highest level, not as a kingdom alongside plants and animals.
3. Archaea as a separate domain, distinct from both Bacteria and Eukarya. — If archaeal rRNA differs from bacterial rRNA as much as from eukaryotic rRNA, the three groups are separated by divergences of similar depth, which supports three domains, Bacteria, Archaea and Eukarya, at a level above the kingdoms.
4. Archaea grouped with bacteria, because cell structure outweighs rRNA evidence. — A student who expects classification to follow visible cell structure picks this. The three-domain classification was proposed from rRNA base sequences precisely because cell structure does not reveal the depth of the split between archaea and bacteria.

Syllabus statement A3.2.9 · Read this in Learn

1. About 20 million years, since roughly half of the differences have accumulated in each of the two lineages. — Sequence differences accumulate gradually in both lineages after divergence, so the 8 differences are shared between the two lineages, about 4 each, and 4 × 5 million years gives an estimate of 20 million years. It is only an estimate, because the rate is affected by generation time, population size, selective pressure and other factors.
2. About 40 million years, because 8 substitutions at 5 million years each took 40 million years to occur. — A student who attributes all the differences to one lineage picks this. Both lineages accumulated substitutions after they separated, so the 8 differences represent about 4 per lineage, giving 4 × 5 = 20 million years.
3. Exactly 20 million years, because the substitution rate is the same in every lineage at all times. — A student who takes the molecular clock to be exact picks this. The arithmetic is right, but the clock can only give estimates: mutation rates vary with generation time, population size, selective pressure and other factors.
4. It cannot be estimated, because the fossil ancestor at the node has not been found and sequenced. — A student who thinks a node is an identified fossil ancestor whose sequence is needed picks this. The estimate uses the differences between the two living species; a node represents a hypothetical common ancestor inferred from the data, and its sequence is not required.

Syllabus statement A3.2.5 · Read this in Learn