A3.2 Classification and cladistics

Biologists have named perhaps two million species and suspect there are many millions more, so we need a system to organise them — otherwise the living world is just an unmanageable list. Classification began as a way to make that list searchable, but modern biology asks something deeper: how are organisms actually related through evolution? A3.2 traces this shift from sorting organisms by surface features to grouping them by shared ancestry. The key idea for the exam is that the best classification is one that reflects evolutionary history (phylogeny), and that molecular evidence has repeatedly forced us to redraw the tree.

The taxonomic hierarchy and binomial naming

Living organisms are classified into a nested hierarchy of taxa. Working from the broadest to the most specific, the main ranks are: domain, kingdom, phylum, class, order, family, genus and species. Each level contains the levels below it, so members of one genus all belong to the same family, order and so on. A useful feature of a hierarchy is that the lower the shared rank, the more features two organisms have in common.

Every species is given a two-word Latin name — the binomial system devised by Linnaeus. The first word is the genus (capitalised) and the second is the species epithet (lower case); the whole name is italicised or underlined, for example Homo sapiens. This gives every organism a single, internationally recognised name, avoiding the confusion of local common names that vary between languages and regions.

Natural versus artificial classification

An artificial classification groups organisms by convenient, observable features that may have nothing to do with ancestry — for example lumping together all flying animals (birds, bats and insects) or all aquatic animals. Such groupings are easy to use but can be misleading, because the shared feature evolved independently.

A natural classification instead groups organisms by their evolutionary relationships, so that each group shares a common ancestor. This is more useful to biologists because it has predictive power: if a newly discovered species is placed in a group, we can predict it will share many other characteristics with the rest of that group, including biochemical and physiological traits not yet examined. The danger to avoid in natural classification is grouping by analogous features (similar because of similar function, such as the wings of birds and bats) rather than homologous features (similar because of shared ancestry).

Clades and the evidence used to build them

A clade is a group of organisms that have evolved from a common ancestor — the ancestor and all of its descendants. Cladistics is the method of identifying clades and arranging them by how recently they shared an ancestor.

Clades are identified using shared, derived characteristics and several lines of evidence:

• Base sequences of genes and the corresponding amino acid sequences of proteins. Because mutations accumulate over time, the more differences there are between the sequences of two species, the longer ago they are likely to have diverged.
• Morphological features, especially homologous structures that share a common origin even when their function differs.

Molecular sequence data are powerful because they can act as a molecular clock: differences accumulate at a roughly steady rate, so the number of differences estimates the time since two clades diverged. This evidence is often more objective than physical appearance, which can be distorted by convergent evolution.

Cladograms and reclassification

The relationships within and between clades are shown on a cladogram — a tree-like diagram in which each branch point (node) represents a hypothetical common ancestor and the tips represent the organisms being compared. The point where a lineage splits in two shows where one ancestral group divided into separate clades. Reading a cladogram, organisms that share a more recent node are more closely related; the length of branches can represent the number of sequence differences or the time elapsed.

Because cladograms are built from evidence, they are hypotheses that can change. When molecular data conflict with traditional classification based on appearance, organisms may be reclassified. The syllabus highlights the figwort family (Scrophulariaceae), which was split apart and its members redistributed once DNA evidence showed the original grouping did not reflect true ancestry. Reclassification ensures that taxonomy keeps pace with the best available evidence of phylogeny.