Cladistics

Clade. A group of organisms that includes a common ancestor AND all of its descendants.

Cladogram. A branching tree-like diagram showing inferred evolutionary relationships:

• Root — the most recent common ancestor of everything on the tree.
• Nodes — points where lineages diverge.
• Branches — lineages connecting nodes.
• Leaves (tips) — the present-day organisms or taxa being compared.

Monophyletic group ("good" clade) — includes the common ancestor and ALL its descendants. Examples: mammals, birds.

Paraphyletic group — includes the common ancestor and SOME of its descendants. The traditional "reptiles" (excluding birds) is paraphyletic because birds evolved from reptilian ancestors and should be included to be monophyletic.

Polyphyletic group — groups organisms that do NOT share a recent common ancestor (e.g. "warm-blooded animals" lumps mammals + birds whose warmth evolved independently). Avoided in modern classification.

Molecular clock. Many DNA and protein sequences accumulate mutations at a roughly constant rate over long periods (especially in regions under weak selection — e.g. silent third positions, certain pseudogenes).

If the rate is calibrated against the fossil record, the NUMBER of differences between two species' sequences can estimate the TIME since they shared a common ancestor.

Worked example. Cytochrome c protein accumulates ~1 amino acid substitution per ~20 million years per site. If two species differ by 5 substitutions in cytochrome c, their common ancestor lived ~100 million years ago. (Simplified — real molecular clocks account for variable rates among lineages.)

Combining data. Modern cladistics uses BOTH:

• Morphological characters — body plans, skeletal features, behaviour.
• Molecular data — DNA sequences (whole genomes when available), protein sequences, gene families.

Statistical methods (maximum parsimony, maximum likelihood, Bayesian inference) find the tree most consistent with the observed data.

Why this matters.

• Surprising relationships emerge — e.g. whales nest within Artiodactyla (even-toed ungulates), so hippos are whales' closest land relatives.
• Conservation prioritises diverse clades to preserve evolutionary heritage.
• Tracking emerging diseases (SARS, COVID, Ebola) uses molecular phylogenies to identify origins and transmission paths.

Limitations. Different genes evolve at different rates. Horizontal gene transfer (especially in bacteria) blurs species trees. Calibration depends on fossil dating, which has uncertainties.