The Molecular-Clock Assumption - Distance Trees Step by Step

UPGMA assumes equal rates across lineages, which is useful but often too strong for real sequence evolution.

highlighted = computed this step

UPGMA assumes a molecular clock

UPGMA assumes every lineage changes at the same constant rate. In that model, all leaves end at the same height, making an ultrametric tree.

\text{same rate} \longrightarrow \text{ultrametric tree}

A distance tree is a hypothesis

Real sequences often evolve at different rates, so UPGMA can place a fast-changing lineage wrongly. Neighbour-joining relaxes the equal-rate assumption. Honesty note: a distance tree is a hypothesis from one distance measure and one clustering rule, not the true evolutionary history.

\text{distance measure}+\text{clustering rule}\longrightarrow \text{tree hypothesis}