Consider five taxa (A, B, C, D, E)
with the following distance matrix. Note that distances involving taxon C are
unusually large:
| A | B | C | D | E | |
| A | 0 | - | - | - | - |
| B | 20 | 0 | - | - | - |
| C | 80 | 80 | 0 | - | - |
| D | 60 | 60 | 100 | 0 | - |
| E | 80 | 80 | 120 | 80 | 0 |
As before, A & B are
most
similar (20 units): join them
into one cluster (AB) joining at 20, and
re-calculate other average distances. This gives:
| (AB) | C | D | E | |
| (AB) | 0 | - | - | - |
| C | 80 | 0 | - | - |
| D | 60 | 100 | 0 | - |
| E | 80 | 120 | 80 | 0 |
(AB) & D are
most
similar (60 units): join them
into one cluster (ABD) joining at 60, and
re-calculate the average distances. This gives:
| (ABD) | C | E | |
| (ABD) | 0 | - | - |
| C | 90 | 0 | - |
| E | 80 | 120 | 0 |
E & (ABD) are
most similar (80 units): join
them into one cluster (ABDE) joining at 80, and
re-calculate the average distance. This gives:
| (ABDE) | C | |
| (ABDE) | 0 | - |
| C | 105 | 0 |
C joins the remaining taxa at 105. This completes the analysis.
The analysis suggests that C is the least similar to the others. If similarity of ABDE in the phenogram (below, left) estimates their relationship to C, then it implies that C is the most distantly related taxon to the other four. In fact, the evolutionary tree from which the data were derived (below, right) shows that C is most closely related to (AB) [they have the most recent common ancestor], but has evolved at twice the rate of other taxa. The violation of the assumption of rate equality in the method is guaranteed to give a wrong answer.
