Figure 1.

The logic and problems of paralogue rooting. In theory (A), two genes that arose from a single parent by duplication immediately prior to the common ancestor of the group under study should yield two identical trees joined together by a line (shown extra thick) between the roots (stars) of each tree. Letters are taxa. In practice (B), stochasticity and systematic biases in evolutionary modes and rates yield trees with partially incorrect topology and often-misplaced roots [1]. Misplaced branches (red) are shown as extra long, but in practice misplaced taxa often do not reveal themselves so neatly. In practice, root positions in paralogue subtrees may both be right (very rare: I recall no examples), both wrong but the same (implying strong systematic biases), both wrong but different (often reflecting stochasticity and poor resolution), or one right and one wrong. When such conflicts occur among different paralogue pairs (or triples, etc.), as is almost invariable, other means are required to decide between them.