The selection problem. Branch length changes to the neutral phylogenetic tree are shown for each type of selection considered in this study: gain, loss, and acceleration. The figure shows a phylogenetic tree composed of a supertree T with root A, containing a subtree t with root A' that is affected by selection. The left side of the figure shows the effects of negative selection on the relative shape and position of t. In the case of "gain" elements the branches within t as well as the branch from A to A' are reduced in length. In the case of "loss" elements, t is unaffected while the rest of the tree is reduced in size (conserved). Both gain and loss events are particular cases of negative selection affecting different lineages in the tree. In the case of acceleration, shown on the right side of the figure, only the branch from A to A' increases in length. Positive selection is one cause, but not the only cause, of this type of increase. Branches within t may decrease in length if there is additional selection within the tree.