The macaque is a better outgroup than the mouse for inferring the history of sequence changes in human and chimpanzee genomes. (a) The scaled phylogeny of primates with respect to the mouse. Over long evolutionary periods, multiple mutations are likely to occur at the same position in the genome, obscuring that base's true evolutionary history. This is indicated here by the change of the initial T to a C and later to an A in the mouse genome, and the change from the T to a G in the primate line, and later to an A in the chimpanzee line only. (b) If a distantly related species (the mouse) is used as the outgroup in a comparison of the human and chimpanzee genomes, this can lead to the mistaken conclusion that a unique mutation has occurred along the human lineage, as demonstrated in the diagram on the left. When the genomes are compared using a more closely related outgroup (the macaque) the more probable history of this difference is revealed, as shown in the diagram on the right.
Disotell and Tosi Genome Biology 2007 8:226 doi:10.1186/gb-2007-8-9-226