When three species are fairly closely related to each other (like human, chimpanzee and gorilla), the trees obtained from DNA sequence data may not be congruent with the tree that represents the speciation (species tree). A and B are two different loci. In the upper figure they fit to the species tree: the DNA that is present in todays gorillas diverged earlier from the DNA that is present in todays human and chimp. Thus both loci should be more similar between human and chimp than between gorilla and chimp or gorilla and human. The lower graph is different, locus A in human and gorilla have a more recent common ancestor compared to the chimpanzee sequence. Whereas chimp and gorillas have a more recent common ancestor for locus B which is therefore more similar in sequence between the two. The gene trees do not fit to the species tree. The shorter internodal time span (T_IN) the more common are incongruent gene trees. The effective population size (N_e) of the internodal population determines how long genetic lineages are preserved in the population. A higher effective population size causes more incongruent gene trees. Therefore, if the internodal time span is known, the ancestral effective population size of the common ancestor of humans and chimpanzees can be calculated (Chen & Li, 2001).

• Chen, F.C. & Li, W.H. (2001), 'Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees.', Am J Hum Genet 68(2), 444--456. [1]