Ancestors can be highlighted in pedigrees e.g. to highlight repeat individuals, or to emphasize common ancestors present of both sides of the pedigree (and which give rise to inbreeding).
This feature is accessed through the Ancestor Highlight pulldown menu (just above the top-right corner of the pedigree as displayed in the main window).
Repeat ancestors are simply those that occur twice or more within any part of the displayed pedigree. Each such ancestor is highlighted with a unique background color.
Highlighting is only applied when an ancestor occurs twice or more within the displayed pedigree. E.g. if a given ancestor occurs once in generation 4, and then again in generation 5, if you display a pedigree to 4 generations then that ancestor will not be shown as a repeat ancestor. However, if you then switch to a 5 generation pedigree it will be shown as a repeat ancestor because both occurrences are then visible.
Common ancestors highlighting is similar to repeat ancestors highlighting but only ancestors that are present on both the sire and dam sides of the pedigree are highlighted. Common ancestors are those that give rise to inbreeding.
When an individual has common ancestors, this raises the possibility that for any particular gene locus, both alleles present are in fact physical copies of the exact same allele from one of its common ancestors. The inbreeding coefficient is the value of this probability. Or, put another way, it is the probability that both alleles are identical by descent.