Identification of lineage-specific insertions and deletions. In this hypothetical region of an amino acid multiple alignment, there are six regions containing gaps. The regions identified by numerals below the alignment can be assigned unequivocally to a particular branch in the species tree: 111 indicates a deletion (EDD) in the ancestral rodent branch; 22, an insertion (EE) in the ancestral primate branch; 3, an insertion (F) in human; and 4, a deletion (L) in the macaque branch. The regions identified by Xs below the alignment involve at least two distinct indel events, the nature of which cannot be established with confidence; regions of this type were discounted from further analysis.
