In DNA and protein sequence alignments, gaps are used to represent positions where insertion/deletion (indel) events have occurred, reflecting the absence of nucleotides or amino acids in specific sequences. Although indels accumulate in most genomic regions, they are more common in non-coding regions (e.g., introns) than in protein coding regions. Intron sequences have typically been used to examine relatively recent divergences (e.g., [1±5]), but there has been a growing appreciation that non-coding sequences also represent a rich source of phylogenetic information at deeper levels in vertebrate phylogeny. Indeed, non-coding data have been used to estimate phylogeny for a number of vertebrate orders (e.g., [6±8]) and classes (e.g., [9±13]).