On gaps

Gaps result from the alignment of sequences of unequal length during primar y homology assessment. Viewed as character states originating from particul ar biological events (mutation), gaps contain historical information suitab le for phylogenetic analysis. The effect of gaps as a source of phylogeneti c data is explored via sensitivity analysis and character congruence among different data partitions. Example data sets are provided to show that gaps contain important phylogenetic information not recovered by those methods that omit gaps in their calculations. However, gap cost schemes are arbitra ry (although they must be explicit) and thus data exploration is a necessit y of molecular analyses, while character congruence is necessary as an exte rnal criterion for hypothesis decision. (C) 1999 Academic Press.