SIMMONS, MARK PITKIN* AND HELGA OCHOTERENA. L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853. - Effects of gap characters on sequence-based phylogenetic analyses.
We assess the effects of gap characters on phylogenetic analyses and
the relative levels of homoplasy of gap and base characters from a
selection of published sequence-based matrices. Our results, based on
structural rDNA, internal transcribed spacer (ITS) of rDNA, intron,
and exon sequence-based matrices, demonstrate that: 1) gap characters
can represent a considerable portion of the potential phylogenetic
information in sequence-based matrices; 2) gap and base characters
have similar levels of homoplasy; 3) including gap characters in
sequence-based matrices often changes the tree topology and/or
resolution of the most-parsimonious trees; and 4) including gap
characters in sequence-based matrices often increases branch-support
values. These empirical results, in combination with the theoretical
bases given for using gap characters and rigorous methodologies with
which to code gap characters, strongly support the use of gap
characters in phylogenetic analyses that include sequence data from
structural rDNA, ITS of rDNA, intron and/or exon regions. Our results
suggest that longer gaps are not necessarily better phylogenetic
characters than shorter gaps.
Key words: cladistics, deletions, gap characters, indels, insertions, molecular systematics