3.3. Combined Analyses of Nucleotide Substitutions and Gap Characters
ML analysis of the combined nucleotide and gap character data (including invariant gap characters) resulted in an estimate of phylogeny (Figure 6) virtually identical to the nucleotide tree (Figure 1). In general, there was a modest increase in the average bootstrap support for groups in the partitioned ML analyses of nucleotide substitutions and gap characters (Figure 6). However, there were also five nodes that exhibited more substantial increases in bootstrap support (>10%); four corresponded to supra-ordinal clades (Figure 6) and the fifth to the Balaeniceps-Scopus clade in Pelecaniformes (which increased to 75%). This general increase in support is consistent with the general assumption that including indel information in phylogenetic analyses would prove useful.