The combined molecular data matrix included 1,651 aligned positions, with 292 parsimony informative characters.
The final molecular data matrix comprised 195 taxa representing 185 mycalesine species and 10 related taxa as outgroups.
Across six genes, the molecular data matrix consisted of 5352 aligned characters, of which 2839 were variable and 2259 were parsimony informative (Table 3).
Similar analyses of a reduced molecular data matrix (3,703 nucleotides, loops and mt third positions excluded) resulted in a more poorly resolved and supported tree (Fig. 6).
Whereas this scenario indeed receives strong support from the two coding regions (rbcL-gene, atpA-gene), the molecular data matrix also yields a strong conflicting signal from three relatively conserved spacer sequences (i.e. atpB- rbcL, rbcL- accD, and trnL- trnF) that indicates an alternative root placement between Leptopteris– Todea and the remaining Osmunda s.l.l
The ILD metrics for all analyses are summarized in Additional file 7. Combined unconstrained analyses of the molecular data and matrix A yielded a single MPT with 10451 steps, CI= 0.432, RI= 0.694 (Fig. 8A).
The maximum-parsimony (MP) analysis was applied to MOR, molecular, and combined data matrices (NONA version 2.0 [ 67]: heuristics, option "hold10000 munconstrained100", unconsearched strategytrategy with TBR branch swapping).
For this purpose our results were compared with analysis combining the molecular data with a matrix produced applying Shultz's [ 22] character statements to the sampled taxa.
It is capable of coding indel events, concatenating sequences, incorporating non-molecular data into matrices, and producing output formatted specifically for the popular analytic programs Garli, MrBayes, RAxML, and TNT.
