A logged output of the PAUP* data for generating phylogenetic trees for the protozoan branch is supplied as an example (Figure S7) and provides information regarding the g1 statistic, number of informative characters (parsimony analysis), treatment of gaps, heuristic search settings, distance matrices, tree statistics, tree lengths and bootstrap support.
In Panax, the trnC trnD region provides a similar number of informative phylogenetic characters as the ITS regions and a slightly higher number of informative characters than the chloroplast ndhF gene.
Table 2 Matrix characteristics of separate and combined datasets ITS trnL-F Combined Number of taxa 43 43 43 Number of included characters 691 1,002 1,693 Number of informative characters 190 43 233 Consistency index 0.56 0.93 0.64 Retention index 0.74 0.74 0.74.
Results from phylogenetic analysis of FLint2 are largely congruent with results using the chloroplast regions rbcL, matK, and trnL, and compare favorably in percentage of informative characters, overall homoplasy levels, number of well-supported clades in consensus trees and resolution of ingroup relationships within Amorphophallus.
Cladistics uses algorithmic and statistical methods to determine these taxonomies, based on a matrix of informative characters.
Overall, our data indicate that outgroup choice can severely influence tree topology in datasets with lower numbers of informative characters, but that the addition of more informative characters can lead to a point where outgroup choice plays a minimal role.
The concatenated data set including the nLTRS locus had significantly poorer statistical resolution than the analysis when this locus is excluded, despite the large number of informative characters.
Although species resolution and the number of informative characters are well correlated, the best single gene regions did not necessarily perform the best in combination.
Gap-coding the matrix results in similar arrangements, except for Cryptomeria, which falls outside the gymnosperms – probably due to insufficient amounts of informative characters.
The lack of informative characters and a slow evolution rate complicates both the differentiation of closely related strains of bacteria as well as the resolution of an evolutionary tree [42].
It remains however important to bear in mind that these rapidly evolving nucleotide sites could quickly be submitted to multiple hits, resulting in the loss of informative characters (i.e. homoplasy or saturation).
