However, introns cannot be regarded as reliable phylogenetic indicators because they are often mobile and can be lost frequently (see next section).
Introns are highly volatile components of the charophycean mitochondrial genome (figs. 3 and 4), making it difficult to trace their origins and use them as phylogenetic indicators.
The presence and absence of such helices are therefore good phylogenetic indicators for these relatively closely related taxa, even though alignment of the primary sequence of these helices (and cladistic or phenetic sequence analysis) between all taxa is difficult due to high evolutionary rates.
We used both statistical support (bootstrap values, quartet puzzling support values, and posterior marginal probabilities) and congruence between the different phylogenetic methods as indicators of the reliability of the different internal branches of the tree.
95% of same-RFLP pairs have SNP distances under 11, indicating that in general RFLP type is a good indicator of phylogenetic relatedness.
A difference of 10% ensures that sequence similarity is a good indicator of phylogenetic affinity (unpublished observation).
Authors' response: BLAST generally is not a reliable indicator of phylogenetic relationships especially for diverged proteins.
Net relatedness index reflects the more general structure, whereas NTI is a more sensitive indicator of phylogenetic extendability or segregation among components.
However, hybridization was a weak indicator of phylogenetic relationship for the African 20-chromosome toads, and seems to be widespread among all species in that group independent of phylogenetic distance [ 40].
Ranking individual genes by their respective contribution to the total PBS values--a rough indicator of phylogenetic utility--reveals that some genes, such as ND5, CR, ND4, CoxI and 16S, are better indicators of galliform evolution than others (Fig. 3A).
