Generally, the modified distances are very close to the distances estimated by the NJ method for just these taxa.
Among these methods, adding taxa to break up long branches is one of the most widely suggested strategies to reduce the effects of LBA bias [ 17, 18].
Adding our data to that from two previous studies [ 2, 3], we produced the longest aligned dataset (Aln-1, 7164 nucleotide sites) so far used with these taxa (see Methods section).
For such pluralists, depending on the approach taken (e.g., the choice of sequence, the choice of the reconstruction method, the taxa of interest), a different evolutionary pattern may be generated (e.g. a reticulated network rather than a vertical tree).
Thus, depending on organisms of interest, investigators may need to apply due caution when using either of these methods on the taxa mentioned above.
For instance, supertree methods consider taxa not present in all compared trees, whereas consensus methods overlook these taxa.
The percentages of reads assigned by the methods to taxa are shown in Supplementary Figures S1 S18.
The MR supertree methods add taxa to the input trees and apply a consensus.
First, we compared the percentages of reads assigned by the methods to true taxa.
However, notable 'position swaps' occur between the placements obtained from different weighting methods of several taxa, including Osmunda pulchella.
