Data from: Robustness of Felsenstein’s versus transfer bootstrap supports with respect to taxon sampling

The bootstrap method is based on resampling sequence alignments and
re-estimating trees. Felsenstein’s bootstrap proportions (FBP) is the most
common approach to assess the reliability and robustness of sequence-based
phylogenies. However, when increasing taxon sampling (i.e., the number of
sequences) to hundreds or thousands of taxa, FBP tends to return low
supports for deep branches. The Transfer Bootstrap Expectation (TBE) has
been recently suggested as an alternative to FBP. TBE is measured using a
continuous transfer index in [0,1] for each bootstrap tree, instead of the
binary {0,1} index used in FBP to measure the presence/absence of the
branch of interest. TBE has been shown to yield higher and more
informative supports, while inducing a very low number of falsely
supported branches. Nonetheless, it has been argued that TBE must be used
with care due to sampling issues, especially in datasets with high number
of closely related taxa. In this study, we conduct multiple experiments by
varying taxon sampling and comparing FBP and TBE support values on
different phylogenetic depth, using empirical datasets. Our results show
that the main critique of TBE stands in extreme cases with shallow
branches and highly unbalanced sampling among clades, but that TBE is
still robust in most cases, while FBP is inescapably negatively impacted
by high taxon sampling. We suggest guidelines and good practices in TBE
(and FBP) computing and interpretation.