Data from: Median-Joining Networks and Bayesian phylogenies often do not tell the same story

Inferring phylogenies among intraspecific individuals often yields
unresolved relationships (i.e., polytomies). Consequently, methods that
compute distance-based abstract networks, like Median-Joining Networks
(MJNs), are thought to be more appropriate tools for reconstructing such
relationships than traditional trees. Median-Joining Networks visualize
all routes of relationships in the form of cycles, if needed, when
traditional approaches cannot resolve them. However, the MJN method is a
distance-based phenetic approach that does not involve character
transformations and makes no reference to ancestor-descendant
relationships. Although philosophical and theoretical arguments
challenging the implication that MJNs reflect phylogenetic signal in the
traditional sense have been presented elsewhere, an empirical comparison
with a character-based approach is needed given the increasing popularity
of MJN analysis in evolutionary biology. Here, we use the conservative
Approximately Unbiased (AU) test to compare 85 cases of branching patterns
of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets
from 55 empirical studies. By rooting the MJN analyses to provide
directionality, we report substantial disagreement between computed MJNs
and posterior distributions on BI phylogenies. The branching patterns in
MJNs and BI phylogenies show significantly different relationships in
37.6% of cases. Among the relationships that do not significantly differ,
96.2% show alternative sets of relationships. Our results indicate that
the two methods provide different measures of relatedness in a
phylogenetic sense. Finally, our analyses also support previous
observations of the statistical hypothesis testing by reconfirming the
over-conservativeness of the Shimodaira-Hasegawa test versus the AU test.