Data from: Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales

The placement of angiosperms and Gnetales in seed plant phylogeny remains
one of the most enigmatic problems in plant evolution, with morphological
analyses (which have usually included fossils) and molecular analyses
pointing to very distinct topologies. Almost all morphology-based
phylogenies group angiosperms with Gnetales and certain extinct seed plant
lineages, while most molecular phylogenies link Gnetales with conifers. In
this study, we investigate the phylogenetic signal present in published
seed plant morphological datasets. We use parsimony, Bayesian inference,
and maximum likelihood approaches, combined with a number of experiments
with the data, to address the morphological-molecular conflict. First, we
ask whether the lack of association of Gnetales with conifers in
morphological analyses is due to an absence of signal or to the presence
of competing signals, and second, we compare the performance of parsimony
and model-based approaches with morphological datasets. Our results imply
that the grouping of Gnetales and angiosperms is largely the result of
long branch attraction, consistent across a range of methodological
approaches. Thus, there is a signal for the grouping of Gnetales with
conifers in morphological matrices, but it was swamped by convergence
between angiosperms and Gnetales, both situated on long branches. However,
this effect becomes weaker in more recent analyses, as a result of
addition and critical reassessment of characters. Even when a clade
including angiosperms and Gnetales is still weakly supported by parsimony,
model-based approaches favor a clade of Gnetales and conifers, presumably
because they are more resistant to long branch attraction. Inclusion of
fossil taxa weakens rather than strengthens support for a relationship of
angiosperms and Gnetales. Our analyses finally reconcile morphology with
molecules in favoring a relationship of Gnetales to conifers, and show
that morphology may therefore be useful in reconstructing other aspects of
the phylogenetic history of the seed plants.