Phylogenomic testing of root hypotheses - demonstrative datasets - Opisthokonta and Proteobacteria

The determination of the last common ancestor (LCA) of a group of species
plays a vital role in evolutionary theory. Traditionally, an LCA is
inferred by the rooting of a fully resolved species tree. From a
theoretical perspective, however, inference of the LCA amounts to the
reconstruction of just one branch - the root branch - of the true species
tree, and should therefore be a much easier task than the full resolution
of the species tree. Discarding the reliance on a hypothesised species
tree and its rooting leads us to re-evaluate what phylogenetic signal is
directly relevant to LCA inference, and to recast the task as that of
sampling the total evidence from all gene families at the genomic scope.
Here we reformulate LCA and root inference in the framework of statistical
hypothesis testing and outline an analytical procedure to formally test
competing a-priori LCA hypotheses and to infer confidence sets for the
earliest speciation events in the history of a group of species. Applying
our methods to two demonstrative datasets we show that our inference of
the opisthokonta LCA is well in agreement with the common knowledge.
Inference of the proteobacteria LCA shows that it is most closely related
to modern Epsilonproteobacteria, raising the possibility that it may have
been characterized by a chemolithoautotrophic and anaerobic life-style.
Our inference is based on data comprising between 43% (opisthokonta) and
86% (proteobacteria) of all gene families. Approaching LCA inference
within a statistical framework renders the phylogenomic inference powerful
and robust.