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. Applyi...