All of our alternatively recovered relationships favor simpler biogeographic scenarios than previous hypotheses and complete the evidence that amphibians experienced continent-scale endemic radiations [11] as the result of a general vicariance history with little overseas dispersal.
All topologies showed moderate to high support values for the recovered relationships.
Overall, the network was characterized by reticulation and little structure to the recovered relationships.
Within each of Canini and Vulpini, the recovered relationships agree strongly with those recovered by a variety of other authors.
Although the four major lineages (Paulinella, Cyanobium-clade, marine Synechococcus- and Prochlorococcus-clades) are recovered, relationships between these lineages remain unresolved.
We further considered the ratio of the observed number of recovered relationships to its expected count as a result of random assortment (O/E).
d The O/E ratio is the number of folds the observed number of recovered relationships (i.e., TP) in excess of the expected count of recovery by chance.
A preliminary phylogenetic reconstruction of these data (not shown) indicated that the sequences falling within the phylum Betaproteobacteria may be an endosymbiont because their recovered relationships were concordant with some well supported relationships within the planthopper phylogeny (based on [ 29]).
However, the majority of recovered relationships have never been hypothesised by earlier authors (e.g., the sister group relationship of apoda and the bipes species group, and of praepedita + humphriesi and the nichollsi species group).
Strong statistical support has been used to argue that recovered relationships should be treated as canonical, but simulation studies have shown that robust statistical support can be assigned to phylogenetic relationships that are incorrect [ 55].
