What if some phylogenies were simply irresolvable? That is, what
if, no matter how much data we collected, it would be impossible
to reconstruct, with a high level of certainty, an accurate
representation of the tree of life? That would suck. A lot. I
have mentioned how this can result from long branch attraction
or lineage sorting. But are there any taxa where this appears to
be a major problem? Antonis Rokas and Sean Carroll have
published an essay in PLoS Biology that addresses the issue of
bushes (or irresolvable nodes) in the tree of life. They point
out four clades in which no single tree has a high level of
support: The types of data considered are gene sequences,
parsimony informative characters (PI-characters), and rare
genomic changes (RGCs; insertions, deletions, and other events
less common that nucleotide substitution). The four clades shown
are (A) human/chimp/gorilla, (B) elephant/sirenian/hyrax, (C)
tetrapod/coelocanth/lungfish (the vertebrate tree), and (D)
chordate/arthropod/nematode (the me