A paper on species numbers and why some taxa have more than others

Been reading this paper: Rabosky DL, Slater GJ, Alfaro ME (2012) Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life. PLoS Biol 10: e1001381. doi:10.1371/journal.pbio.1001381.t002.

In a way I like it because the result, basically the time a taxon is around does not say anything about the number of species in that taxon, fits into what I would have expected. However there are some general concerns with this work:

• Look at the time tree: where are the worms? Okay, that's asked from a wormy point of view, but it's a general thing. The evidence is based on a subset of taxa, where estimates about evolutionary age are at hand. Even more so in the data set four groups, Angiosperms (Flowering Plants), Mammalia, Aves (Birds, Dinosaurs?) and Coleoptera (Beetles) are featuring prominently (because they are species rich and wells studied). Out of 1,397 major clades 825 fall into these four.
• Figure 3 is weird in some way as well. The time scales in the plots seem to be wrong, why are Chondricthyes ('sharks') displayed with a bit more than 300 million years (Ma), while Actinopterygii (your 'normal fish') with more than 400 Ma? The former ones are at least 50 Ma older than the latter ones. The other thing, how is species richness measured in the past? Fossils of course, but then some organisms (like water living vertebrates) fossilise much better than e.g. land dwelling invertebrates (think of little flies).
• As mentioned by the authors themself 'we know very little about the consequences of [...] taxonomic ranking'.
• The closing sentence 'large-scale phylogenetic diversity patterns reflect constraints on species richness within clades rather than sustained diversity increases through time' is very interesting, as it raises the question: which constraints?