Scott,
The answer to all your questions is: because, as the title indicates, it is in the first instance a biogeography paper, not a detailed taxonomy paper. Therefore, we only included samples that were relevant for the biogeographical question at hand, concerning biogeographical relationships between Aussie and NG representatives of these genera. Yes, we did draw the taxonomic inferences our data allowed, but also indicated the many issues that remain unresolved.
Cheers,
WW
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