G.F. Guala
The time scale issue.
If a vicariant event occurred for one species, then it is likely that the entire community present at the time was effected. Thus, one should see a biogeographic pattern across multiple taxa.
Exactly which taxa should we see it in (community assemblages)?
What if no speciation happened? What if we have extinction?
With the foundation of Vicariance Biogeography technique as well as the extraordinarily useful and simple optimization algorithms available now, we can apply all of the data to the cladogram and really, for the first time, rigorously explore the relationships of habitats, traits and areas to taxa.
If Vicariance Biogeography explores the relation of taxa to areas, Historical Biogeography and Historical Ecology explore the relationships of taxa to everything (including areas).
You can hang anything on a cladogram.
Because a cladogram is a representation of relative relationships and not a complete phylogeny, it can be used as a framework on which to test hypotheses of evolutionary directionality or series.
1. The C4 Carbon fixation pathway is much more complex and efficient and therefore must have evolved from the C3 pathway.
2. The C4 Carbon fixation pathway is a very complex (and therefore unlikely) evolutionary shift and must have therefore evolved only once.
Using a cladogram generated by the Grass Phylogeny Working Group
(1998) we can test these hypotheses.
We can see that the first hypothesis is supported and the second is rejected.