TRH, Birds are more closely related to crocs than they are to other reptiles. After that, I'm uncertain about the degrees of relatedness among other herps, but I think your speculation may be wrong. I just can't say for sure. Cold blood critters leave me cold. Sad sad pun.
As you work back into the basic framework of the phylogenetic tree, you will find that the relationships among groups is more and more difficult to discern. In some ways that makes sense because they diverged long ago. On the other hand, this seems singularly odd since the differences between some groups seem so fundamental (warm vs. cold blooded for instance) and thus the separations should be easy to locate. But when you get back a good long ways, where you attach, for instance those crazy sponges, is not obvious. One of my colleagues however, is puzzling that out right now (among many other things).
I am lucky to be in a place where folks are working on such strange and seemingly esoteric issues. But in the end, the answers they come back with provide, in combinations with others, provide the essential understandings of how life works and how it got to this point, and where it is going. Damn cool. Another friend works in the developmental, evolutionary genetics of vision in mollusks. Both of these research programs require a solid understanding of who is related to what. And that doesn't exist for their study organisms. So that has to be developed along the way. I never thought something like that could be so interesting but it is.
Meanwhile I work on some crazy mice that do really bizarre stuff, both evolutionarily and ecologically. Life is cool.
