In article <badger.766127909 at phylo>, badger at phylo.life.uiuc.edu (Jonathan
>>Doug Eernisse <Doug_Ee at um.cc.umich.edu> writes:
>>>Am I missing something or does anyone else think this is a basic
>>problem with not being able to say anything about the relative
>>cladistic branching pattern of a three taxon statement? That
>>is, without using rocks for an outgroup, and assuming each
>>of these is more or less a cohesive group itself (which may
>>not be true, for all I know).
>>Trees are based on sequences, not organisms. The "Tree of Life" can be rooted
>by the use of paralogous genes such as the Alpha and Beta globins. All Alpha
>globins are more closely related to other Alpha globins than they are to Beta
>globins, even the Beta globin from the same species. So every species contains
>its own outgroup -- neat, eh?
So then, which B globin sequence do you choose to use in the actual
analysis, given that there are as many different ones as there are
species? And, more globaly, what do you do if the available paralogue
of the gene of interest is too saturated with change to be of use?
I think the original poster's comment is to some extent valid.