Immortal cells, horizontal gene transfer and the tree of life

Had an interesting phone conversation with Aldo last night, talking about horizontal gene transfer amongst single-celled organisms (yes it also happens in multicellular organisms, but I guess it's not so important there unless the new material gets into the germ cells). He mentioned that the traditional tree-of-life style classification of the prokaryotes is a bit ... can't remember the exact word he used, let's say provisional ... when compared to its application to multicellular organisms. I replied that, with multicellular organisms, there's a clear sense in which offspring are not the same individuals as their parents, but there's no such distinction in the case of single-celled organisms. In a sense, a single-celled organism today is the same individual (or at least, one of many clones of it) as its parent from a billion years ago — a parent which we might not even classify as being in the same species as its "descendant"!