I apologize if this seems naive, but I was asked a question that appears to me to be kinda deep, but might just turn out to be a detail about terminology.

I had been discussing evolution with my son when he raised the question, did the common ancestor of humans and chimps and bonobos "really go extinct"?  I immediately understood his query, though he further clarified it by adding "...like the dodos did."  And I had to say, technically, "I don't know!"

Clearly, that common ancestor (or any of our evolutionary ancestors for that matter) is extinct in the sense that there are no longer living creatures of that species in existence today.  But did they technically "go extinct"?  It seems to me they survived - I'm living proof!

When I think of the tree or bush of life, I think of that common ancestor as a branching point, with humans evolving along one branch, and chimps and bonobos along another (perhaps I've got the ordering messed up or simplified, you get my point) - the species didn't die out per se, it diverged and evolved along different paths.  But when I think of the dodo, it's the end of a twig.  That's it, lopped off, no more of them, no more of their genes being directly passed on, the end of the line - it didn't evolve, it was snuffed out.  

The extinction of the dodo seems like a very different kind of thing than the extinction of a species with evolutionary descendants.  Our ancestors' genes are still "with us", the dodo left no ancestors, so they are not.  Extinction seems like a negative thing, like a failure to adapt to changing environment or to succumb to a given evolutionary pressure.  But our ancestors didn't succumb, they succeeded, and their descendants evolved and adapted and continue to successfully reproduce and thrive.  Am I just dealing with a terminological distinction for which there is a simple, technical nomenclature?  Are there really different words for these seemingly different things?  (If so please tell me!)  Perhaps it's as simple as 'evolution' versus 'extinction'?  Should we just say that whereas the dodo truly went "extinct", our ancestor species actually "evolved" (and maybe it's wrong to say they went extinct at all)?  Or is the difference more elusive than that...

I started rereading bits of The Selfish Gene and The Extended Phenotype for some guidance.  OK, I realized this tree image is perhaps too linear, and it might even be a tad group- or species-selectionist.  The gene-tree picture would be much more complicated, with gene lines looping in and out of organisms, like strands woven through individuals, through species.  And as the genes flow through time, species would look more like fluid rivers than solid tree trunks. And then the whole thing gets even more complex when extended phenotypic effects are introduced, with rivulets spilling over banks affecting other rivers' gene-flows!  That's one messy tree!

From this I envision (though am by no means certain) that from a gene's point of view, there might not be much difference at all between these seemingly very different types of species-level extinction.  (I don't know if the following points are in fact true of the dodo specifically, but) assuming that most of the genes of the dodo continue to exist in its cousin species (albeit in different configurations), then the gene lines passing through the dodo river might not look significantly different in (mathematical) character from the gene lines going through the river that was our common ancestor with chimps and bonobos.  From the gene point of view, the extinctions of individual species aren't necessarily causally connected to the ends of gene lines (any more than they are connected to the deaths of individuals), and so might not appear to be significant events in the 'life' of a gene at all, let alone appearing to be significantly different events.  (Barring mass extinctions, of course.)  That is, if bonobos and chimps share 99% of their DNA, then 99% of the genes don't care and don't even notice if one of those species goes extinct, for they continue into future generations via the genes in the successful cousin anyway.  The death of any one species doesn't really impact gene lines any more significantly than the death of an individual impacts the continuation of a species.

So back to my original query, is there really a difference between the two types of extinction? -- is this just a species-centric way of asking a question that doesn't really have meaning at the gene-selection level of evolution?  Or am I just being misled by the group-selectionist fallacy instilled by the image of the tree?

It's been two weeks now, I still haven't answered my son.