Mailbag: mtDNA ancestor and speciation?

I've got a question about something I wrote in a newsgroup in 1995. Okay, that doesn't sound overly urgent, right? The general subject has come up again for me though, and so I would like to find out if I am right about this, and figured the best way to be sure is to ask someone who will likely know right off. Hence this email.
One other problem has been the assumption (I don't remember any compelling reason being given to assume this) that the end point (going backwards) of the MtDNA trail *must* be a speciation point. This sort of thing also happens with changes in tool industries; there is often an unsupported assumption that it must mark a change in species. The MtDNA trail is just that, it's a trail like tracing surnames that always pass through one side of a family. The trail just fades out, but that doesn't necessarily mean that it marks a major change (mind you, it *might*, but it doesn't *necessarily* do so).
The first paragraph is where I wonder if I am right or wrong, or some muddled middle ground that I'm not aware of.

Heh..that’s taking it to a new level – someone was WRONG on the INTERNET in 1995!

Nowadays it’s pretty clear that the mtDNA ancestor was not a speciation point, because Neandertals didn’t have the same mtDNA ancestor and they interbred with us (new paper tomorrow reports that a large fraction of people today have Neandertal and Denisovan-derived HLA types, for example).

There’s still a serious disagreement about the meaning of these recent common ancestors. Most genes aren’t like this, but it’s not clear whether mtDNA and the Y chromosome have these recent ancestors because of a population size bottleneck, or natural selection, or some kind of population structure. Humans don’t look very much like most other primates in this aspect of our biology, but when you combine us with Neandertals and Denisovans, we do look pretty much like ordinary apes in population structure. So maybe this is an aspect of how we became modern humans, something about our population structure or biology.

Here’s a recent review paper where I discuss these issues in some more detail.

http://johnhawks.net/research/hawks-2008-genes-numbers-effective-size

Hope that helps –

–John