Over at John Hawks, Has the dam broken on mtDNA selection?. I don't know if this matters that much scientifically since non-human phylogeography tends to be more cautious than the field of historical human population genetics, but it matters a lot for the public which has been habituated to a steady stream of mitochondrial data being interpreted by popularizers and the press since African Eve.
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I think you were trying to point here.
fixed now.
The part about mtDNA diversity reflecting only the most recent selective sweep was pretty interesting.
Maybe OOA is right, but it's only the most recent layer of the cake.
With regard to homogenization of mtDNA, I found this comment interesting:
"perhaps hitchhiking with a maternally transmitted parasite"
To the degree that parasites cross specie boundaries, wouldn't that imply some horizontal mtDNA gene transfer across species? Should someone be looking for mtDNA similarity between species that share common parasites? (Or are there mechanisms by which the fertilized egg actively breaks down the "wrong" mitochondria...as happens in some species with the sperm mitochondria that get into the egg.) (Selection would also tend to eliminate foreign mitochondria that were poorly adapted to the new species.)
A comparison between rat and human mtDNA might show mtDNA horizontal gene transfer.
Hmmm...what happens if a fertilized mouse egg has its mitochondria replaced with human mitochondria? Have any mouse cell lines been created with human mitochondria?
Viability of mitochondria transfer between species:
http://news.scotsman.com/topics.cfm?tid=10&id=57822006
"Dr Huizhen Sheng, of Shanghai Second Medical University, said in a paper two years ago that she had created more than 100 embryos by fusing human skin cells with rabbit eggs whose nuclei had been removed.
The embryos are said to have survived to the blastocyst stage - a ball of no more than about 60 cells the size of a pinhead."