An excellent article from @Agauger on the mitochondria barcodes story (Mitochondrial Barcodes: An Adam-Eve Bottleneck 200,000 Years Ago?). Great job explaining the complexities here, and I think your conclusion is empathetic and correct:
What to Make of It?
Well, I am unwilling to dismiss the article flat out, but neither can I endorse it. I don’t think the study can claim all the things it does based on the evidence they have. That I take this approach is ironic. I myself am investigating the possibility of our origin from a single human pair, so my opinion is not because I exclude the idea a priori . Yet I must confess I have reservations. Too many unanswered questions.
I am also sympathetic because I have seen tactics used on Stoeckle and Thaler similar to those that have been used on ID proponents. Denigrating the journal the article was published in, and therefore declaring the work is junk, is erroneous as an argument, because controversial papers may not ever see the light of day except in non-conformist journals. Saying they are ignorant or worse, dishonest, without first examining the work on its own terms, is simply unfair, and ad hominem .
I agree that focusing in on the Journal is an ad hominem. It is worth noting, but it does not tell us much about the quality of the argument or the nature of the evidence. My only critique with this article is that they have wildly extrapolated to conclusions that the evidence does not support, revealing basic misunderstanding of population genetics. It seems that @Agauger agrees.
Great job @Agauger, your graphic showing how coalescence works is important education for your readers too:
Look at this figure. It traces the lineages of women going back eight generations. At the top is the ancestral generation with eleven individuals. I have colored the arrows for one woman’s lineage red. In the final generation, only her lineage persists. Working from the present backwards, you can follow the pattern as it coalesces into one lineage, that one woman’s on the first line. Note also that mitochondria, because they are passed from mother to daughter, never have an admixture of the paternal and maternal DNA. This speeds up the effects of beneficial gene sweeps.