Mitochondrial Barcodes: An Adam-Eve Bottleneck 200,000 Years Ago?

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(Timothy Horton) #31

I looked into this a bit more. Human Evolution where this paper appeared is an online science vanity journal published by Angelo Pontecorboli in Florence, Italy. Pontecorboli’s background is in Architecture and there appears to be little to no scientific oversight or review.

According to their website the services offered are

Human Evolution

The e-zine is not listed in the 2018 Journal Citation Reports list which supplies index factors for scientific journals and papers. Not very impressive.


(Steve Schaffner) #32

Web of Science doesn’t include it, but Harvard does have a subscription. A decidedly eclectic journal. . . Some titles from one issue: “Africa: Genital Stretching”, “Factors Influencing the Academic Performance of Undergraduate Students of Private Universities in Bangladesh: Modeling Approach”, “Humanoid fossil of Sansan revealed during ‘A Journey to the Center of the Earth’ by Jules Verne”, “What went wrong in cross-cultural psychology over the last 40 years”, “Laicality and secularity of Bioethics: why I believe in a biologically rounded ethics”.


(Joel Duff) #33

I find myself straddling the fence a bit here compared to some of you. Everyone seems to agree - as do I - that the popular press has mangled the original research in its reporting. Some place the blame on the original authors lack of clarity and/or their own incorrect interpretations. I’ll grant there has been some unfortunate quotes from the authors that have led to some of the problems. When I reviewed the situation and focused on the YEC response I provided a fairly neutral response to the actual research and even provided a simply case of bottlenecking as an example of how some of their results could be understood. I knew then but have regretted more since,using such a simple example as if were the explanation.
The recent flair up of press again has made me go back and take another look. I’ve been working my way through literature I had not seen before when I wrote my response on BioLogos. I’m a bit more sympathetic to the original authors. Sure, I think they are ignoring some things and we have had many criticisms of their conclusions but their concerns and results they present are not without precedent. The “barcode” gap between species has been the subject of a fair amount of discussion and there is a really interesting set of literature that suggests that there are processes involved in mtDNA selection/sorting or a “scouring mechanism by which the within-species diversities of mtDNAs are decreased…” that isn’t fully appreciated to this point. The point being that there are still unknowns and while they may be wrong in their interpretation of the significance of similar amount of variation in many species the observation in mtDNA seems to be real and worth exploring and debating. They aren’t alone in this quest but the whole barcoding thing seems to have taken on a personal angle that causes strong opinions about studies such as this one. Those strong opinions result in the inflated and over-the-top claims.
I do know that the authors feels that most of the coverage resulting from their paper is far from what they were trying to say and they were very surprised that this paper has taken on a life of its own.
Just a few of the papers I’m reading that are relevant to this study:

Hill, Geoffrey E. "Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap." Ecology and evolution 6, no. 16 (2016): 5831-5842. https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.2338

Hill, Geoffrey E. "Mitonuclear Mate Choice: A Missing Component of Sexual Selection Theory?." BioEssays 40, no. 3 (2018): 1700191. https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.201700191

Gershoni, Moran, Alan R. Templeton, and Dan Mishmar. "Mitochondrial bioenergetics as a major motive force of speciation." Bioessays 31, no. 6 (2009): 642-650. https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.200800139

Forsdyke, Donald R. "Base composition, speciation, and barcoding." Trends in ecology & evolution 28, no. 2 (2013): 73-74. Base composition, speciation, and barcoding - ScienceDirect


(S. Joshua Swamidass) #34

@Joel_Duff, I’d like to know how you came to this conclusion. It does not appear to be supported by the data. It appears to echo the incorrect interpretation of the authors, amplifying the negative consequences to public understanding.

Reading their original paper, it is hard to be sympathetic to them. Here is what they right about human evolution:

More approaches have been brought to bear on the emergence and outgrowth of Homo sapiens sapiens (i.e., modern humans) than any other species including full genome sequence analysis of thousands of individuals and tens of thousands of mitochondria, paleontology, anthropology, history and linguistics [61, 142-144]. The congruence of these fields supports the view that modern human mitochondria and Y chromosome originated from conditions that imposed a single sequence on these genetic elements between 100,000 and 200,000 years ago [145-147]. Contemporary sequence data cannot tell whether mitochondrial and Y chromosomes clonality occurred at the same time, i.e., consistent with the extreme bottleneck of a founding pair, or via sorting within a founding population of thousands that was stable for tens of thousands of years [116]. As Kuhn points out unresolvable arguments tend toward rhetoric.

In your opinion, is this a valid or rational interpretation of the data? Do you think it wise to claim there is no evidence against a bottleneck before 200 kya without actually referencing the immense number of studies demonstrating there is evidence against it?

Honestly, I do not know how to read this sympathetically. They were out of their depth, and choose to disparage the whole field of population genetics. Not good.


(S. Joshua Swamidass) #35

An article getting it right was published in Forbes:


(S. Joshua Swamidass) #36

I will point out another example, at the very least, of confused writing. They lay out to options:

  1. mitochondrial and Y chromosomes clonality occurred at the same time, i.e., consistent with the extreme bottleneck of a founding pair,

  2. or via sorting within a founding population of thousands that was stable for tens of thousands of years

These are both the same scenario. This is not an either-or, so of course science can’t discriminate it. Moreover, mitochondrial and Y-Chromosome “clonality” (but they must mean coalescence, not clonality) does not need to be at the same time to be consistent with a bottleneck. It is nearly impossible to untangle their meaning in sentences like this because they do no appear to really understand population genetics.

It bears repeating and redisplaying some prior discussion on this with @AJRoberts about @purposenation’s podcast.

Of note, William Lane Craig emailed me the other day with NewsMax article (someone had forwarded it to him). He immediately recognized it was bogus, to his credit, and new exactly why. This is not rocket science.


(S. Joshua Swamidass) #37

8 posts were merged into an existing topic: Introducing Matt Mirecal


(Steve Schaffner) #43

The barcode gap background that you point out is interesting, and is something I hadn’t known about. Even if the hypothesis is correct, though, that this gene is frequently involved in speciation, it still doesn’t follow that the coalescence time within a species corresponds to the time of speciation. It would only set a lower bound on it.


(Steve Schaffner) #44

Sure, I’m familiar with the case. But that really was a hugely significant discovery.


(Joel Duff) #45

Absolutely agree


(S. Joshua Swamidass) #48

Not at all. I would make use of it and add it as a new model.

@mattc_mirecal did you know that we have been evaluating the evidence very closely, and have found three new ways of thinking about Adam and Eve in light of the evidence?

Would you be interested in learning about these?


(S. Joshua Swamidass) #49

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(S. Joshua Swamidass) #50

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(S. Joshua Swamidass) #53

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(S. Joshua Swamidass) #54