Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)

You’re correct in your guess - the human / (Neanderthal - Denisovans common ancestor) split at ~ 700KYA. There’s also the fact that that Denisovans genome has some parts that seem to be around 1MY old, but that’s more up for debate.

I just don’t find the sudden bottleneck to two compelling either. For multiple reasons: 1. Hominins have always been pretty widespread so what kind of event can cause a severe bottleneck of two? What kind of natural disaster? Now I guess you could argue the event happened to a local population and that population dipped to two and then they outlived the other populations and didn’t reproduce with them. Which leads me to my second issue
2. If it happened to a local population what in the world could keep them isolated from the other populations? Like I said hominins moved around.
3. It seems the prior probability of a population dipping to two and not going extinct would be very low. And these two individuals would have to be male and female and at the right age to reproduce. A 40 year female and an infant aren’t going to do you much good.
4. I also have theological concerns

It’s an interesting idea but I don’t find it compelling at all.

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I’m hoping to meet both of you!

Hi Dennis,

I think that you and @RichardBuggs might be working from different definitions of the problem.

The hypothesis under scrutiny is that all of humanity on the planet today is the genetic (not genealogical) offspring of a single couple. Your view is that this implies that 100% of our genome must be traced back to that couple. So the couple would have to be the exclusive genetic forebears of H Neanderthalis as well, because over 1% of the genome of non-African populations comes from Neanderthals. Since the Neanderthal/H Sapiens split was 700kya, that is the earliest possible date for the single couple.

On the other side, @RichardBuggs seems to believe that the claim of single couple sole genetic ancestry does not imply that 100% of humanity’s DNA must trace back to that couple. He would thus allow hybridization between humanity and non-humanity (Neanderthals, Denisovans), and logically the date could be earlier (500kya).

It seems logically incoherent to claim that humanity is solely descended from a single couple, and also to allow for hybridization with creatures that are not descended from that couple. I note that Hugh Ross stated about 10 years ago that the Bible predicted that there was no hybridization between H Sapiens and Neanderthals; the Bible claimed (in Ross’ view) that 100% of humanity’s genetic code must come from that single couple. So I would accept your definition of the claim, Dennis. (And Ross’ 10 years ago.)

Moreover, if anyone is willing to permit humanity to have less than 100% genetic descent from that couple, then the vastly more sensible solution is @Swamidass’ genealogical Adam and Eve hypothesis, which would easily put the couple in the timeframe of the capabilities we associate with humanity.

Pax Christi,
Chris Falter

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@Swamidass (and @DennisVenema ):

Joshua, I think you have made a category error in your thinking here… and this is the post I just made back where your “…Against a Bottleneck of Two?” first appears. And you made it quite some time ago!

I, like @glipsnort, didn’t even notice you doing this so many months ago!

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Continuing the discussion from Heliocentric Certainty Against a Bottleneck of Two?:

@swamidass

This is the kind of distortion that I would have expected from a YEC, not from you.

You appear to be attempting to “divine” a dividing line between Homo Sapiens and NOT-Homo Sapiens… but this has nothing to do with a regression analysis of genetics back through the common ancestry!

Whether there is a “first” Homo Sapien in God’s eye rather than in the view of human operated sciences, (made through evolution rather than through special creation), the first “man” would still be part of a fairly large population!.. say 10,000 or more!

You need to straighten out your description of this key part of your operating scenario… because right now you are mixing apples with oranges…

Hi all, I have been a bit distracted from the bottleneck issue by the human-chimp genome similarity issue that @DennisVenema raised. This has now moved to another thread here: Human Chimp Genome Similarity
I will try to get back to the bottleneck issue soon!
Richard

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Hi all, this paper, by some of my close colleagues and collaborators, came our yesterday in Nature Evology and Evolution "The ash dieback invasion of Europe was founded by two genetically divergent individuals"

@RichardBuggs

This is a portion of what the article discusses:

You aren’t trying to suggest that the 2.5 million haploid individuals have disappeared from the Earth, are you?

Hi Dennis,
Sorry to take a while to respond. You have quite distracted me by bringing up the human-chimp similarity issue, which is very interesting. I had been wanting to re-visit that issue for some time. But back to bottlenecks…

This is an “argument from personal incredulity” (to borrow a phrase from Richard Dawkins). I am interested that this now appears to be your strongest argument against a bottleneck. I suspect that many people will find argument this less compelling than the “certain” case from population genetics that you appear to make in Adam and the Genome.

As far as I can see, a step-by-step evolutionary pathway for a lineage passing through a bottleneck is clear, and you just have doubts about the selective forces that could drive it. As arguments from personal incredulity go, that is not a very strong one.

I am sorry, but I don’t think this is a complete summary of your claims in Adam and the Genome. You made very specific claims about what the literature was saying, and these have not stood up to scrutiny.

In addition, I think that most readers of Adam and the Genome pp45-65 would conclude that your major claim was that a bottleneck of two in the human lineage is almost impossible on the basis of analyses of current human genetic diversity.

But we have discussed these issues before, and anyone can read your book and make up their own mind, so I won’t belabour the point.

No, as we have discussed, methods applied to date suggest that effective population sizes have not dipped below several thousands, but they do not show that census population sizes have not dipped below that figure.

As I say, I think that most readers of Adam and the Genome pp45-65 would conclude that your major point was that a bottleneck of two in the human lineage over the last 18 million years is almost impossible on the basis of analyses of current human genetic diversity. Your new view is a significant departure from this point.

So have I! Thank you for coming to the table.

May we all be more and more like Chaucer’s Clerk: “And gladly wolde he lerne, and gladly teche.”

Good to hear that. It would be a very different chapter, to be sure.

You would do your readers a service if you wrote a blog to tell them now, as far as you are able, that present day genomic diversity in humans does not preclude a bottleneck in the human lineage between approx 700K and 7myr ago. I think you owe this to them, and to everyone who has taken the time to participate in this discussion.

@RichardBuggs

This is certainly not @DennisVenema’s “strongest argument against a bottleneck.”

The strongest argument against a bottleneck, is that a bottleneck of a single mating pair would have left genetic traces well past 10,000 years ago.

And isn’t that pretty much the litmus test? You seem to indicate that if Dennis can’t prove there was never ever a bottleneck of a single mating pair … even further back than 300,000 or 400,000 years ago… then he must be grand-standing.

I would suggest that the grandstanding is going on from another vector… Dennis has convincingly demonstrated that there isn’t a trace of a bottleneck of a single mating pair for as far back as any convincing understanding of “humanity” can be thought to exist. 300,000 years should pretty much cover that, yes?

Since you have returned to this thread less than an hour ago, perhaps you could take a moment to answer my question from quite some time ago:

I’ve already agreed with this, and it’s been up there ^^ for weeks now. You’re welcome to publicize it as you wish. I no longer write in an official capacity for BioLogos, except by invitation from time to time. This means I’m just another commenter like you for the time being.

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I beg to differ. It is not @DennisVenema’s personal incredulity you have to worry about, but the incredulity of a great deal of people. We have evidence of a number of hominin species existing between 1 My and 500 Kya. (Assuming that 500 Kya is still the threshold for detecting a bottleneck.) The speculation that all of them disappeared into a bottleneck of two breeding individuals has no evidence to support it, and you are not even willing to speculate how it might have occurred.

Moderators, can you please return the hours that I’ve wasted reading this thread?

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Agreed. Provide a plausible mechanism for this event and there might be something to discuss. So far, I’ve seen nothing remotely plausible. I’m willing to entertain your ideas, @RichardBuggs - but you haven’t shared any.

In the words of Miracle Max, “It would take a miracle.”

Actually, while I do not see that we have come to any amazing conclusions, I think it has been educational both in the subtleties of how the data is interpreted, and how the discussion of ideas takes place in science. Thanks to all involved in contributing, as I have learned quite a bit (though still quite lacking in understanding it all)

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Personal incredulity? Seriously…? It’s a valid request and if we are supposed to take an ancient bottleneck seriously then mechanisms need to be put forward. As IDer’s love to say, “show me the mechanism!”

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It’s not even a matter of personal incredulity at all. As you’ve pointed out, it’s a matter of there being no evidence to support the claim, no proposed mechanism, and a far more efficient explanation for the available evidence. This isn’t a matter of personal incredulity, it’s a matter of preferring an explanation which is supported by the available data, and for which there is a demonstrable mechanism.

It must be remembered that the only motivation for this bottleneck theory is theological; it is not scientifically motivated. No outstanding evidence has been presented which can best be explained by proposing a bottleneck. A bottleneck does not provide a preferable explanation for the available evidence. A bottleneck is a solution looking for a problem.

Indeed.

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Love it. I try to work Princess Bride quotes into my lectures wherever possible. Almost the whole movie is quotable lines.

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Your turn to stump me on a pop culture reference, I guess. Lol. (Inside joke. Don’t ask.)

Oh, quite educational. The conclusion seemed straightforward, simply ruling out a 2-person bottleneck for as far back as the models allow (500 Kya). On how the discussion of ideas took place to arrive at this conclusion, it seemed to occur mostly via browbeating and chest thumping, and when the time came to interpret the data, Swamidass attempted to state it in terms that favored his genealogical thesis, and Buggs attempted to state it in terms that favored his bottleneck thesis. That in itself was educational, I suppose.

Regardless, I also thank those who contributed their time, energy, and thought to the discussion.

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All the above is very helpful. I believe it wa Dr Buggs who wrote: “human genome is 84.4% the same as the chimpanzee genome [note added 23/4/18 to avoid disambiguate: i.e. this is our minimum lower bound]. Regarding the regions that are not one-to-one orthologs, I would explain that about a third of it (a little under 5% of the whole genome) appears to be duplicated.”

My question is does this include exons and introns, or just exons in the comparison ?

They continued that part of the discussion in a new thread: