Dr Bugg's latest analysis is seriously flawed

Dr Bugg’s latest analysis where he pushes back the possibility that a single couple could explain the diversity of the genomes of present day people to no later than 700KYA to 7 MYA is seriously flawed. Dr. Bugg’s analysis does not include the DNA data from whole genomes of ancient humans. The whole genomes of over 3700 individuals from all over the world who died from 1000 years ago to over 430,000 years ago have been sequenced and analyzed. (See David Riech’s 2018 book "Who we are and How did we get here. The genomes sequenced include Neanderthals and Denosivans who’s admixtures we see in today’s Eurasian in the 1-2% range for Neanderthals and the 5% range for Denosivans in Oceanic people. If Dr. Bugg would include the DNA from ancient humans he would find that a two person bottleneck in human history never occurred.

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Do you have a link to that analysis Patrick?

I guess I meant the actual Buggs study which you say is flawed. If we could see the study we could scrutinize the methodology for ourselves. As it is we just know that you don’t like it but have no way to verify why.

http://richardbuggs.com/index.php/2018/04/18/adam-and-eve-lessons-learned/

In the above, Dr. Bugg’s writes:

(7) Introgression from Neanderthals and Denisovans makes everything more complicated
Evidence for introgression from Neanderthal and Denisovan populations into modern human genomes provides a major complication for the “Adam and Eve” hypotheses. If Neanderthals and Denisovans are defined as being within the “human” lineage, then a two-person bottleneck could only have occurred before the divergence of modern humans, Neanderthals and Denisovans. If, on the other hand, we define only modern humans as truly “human”, and posit a bottleneck within the human lineage, with later admixture of DNA variation from “non-humans”, then a more recent bottleneck is possible, and the AFS and TMR4L approaches will be made very difficult to apply, unless admixed alleles can be filtered out.

Conclusions
To my mind, the question has now moved on from “Is an ‘Adam and Eve’ bottleneck inconsistent with human genetic diversity data?” to “At what timescale could an ‘Adam and Eve’ bottleneck be consistent with human genetic diversity data?” It would be good to see the AFS and TMR4L approaches followed up with published analyses, and I would be very glad to know of other approaches that could be used to test or date the hypothesis.

See the Reich book for real data showing that an “Adam and Eve” bottleneck never occurred. Dr. Buggs question "At what timescale could an “Adam and Eve” bottleneck be consistent with human genetic diversity data has been answered. Answer: never.

Thank you. Might I suggest going forward that it would be even easier for folks to follow if you put the links to the studies you are discussing in the original post rather than down in the comments?

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@Patrick, @Revealed_Cosmology and @swamidass:

Do any of you know of any data which is inconsistent with the following hypothesis?

There was a two-person bottleneck in the line leading to Homo sapiens, about 430,000 years ago. (I understand that’s consistent with the TMR4L data.) Later on, there were several episodes of introgression from Neanderthal and Denisovan populations, neither of which experienced a bottleneck.

Thoughts?

If we say there was a bottleneck with later admixture, we do not need to take into account Neanderthals and Denisovans. Moreover, it is likely all these groups share a common ancestral population sometime between 1 mya and 700 kya.

The bigger error in his analysis is regarding chimp and human similarity. But that is not referenced here.

That is not an easy hypothesis to test. I’m sure no one has done it yet, and I’m uncertain if it is possible to test.

I don’t know of any scientific data which is inconsistent with it, but I do know of scriptural data which is inconsistent with it. Gen. 2:1 says that God created a “host” on the earth. And there are many other hints in scripture as well that other humans preceded Adam and Eve.

And of course just because the scientific data is “not inconsistent” with it does not mean that it happened that way.

I would also suggest, if you really want to look at this from outside the box, that even if there was a single couple of somethings (not homo sapiens sapiens at that date) who were a two-person bottleneck, then the formation of Adam and Eve 6-14K ago with their contribution to our line would be another introgression, a human one, into our species. Depending on what Reich’s “Basal Eurasian” turns out to be then there could be scientific evidence against a “two-person bottleneck 430,000 years ago” because “Basal Eurasian” is the genetic signatures of Adam and Eve, two new persons combining with the rest of humanity.

Hi @Revealed_Cosmology.

As far as I can tell, Reich’s “Basal Eurasian” originated much more recently than 430,000 years ago - perhaps ten times more recently, judging from Reich’s paper on the subject.

The NIV translation of Genesis 2:1 reads: “Thus the heavens and the earth were completed in all their vast array.” Nothing here about other humans preceding Adam and Eve. Indeed, Genesis 3:20 tells us that “Adam named his wife Eve, because she would become the mother of all the living.” On a straightforward reading, that sounds as if Eve is the sole human female progenitor of the human race.

I didn’t want to comment on events happening 6,000-14,000 years ago, because I haven’t read widely enough on that particular subject. Cheers.

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@Revealed_Cosmology (and @Patrick):

Dr. Buggs (yes, 2 g’s and and an “s”) has been very interested in what I call the “Genetic Wall of Noise”. He did demonstrate to a BioLogos audience that as one regresses genetic change back in time, the “noise” of competing genetic factors starts to obscure the clear signal of a 2-person bottleneck. This was an important realization, and I wouldn’t want to minimize it.

But then the task became developing a realistic estimate of how far back you have to go before the 2-person bottleneck “signal” is sufficiently drowned out that it is undetectable. According to the latest news, this is 700,000 years ago! That’s impressively distant!

It takes us well into the non-human primate history. So, it essentially makes it irrelevant to any discussion of humanity!

As for the conceivable “intrusions” mentioned by @Patrick (Denosivans, Neanderthals, etc), what this represents is an injection of genetic novelty, in presumably small chunks, that complicate the math, but do not do anything to pull the “wall of noise” closer than 700,000 years ago. Why? Because the mathematical regressions presented by Dennis Venema and others is not attempting to compensate for any such possibilities. This means that if there were chunks of novelty to back out, the wall of noise would be even further back!

It is by ignoring the possibility that we calculate a “Wall of Noise” that is closer to the present day, not further way.

@vjtorley, I think your 430,000 time frame is not the current “best number”. In fact, I would have to wonder exactly how you calculated the number, or from where you obtained it.

There is no evidence of a 2-person bottleneck anywhere in the data. The only bottleneck indicated in the data is a 10,000 person bottleneck - - and at the moment, I do not recall the approximate time frame for that one.

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Yes, all the data from ancient genomes is inconsistent with your hypothesis.

Realize that TMR4L is just one gene with different alleles (variations). The whole genome of the thousands of people that have been sequenced have millions of SNPs and other variations within populations. So studying AFS or TMR4L is kind of moot considering the data from millions of SNPs.

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It’s never been found in a sample more than 14K old so far as I can tell. It just shows up and then spreads all around the world with farming and animal domestication.

Yes, these translations are awful. One could never hope to find the truth just by reading them. I invite you to click on the word translated “array” in this interlinear of the verse. See what the Hebrew word is and how it is defined and used in scripture. And remember the host was not just in heaven but on earth.

That is not a Christ centered straightforward reading of the verse. A Christ centered straight-forward reading would connect this statement to the immediate prior verses where they learn that Eve would bear a Seed which would crush the serpent’s head. All the living will be in Christ. Otherwise, it is a weird thing to say to her after she had basically gotten them both killed.

@vjtorley

In fact, it sounds like Eve is the female progenitor of all the animals! This is obviously not a good translation. The phrase “All the Living”, if not entirely poetic (and I’m inclined to think it is) would better mean “all the [human] living.” Using conservative “genealogical assumptions”, she will qualify in less than 2000 years of God-guided dispersion of her offspring into a general (pre-existing) human population.

The science says the population could be as small as 10,000 (depending on which time frame you want to insert Eve into)… or it could be millions.

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That is not correct. The median TMR4A is a genome wide measure, across all genes. However it is limited to just the complete genomics data, and would likely increase if more genomes were included.

It does not, however, remove alleles from introgression, which might reduce the estimate too.

I’ve been saying all along that the biblical model doesn’t require a genetic bottleneck of just one couple under the genealogical Adam understanding. Adam and Eve were comparatively recent; their traits became spread throughout the genome rapidly through interbreeding, outcompetition, or success in warfare. That’s all a biblical model requires. The flood put the brakes on the rapidity with which this “takeover” proceeded.

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Well, if you believe the flood is global, it actually STOPPED the process, and wiped the board clean.
Now, everyone descends from Noah… no muss … no fuss. Problem solved.

It gets a little messier if the Global Flood is really just a regional flood.

Does it need to be said the genomic record of humans, plants, and animals does not show any global bottleneck to eight human beings, and two of each land animal kind 4350 years ago. And it doesn’t show anything of Ken Ham’s hyper-common decent of kinds from that time to the present diversity of genomes not to mention languages and cultures. The problem with Bible stories is that if you force on one piece to be factual history, there are hundreds of examples where it falls apart.

I totally agree. That is an entirely correct assessment that Richard Buggs and @Agauger would agree with. It is critical that people come to terms with this.

I also totally agree with this. @Joel_Duff has done a lot of work on this here:

It is all about reading it correctly. You are atheist who thinks it is hogwash. I respect that, however, you do not really know how we read Scripture in a more sensible way.

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