Sanford and Carter: Allele Frequencies and a YEC Adam and Eve

So I read Sanford et al’s 2018 paper where they attempt to reconcile the allele frequency spectrum (AFS) with a YEC model, and I have a few questions/points to make.

First, can we talk about how they simulated the “evolutionary model” in the paper? They simulated mutation and drift over 10,000 generations in a population of a constant size of 1000 individuals. This would be fine as a simple benchmark for comparison, but they repeatedly commented on how the results of this simulation diverged from the observed AFS, as though it was supposed to call into question the evolutionary model.

I kept waiting for them to comment on the obvious problem with this comparison, but it never came. The obvious fact is that no one is suggesting that the human population has been constant for the last 10,000 generations (never mind at 1000 individuals)! The “evolutionary model” includes a significant recent population growth, which can trivially be shown to shift the AFS to the left (more rare alleles) and produce a sharper bend between the far-left and middle-left of the AFS. Sanford et al. instead suggest that the evolutionary model must invoke a post hoc long-term bottleneck in the distant past. I suppose the more constant population size that existed for the many generations prior to the agricultural revolution and population explosion could be called a “bottleneck”, but that doesn’t really sound like what they’re saying, and it certainly wouldn’t be post hoc on our part.

Second, the “biblical model” simulations include scenarios like starting with 2 individuals, letting the population grow for a few generations, then bottleneck to 6 individuals, and then grow for a couple of hundred generations. The final simulated population size is obviously very far from the current human population size - they don’t include enough population growth. It seems to me that this would significantly change the AFS expected from their model, to produce a much steeper AFS (more rare variants). They discuss this briefly in the paper, in the part about “demographic stirring”, but I don’t think they’ve adequately answered this question.

Third, while the AFS in terms of proportions of alleles with different frequencies in the population might be possible to get in their model of created heterozygosity, what about the actual number of different alleles? The more alleles you deem “originally created”, the smaller the proportion of “mutational alleles” becomes, flattening out the AFS.

To tie this point into Nathaniel Jeanson’s work, consider the proportion of SNPs required to be “originally created” versus the proportion required to have arisen by mutation. Figures 6b and 7 of Sanford et al’s paper suggests that between 30-60% of all SNPs (discounting the rare alleles) in extant human populations would have been the result of mutations in the last few thousand years. On the other hand, in chapter 8 of his book “Replacing Darwin”, Jeanson argues that “originally created” SNPs accounts for 99.6% of the variation in modern human populations, leaving just 0.4% of SNPs as the result of mutations (~15,000/4,000,000 - Figure 8.11 of the book). He does this because only around 15,000 mutations can separate the 2 most divergent living humans today given a 6,000-year timeframe, given current mutation rates.
I don’t see how Jeanson’s claim can be reconciled with Sanford et al’s simulations of the AFS. I agree with Sanford et al’s logic in how the originally created SNPs would have to spread over the AFS from their original distributions at a frequency of 25% or 50% in Adam and Eve to form the low, flat distribution in the AFS, and I don’t see how that’s compatible with the vast majority of SNPs being pre-existing. Or am I mistaken in trying to compare these 2 things, because one is the AFS across a whole population while the other is the proportion of variants separating 2 individuals in a population?

Finally, the Y and mitochondrial chromosome AFS. Sanford et al. note that the actual AFS for these are distinct from the autosomes (figures 1b and 1c), and say that the AFS indicate these chromosomes are “young”. I suppose that’s true, relatively speaking. The Y chromosome and mtDNA have a more recent common ancestor than the entire autosomes do. However, can their “biblical model” account for the alleles in a medium frequency in these chromosomes? For example, in their figure 1b, the bars between 15 and 30 on the x-axis? How about the actual number of SNPs? Jeanson shows in his book (based on his “papers” in ARJ) that the variation in the mtDNA can be (if he assumes a mitochondrial mutation rate that’s about 4x higher than observed, mind you), but what about the Y chromosome? Surely there are more SNPs on the Y chromosome in modern human populations than could be explained in just 6,000 years, given current mutation rates?

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Great work @evograd.

Why is it six individuals, not 5? I’m counting Noah, his wife, and the three wives of his three sons. Who am I a missing?

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I assumed he was referring to Noah’s 3 sons and their 3 wives. The inference being that Noah and his wife had no more children post-flood.

That still means it is just 5, because his sons still derive from just Noah and his wife, right?

Oh right, I see what you mean. Not sure, you’d have to ask Sanford or the other authors, I’d hazard a guess that it was a mistake.

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Thanks, do you have any feedback on the points/questions I raised? I especially interested in how the paper relates to Jeanson’s claims. I still have to try and understand the contents of Heliocentric Certainty Against a Bottleneck of Two? relating to TMR4A and recombination, but for now the AFS seems like a simpler angle to tackle his claims.

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AFS is very weak evidence against a bottleneck. I would not make this argument. There is quite a bit of ways to get around it. Notice also how they hold mosaicism of Adam and Eve in their back pocket. There is a lot of literature on AFS showing it is often very misleading.

Why is Sanford trying to defend a 6000 year old bottleneck? Shouldn’t it be a 4500 year old bottleneck from the survivors on the Ark? Also why don’t ALL extant species show a severe genetic bottleneck only 4500 years ago if all extant species came from the pairs on the Ark?

The whole thing is really silly because we have sequenced DNA from not only humans but dozens of ancient species going back way earlier than 6000 years ago. I believe the record is 700K years for DNA from a Siberian horse fossil. DNA from human remains dating back 45,000 years has been recovered.

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I understand all that, especially after reading Sanford et al’s paper, but I’m thinking specifically in reference to Jeanson’s claims, which aren’t as nuanced or thought-out as Sanford et al’s.

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Sanford does include a bottleneck at the time of the flood.

Of course we have older DNA, but that argument implies they would accept dating methods, which they obviously don’t.

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That’s one trait I’ve never been able to understand about otherwise very intelligent scientific minds like Sanford’s. The ability to ignore 99.9% of the contradictory evidence against the YEC hypothesis while demanding we look at just one isolated data point at a time. The strongest evidence for evolution (IMHO) is that it’s not based on one piece of evidence but on the strong consilience of millions of independent pieces from hundreds of different scientific disciplines. Like a huge jigsaw puzzle we can tell the picture from the large number of interlocking pieces we’ve found without having every piece in place. YECs demand we look at each jigsaw piece separately, in a vacuum away from all the other pieces.

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I’d also appreciate any comments from @glipsnort, your comments in the biologos thread were very informative on this subject.

I largely agree with you @Timothy_Horton, though I do think it is valid to look at the problem in bite size pieces, as long as we acknowledge all that is unsolved from their point of view. Ultimately, they have to resolve all or at least most the puzzle pieces to have a valid position in a limited context. There is no harm, though, in looking at puzzles independently, and granting when they have a partial solution. This does not undermine the case but gives us more credibility when we point to the puzzle pieces they have no solution to offer.

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I looked into this, and I was right. The Y-chromosome SNV mutation rate is estimated to be approximately 0.8x10^-9 mutations/bp/year. This figure is arrived at with good agreement between pedigree studies and studies that use various calibration points in human history, all the way from human-chimp divergence to the peopling of the Americas, to a particular tribe being founded 600 years ago. Even ancient DNA studies give this mutation rate based on their divergence from modern humans and the age of the specimen (estimated using C14 dating). The concordance in the mutation rate between all these different types of studies is very reassuring, and even lends further credence to the validity of C14 dating and the established dates for human migratory events tens of thousands of years ago by extension.

All that aside though, we have a mutation rate. If the YECs are right, this mutation rate should be able to account for all the Y-chromosome SNV diversity in modern human populations, so studies using this mutation rate to estimate the coalescence time to a MRCA should arrive at a figure of approximately 4500 years (Noah). Does it? No, they arrive at a figure of approximately 140,000-190,000 years ago. In other words, there’s about 37 times too much diversity on the Y chromosome for YECs to account for without bringing in post hoc devices.

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Surely, Jeanson must be aware of these papers and their results and so his begging off not addressing Y chromosome variation in the book must be that he is still looking for ways to fit this data into his model rather than using this data to inform him that his model is wrong and he needs to find ways to change his model. BTW, somewhere I saw that Jeanson has a paper about Y chromosoms and the slave trade coming out soon. I presume that will present his Y-chromosome hypothesis.

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Presumably. I look forward to seeing how he tries to square this circle.

Do you have any thoughts on what I said above Joel?

I’m really interested in how Sanford et al’s paper jives with what Jeanson says in his book, so I want to be sure I didn’t make any errors in what I said in that comment.

Sometimes the errors are so large that it is tempting to think that we are missing something because “they simply couldn’t have missed this.” So we find ourselves feeling unsure when, in fact, the obvious criticism really is that obvious. I believe that is what we have here though I have only glanced at Sanford ICC paper. BTW, notice that they do include two references to Jeanson but they only tangentially use them early in the introduction. They don’t interact with Jeanson’s ideas. I think that is partially because it is hard to say that Jeanson has a model to interact with. Despite his insistence that he has a testable model other YECs don’t seem to find it useful to talk about and test.

Exactly, that really hits the nail on the head. Especially since I’m commenting outside my area of expertise, it’s nice to just get some reassurance that I’m not missing something obvious.

@evograd this is the crux of Jeanson’s argument. Everything else is a distraction. He has an incorrect way of computing mutation rates. He uses this incorrect mutation rate, which is far too high, to estimate m-MRCA, and it ends up very recent. He ignores autosomal-MRCA and y-MRCA because he can’t pull out of a hat such an absurd mutation rate.

Without his mito-mutation rate he has nothing new to add.

Now I’m second-guessing myself again (third-guessing?).

In this 2016 article in ARJ, Jeanson draws a distinction between the AFS and the variants present in each individual:

To clarify, within the world-wide human population, over 84 million total SNV sites have been identified (1000 Genomes Project Consortium et al. 2015). Rare variants, by definition, represent most of these 84 million sites. Since common variants would be present at identical sites in a variety of different individuals, common variants would constitute the minority of sites—they show up frequently but add little to the total number of different sites. By contrast, within each individual, only 3.5–4.3 million SNVs exist on average, and the vast majority of SNVs (>80%) within a single individual are common variants (1000 Genomes Project Consortium et al. 2012, 2015). Thus, within each individual, >80% of the nuclear SNVs (80% by the “common variant” criterion; >98% by Fig. 3B) are due to inheritance of alleles that arose via fiat creation during the Creation Week in Adam and Eve, and a small but significant minority of nuclear SNVs within an individual are due to mutations since Creation.

This seems to suggest that I was right (yay?) earlier when I said:

Or am I mistaken in trying to compare these 2 things, because one is the AFS across a whole population while the other is the proportion of variants separating 2 individuals in a population?

Anyone else want to weigh in on this?