Gauger: A Single-Couple Human Origin is Possible

[John_Harshman]

@swamidass

Those questions have to be articulated and engaged in a sensible way for them to make their case. As far as I can tell, they do not do this here, or elsewhere.

How would one even start?

[glipsnort (Steve Schaffner)]

@swamidass

@glipsnort, this explains why they did not use the derived frequency spectrum. It looks like they are really going for a de novo creation model here.

I assumed they were going for de novo creation. That’s no reason to use the folded spectrum – you don’t have to accept common descent to do so. Just call one allele the ‘non-chimp allele’ if you don’t want to call it ‘derived’. Whatever you call it, it’s an empirical fact that the frequency distribution of the non-chimp allele continues to decline past 50% and therefore imposes a constraint on how much initial diversity there can have been in this model. (Or maybe it imposes a constraint – hard to know without looking.)

@swamidass

Unlike the GAE, however, in this case, they do fall prey to the “appearance of common decent” problem. Why did God create AE such that it appears we share common ancestry with the great apes?

Along those lines. . . In their model(s), primordial diversity (diversity appearing in the first couple) contributes negligibly to low frequency alleles but represent more than half of alleles with frequencies around 50%. One might guess, therefore, that the genetic variants in the two frequency ranges would have different characteristics. Of course, they don’t. Here’s the breakdown of the different classes of single-base substitutions for high frequency (40-50%) and low frequency (<1%) alleles.

The all look like mutations.

[glipsnort (Steve Schaffner)]

Sorry, I got the labels wrong on those plots. The classes in order are

1. transition, non-CpG
2. transition, CpG
3. G-C, non-CpG
4. G-C, CpG
5. AC/GT, non-CpG
6. AC/GT, CpG
7. A-T

[swamidass (S. Joshua Swamidass)]

@glipsnort, that is a very good and interesting test of the genetic-bottleneck-de-novo-creation model they are proposing. That is worth writing up more carefully so people can understand it better. Looking forward to seeing the numbers in a table and the revised graphs.

[Patrick]

Does this paper shows that the Mathematical Conjecture is false and that there wasn’t a single pair of humans for over a million years?

674986.full.pdf

[swamidass (S. Joshua Swamidass)]

Very nice study. It also provides no support for the so called Venema conjecture. He equivocated average with minimum. Effective population size, it turns out, is not a minimum.

[Patrick]

But doesn’t the study lead one to accept that the mathematical conjecture of a human bottleneck of precisely two is highly unlikely to such an extend that it can be ruled out as not historically accurate?

[swamidass (S. Joshua Swamidass)]

No, it does not tell us it is unlikely unless the prior says it is unlikely. The evidence does tell us one way or another.

[glipsnort (Steve Schaffner)]

Updated plots:

The motivation for these plots is that different kinds of mutation happen at different rates, which means that we should see more of some kinds of genetic variant than other kinds, if the genetic variants are the result of previous mutations. What’s shown in the plots are different classes of single-base differences and how frequently they occur in a human population. The details of the different classes are explained in a blog post by me, here.
I have made the plots for two different frequency bins; that is, one plot show variants that are rare in the human population (0.5% to 1.0%) and the other variants that are common (40% to 50%). (I pulled the variants for the different frequencies when @evograd was preparing this post.) According to the model that is the subject of this thread, rare variants are all the result of recent mutations, and should show the characteristic pattern expected of mutations – which they do. In the same model, however, most high frequency variants were created along with the original couple – but they also show exactly the same pattern, which is what we would expect if the human lineage is older than 500,000 years and high frequency variants are also the result of mutations.

[r_speir]

@glipsnort

human lineage is older than 500,000 years and high frequency variants are also the result of mutations.

This is the part that I would like to hear more about. Can you elaborate some on this statement and this kind of reasoning?

[glipsnort (Steve Schaffner)]

@r_speir

This is the part that I would like to hear more about. Can you elaborate some on this statement and this kind of reasoning?

Can I? Sure. I’ll be happy to do so as soon as you explain why genetic differences between humans and baboons show the same pattern as genetic differences between humans and chimps, despite there being five times as many of them. (I wouldn’t be a very good steward of my time if I spent it on explaining things to someone who didn’t want to engage with the issues, would I?)

[swamidass (S. Joshua Swamidass)]

I think I missed these point from @Agauger:

So why make “parsimonious” a threatening word? Maybe I should have said “simple” instead? I think they all missed the point of the title. Our whole point was not that the single-couple model was true or to be preferred, but merely possible. Just possible. 500,000 years ago, or 2 million years ago, with ad-mixture, without, still possible. Unique or from a bottleneck, take your pick, the model doesn’t distinguish. All we set out to show was that it was possible to account for current diversity starting from two. Which, by the way, Josh Swamidass has kindly reminded me, he has already done. Now we have done it a second way.

First off, thanks to @Agauger for acknowledging the TMR4A work. Also she substitutes “simple” for “parsimony” which I have to think about.

[John_Harshman]

Neither word seems like what she’s trying to say. Why not just “possible” if that’s what she means?

[swamidass (S. Joshua Swamidass)]

That makes sense to me. Or “not ruled out” by the genetic data?

[John_Harshman]

Just happened to revisit this old thread and the Biocomplexity article that started it. And one thing quickly struck me:

For instance, some recent qualitative discussions suggest that genetic data might be compatible with an extreme bottleneck from a previously evolving large population to a single-couple around 500kya ago [16}, whereas other authors suggest a primordial couple that lived much more recently [17-19].

Here are the references:

17. Sanford JC, Carter RW (2014) In light of genetics … Adam, Eve and the Creation/Fall. Crist Apol J 12(2):51-98.

18. Jeanson NT (2016) On the origin of eukaryotic species’ genotypic and phenotypic diversity: Genetic clocks, population growth curves, and comparative nuclear genome analyses suggest created heterozygotisy in combination with natural processes as a major source mechanism. Answ Res J 9:81-122.

19. Sanford JC, Carter RW, Baumgardner J, Potter B (2018) Adam and Eve, designed diversity, and allele frequencies. In 8th Intl Conf Creationism, 200-216.

[Roy (34-year veteran)]

Was it that ID is creationism with biblical references removed?

[misterme987 (Andrew P.)]

They didn’t even try to hide it here. They just cited unapologetically creationist sources to support their claim that a primordial couple may have lived less than 500 kya.

(As an aside, wouldn’t “500 kya ago” mean “500 thousand years ago ago” which is pretty redundant? Wonder how that got past the editors.)

[John_Harshman]

I will also point out that they recognize a difference between a primordial couple and a bottleneck of two. The only logical justification for such a difference would be that said primordial couple was without ancestors, i.e. a de novo creation. A primordial couple with ancestors would in fact just be a bottleneck.