What Genetics Says About Adam and Eve

Many thanks Steve for this helpful article.

It could be interesting to extend the reasoning to the 8-person bottleneck at the end of Noah’s flood.

On the basis of the data we find in Genesis it is fitting to date the flood at the end of the Neolithic and dawn of civilization.

On the other hand, the estimate range of the whole Homo sapiens population at that time is 10-14 million.

From your essay I infer:

Computational population genetics rules out such a recent 8-person bottleneck, and rather supports that today’s humanity descends from a several million population at the end of the Neolithic.

Is this conclusion correct?

I believe your conclusion is correct, but I have not personally looked into the time range over which population genetics can rule out an 8 person bottleneck. You might want to inquire about it on Josh Swamidass’s site (https://discourse.peacefulscience.org/), since I know he has looked into this specific question.

2 Likes

Everything I have been reading about population bottle necks in the human species reveals a terribly complex situation because of migration where large populations are descended from fairly small populations which migrated to different areas. For example, it is thought that all the Native Americans are descended from a population of 70 which came across the Bering Strait.

I also saw a claim that there was a worldwide population bottleneck around 70,000 years ago possibly due to effects of a massive volcanic eruption in Indonesia.

Are models to estimate a minimum population bottleneck that complex?

I was looking at this study which suggest that some of the work uses some pretty complex models. But with so many variables and unknowns it may take many studies like this before we come up with one that gives a high degree of confidence.

My conclusion is that we are perhaps in early days yet with the means to make such calculations.

I was also looking at this study of population bottlenecks from earlier in human evolution. They talk about many such population bottlenecks. It seems to support my own idea that a great portion of evolution happens in small populations struggling for survival on the brink of extinction.

Hi @glipsnort thanks for posting this blog about genetics and Adam and Eve. It is good to see how constructive the discussion on this issue three years ago on this forum has been in the longer term. I have not done much fresh thinking on this issue since then, but every so often I have noted a paper newly published in the literature that has relevance. Your blog prompts me to have another think about all this. Would you mind pointing me to the exact datasets you used from the 1000 genomes project, please? Was it the exome data, or more recent whole genome re-sequencing?

1 Like

I thought the human population has never been below 10,000. I think it was Darrel Falk who said this.

Hi @RichardBuggs. I used the whole-genome sequence data from Phase III of the project. I think the portal for accessing the data has changed, so I’m not sure exactly how to go about finding it again. The data files I used have catchy names like ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

1 Like

This was the subject of intense debate some time ago. The consensus is that we can’t really say that. I attempted to sketch the limits of what we can say with confidence in the blog post linked above.

2 Likes

And isn’t the estimated minimum population dependent on how far back you go? This seems to be a reason for some people to put Adam&Eve or Noah (as progenators of all) much earlier in history than previously. I do not support such an idea, just to be clear.

2 Likes

Yes, very much so.

1 Like

28 posts were split to a new topic: Original sin if there is no historical Adam

Thanks @glipsnort. Do you know how many individuals and how many SNPs it was?

I don’t know the number of individuals offhand – it was whatever was included in the defined superpopulations. Probably somewhere between 500 and 1000 individuals for each. For the SNPs, I included everything with a minor allele frequency > 1%, which amounted to 14,063,876 for the African population and 8,100,227 for the European pop.

A post was merged into an existing topic: Original sin if there is no historical Adam

Thanks @glipsnort for clarifiying this. If I understand you correctly, the African sample is several hundred individuals from each of the following populations:

YRI Yoruba in Ibadan, Nigera
LWK Luhya in Webuye, Kenya
MAG Mandinka in The Gambia
MSL Mende in Sierra Leone
ESN Esan in Nigera
ASW American’s of African Ancestry in SW USA
ACB African Carribean in Barbados

I think this is the same population set as in the 2015 Nature paper from the 1000 genomes project, with the addition of the MAG population, which I don’t think was in the 2015 paper.

I note that in the supplement for the 1000 genomes paper in 2015, the authors said (p. 5): “The amount of divergence among African populations is much higher; it would require sampling many more populations to capture rare variation adequately.”

Do you have any concerns that such a limited number of populations, (two of which are outside of Africa and perhaps to some extent admixed?) might not accurately portray the true African SFS?

The dataset I used did not include MAG but did include GWD (Gambian Mandinka) as an AFR population.

Note that in that paper we defined ‘rare’ as MAF < 0.5%, which means I discarded all rare variants for my exercise.

I’m not at all concerned about the limited number of populations, since the number sampled here is adequate to capture variants reflecting the shared deep ancestry of the populations – which is what we’re interested in. Rare variants unique to a population are almost always recent additions.

I would exclude the two admixed populations if I were doing a rigorous study, as they will distort the allele frequency spectrum. The distortion should be quite small, however. They might contribute 3 or 4% non-African (mostly European) chromosomal segments to the total set. You can get an idea of the effect of excluding them by increasing the African data points in the plot by 4% of the difference between the African and European data points. For the purposes of the illustration, it doesn’t matter at all.

4 Likes

Thanks Steve. Would it be worth looking at the SFS the H3Africa Consortium just to check that better sampling does not change the shape of the curve, or are you completely confident it would not make a meaningful difference?

Typically when this discussion comes up I always see people trying to argue for a single couple that is all of our ancestors. But I don’t think anyone in the relative scientific fields are saying that. Swamidass says that theoretically it’s possible that all humans can trace their genealogical history alive now back to a man and a woman but that these two would not have been a couple or even alive at the same time.

As soon as you step into even a tiny bottleneck population with two ancestors who are not an actual couple you have changed the genesis story of Adam and Eve completely since it paints them as a couple. So that would be a non literal interpretation and these non literal interpretations span from completely mythological and they are just metaphors for mankind as whole to beliefs thst it’s an ahistorical highly hyperbolic narrative written as a myth.

Theologically speaking, there is some reasons to be able to justify either of those positions. Genetics would obviously play no role in the two if they are just fictional characters snd if they were just a couple out of many being used as the characters in a historical fiction similar to Job then science would probably not be able to detect it.

What would constitute a meaningful difference for you? I’m quite confident that looking at a different dataset would not change the broad conclusion, and if you’re looking to set a firm limit there are better approaches.

2 Likes

I guess I would see a difference in SFS that would lead to a change of 100,000 years or more in the minimum time to a bottleneck of two as “meaningful”. I looked into downloading the H3Africa data, but it seems quite a process to get the right permissions, so I did not pursue it further.

“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6

This is a place for gracious dialogue about science and faith. Please read our FAQ/Guidelines before posting.