What Genetics Says About Adam and Eve

Faith & Science Conversation
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Thanks, @glipsnort. Had to bookmark this one. It was pretty well written for a guy with just two English degrees. :wink:

Question: Population genetics’ tools and methodology to measure a two-person bottleneck all seem to peter out around 500,000 years ago. Do you think this will change in the foreseeable future? In other words, are technological or methodological breakthroughs likely to change that date?

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I doubt the limit is going to change very much. When you go that far back, you start to get down to a handful of lineages that we all descend from, and it becomes impossible to distinguish four ancestral lineages that happen to survive from four created genomes.

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Great article. The figures were very helpful. I understand population genetics a little better now

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Thanks.
. .

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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?

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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.

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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.

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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?

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

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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

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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.

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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.

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Yes, very much so.

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

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

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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.

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

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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?

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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.

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