Do “Humans” arise from a single couple?
It is a deceptively simple question, with a great deal of subtlety. Some claim “no,” with certainty approach that of our certainty that the sun is the center of the solar system: “heliocentric certainty.”
This, however, is a subtle question. Most important to be careful about is the equivocation between genetics and genealogy, which does arise here (see TMRCA vs. TMR4A). More significantly, we find that all “humans” do descend each individually from many single couples (see the Genealogical Adam). That, however, is a conversation for another day.
Instead, here, I wanted to focus on understanding why scientists are convinced our ancestors arise as a population that never dips down to a single couple. What is the evidence behind that finding? What are its limits? How strong is that case? Most of my work takes this for granted, but it is worth pressing further into the population genetics.
On this question, there has been some very interesting discussion lately about population genetics. It deserves a deeper dive, which I want to give here. It is generally thought that the evidence against a bottleneck of one couple in our ancestors is overwhelming. In the recent past (less than 100 thousand years), this certainly seems to be the case. This question about ancient bottlenecks though.
Going forward, we should keep in mind:
No estimates of population size in the distance past (which are a geometric average over time windows) ever goes below a few thousand. The real question here is if the population size estimates are good enough in the distant past to detect a brief bottleneck.
There appears to be overwhelming evidence against a recent bottleneck less than (for example) 100 kya.
The case against a more ancient bottleneck is what is at question here, but even if its possible, there does not appear to be any positive evidence for an ancient bottleneck. We are discussion, instead, whether there is strong evidence against it.
As yet, no mathematical theory of a bottleneck has been put forward yet that explains the full range of data. The only theories offered right now validated on the data do not include a bottleneck. That could change, but that is where things stand.
The consensus of population genetics is solidly against any notion of a bottleneck of a single couple. Perhaps they are wrong, but the consensus is solidly against a bottleneck.
Therefore, it is correct to say the consensus is against a bottleneck of two in both our recent and distant past. This seems to be bad news for those affirm a historical Adam, ancestor of us all. Of course, this is not really important if we think Adam’s line could have interbred with others, because we do not expect there to be a bottleneck in the genetic data with a genealogical Adam, ancestor of us all.
It is still worth asking how certain we should understand this scientific claim. Is it to heliocentric certainty? Or less sure?
Richard Buggs (a UK geneticist) has been pressing on this (
https://natureecoevocommunity.nature.com/channels/522-journal-club/posts/22075-adam-and-eve-a-tested-hypothesis ). The conversation quickly became interesting. First, I pointed out that if we allow for interbreeding and keep in mind the difference between theological “human” and Homo sapiens, then we do see genealogical universal ancestors very early (see the Genealogical Adam). Second, and to the point right now, Richard Buggs raised some interesting questions about the evidence. His point is simple. We cannot know for sure, because we never tested the bottleneck hypothesis, and the evidence is not a definitive as we move past a few hundred thousand years ago.
The conversation has become technical, but I wanted to highlight on some of my thoughts here. What does the evidence tell us about a “human” bottleneck of one couple? Of course, all the same caveats regarding the definition of “human” apply. “Human” is an ambiguous term in the distant past.
Stated more precisely, what does the evidence tell us about a bottleneck in our ancestors since it seems we diverged from a common ancestor with the great apes about 6 mya?
Clarifying This Conversation’s Question
In this conversation we are not allowing for any miracles. For example, the bottleneck couple would not be specially created or be genetic mosaics (with different genomes in every sperm/egg). Instead, they would be biologically normal individuals, but the only ones alive at their time that produce surviving offspring till today.
Also, we are not looking for evidence for a bottleneck, but rather testing the strength of the evidence against a single-couple bottleneck. The bar here is really low. We are just asking the degree to which we really know from the evidence that there was no bottleneck in our lineage.
Finally, we are only considering bottlenecks from 100 kya to 3 mya (kya=thousands of years ago, mya=millions of years ago). We are not considering very recent bottlenecks (say 50 kya or 10 kya). Those recent bottlenecks seem to be inconsistent with the data. Instead, we are wondering about the strengths and limits of the scientific claim that “humans” arise as a population that never dips down to a single couple. The place that claim is the weakest is in the distant past, for example 500 kya ago.
So, no miracles. No positive proof. Not recent. This is, instead, a question about the limits of the scientific claim. Other questions, of course, are interesting. We, however, have a more sharply delimited concern on this thread.
To Summarize this exchange, Richard Bugg’s suggests this text, which is currently under revision…
As Christian biologists, we have over the last few months reviewed the population genetic literature, asking if it is possible that all modern humans could descend from a single couple within a theistic evolution (or evolutionary creation) framework. We have assumed that humans share common ancestry with apes, and that God has not intervened with physical miracles. Our task has been difficult because the hypothesis of a bottleneck of two in the human lineage has not been directly addressed in the scientific literature using genome-wide human diversity data. Nonetheless, from those published studies of human diversity that we have reviewed, and based on our understanding of current theory, we have drawn tentative conclusions. We conclude that current human genetic diversity data does not rule out a bottleneck of two individuals in the human lineage between approximately 400,000 and 7,000,000 years ago, but neither do they show that such a bottleneck has happened. Current analyses and models suggest that a two-person bottleneck has not occurred below a threshold of approximately 400,000 years before present. More research is needed in this area, and we are open to new analyses moving this threshold up or down.
I would point out, however, that the results here do not depend on evolution, or the assumption of common descent. The conclusions here apply just as strongly to OEC and YEC models.
Guide to Contents
Claims of Heliocentric Certainty. What are the scientific claims in question?
The Ecological Fallacy.: Homo sapiens go to zero, so why couldn’t they go to two?
TMRCA or Time to Most Recent 4 Alleles? TMR4A (not TMRCA) puts the bounds on a couple bottleneck.
Estimate with Median or Max? The statistically sound approach is the median.
TMR4A from Genome-Wide TMRCA. An initial estimate of TMR4A.
The ArgWeaver Genome Wide Phylogenies 424 GB of data with genome-wide answers.
Genome-Wide TMR4A. A better estimate of TMR4A.
ArgWeaver Does Not Assume Large Population. The computed TMR4A is biased downwards, not upwards, by the prior.
The Correct Mutation Rate. ArgWeager is using an experimentally confirmed mutation rate.
Correctly Weighting Coalescents. An improve esitmate of TMRCA is about 500 kya.
ArgWeaver works like MAP and MrBayes. Really, no assumptions of population size are made, and this is just a measure of human variation, converted to units of time.
An Estimate Robust to Correction. The TMR4A estimate is exceedingly stable. AJ Roberts from Reasons to Believe would want a correction for the amount of genome that is not yet sequenced.
What about Recombination? The errors we see in ArgWeaver do not effect TMR4A estimates.
Trans-species variation. The evidence against an ancient bottleneck in trans-species variation is not as strong as I had thought.
Convergent Evolution or Trans-Species Variation? A deeper look indicates convergent evolution, which violates the assumptions required for genetic clocks and undermines substantially the argument against a bottleneck using this line of evidence.
This topic will not open to general comment, as it is technically detailed, and I do not want it to get confusing. However, please comment on the companion thread: https://discourse.peacefulscience.org/t/comments-on-heliocentric-certainty-against-a-bottleneck-of-two/62?u=swamidass