Are Population Bottleneck Estimates Decreasing Towards Two?

I was in a talk today and the claim was mentioned by Hugh Ross (similar to here):

Personally, I have observed the ancestral human population derived from genetics models decline over the past fifty years. Fifty years ago, geneticists were claiming an ancestral human population of about one million individuals. Thirty to forty years ago, that number declined to about one hundred thousand. Ten years ago, Biologos’ Francis Collins wrote that it was about ten thousand individuals. When my colleague Fazale Rana debated the Biologos geneticist Dennis Venema, Venema said the number was 1,200 individuals. When i had a public dialogue with the president of Biologos, Deborah Haarsma, she said the Biologos biologists could go as low as 132 individuals. I suggested in that dialogue that we should plot a graph and that the graph would indicate that geneticists will be done to the biblical two in less than two decades.

I’m not sure about the particular exchanges he is referring to from @DennisVenema or from Deborah. I’m also not sure why or how he concludes that this is a trend in particular. From what I can see, population size calculations tend to look something like this:
image

Even if there was a historical ‘trend’ downwards for several decades, I don’t see this trend continuing with a growing consensus/evidence towards well over 10,000 around the time of Reason to Believe’s Adam and Eve (~50 kya). Am I missing something here or where is the RTB argument coming from? @SWilling maybe you know more on this topic. And yes, the Mouflon Sheep were mentioned once again!

I would love to hear what Dr. Venema and Dr. Haarsma have to say, and will follow closely. My understanding after the last long post on the subject, is that there is no evidence of a severe bottleneck below 5,000-10,000 in recent ( last hundred thousand)years, but we simply do not have the data to state that it did not in the more distant past, but neither is there any evidence it did. Perhaps my memory is flawed, and I am sure some here can do better.
Interestingly, I am also reminded that effective population size genetically may also be far less than actual population size. I read recently that all those Holstein dairy cows you see (numbering over a million) have an effective population size of roughly 50 due to lack of genetic diversity.

The genetic evidence could never show a bottleneck of only two for the simple reason that at the time of the lowest population there were at least three separate populations which eventually contributed to human beings today. Besides the “cro-magnons” (modern humans) coming up from southern Africa, there were Neanderthals in the north and the Denisovans in the east.

I don’t believe those from southern Africa were ever down to two, but considering how small the contributions of the Neanderthals and Denisovans were, I suppose it is possible in those cases. But even the Bible doesn’t support this idea of a population of only Adam and Eve. Cain was well aware that the world was full of people so that by itself points to a much later time period for Adam and Eve, when they were not the only people on the Earth.

I find it amazing that people can think they have a literal understanding of the Bible with this anti-science approach, when the fact is to make it work they have to insert things in the Bible which just are not there. Not only adding sisters of Cain, Abel, and Seth never mentioned in order to provide wives, but many many more children than what the Bible talks about in order to fill the earth in a remarkably short period of time. Why do they go so far as rewriting the Bible just to contradict the science? It is as I said before, they don’t want science investigating questions like this. They want to dictate the answers – even if those answers don’t even agree with the Bible.

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The genetic effects of the population bottleneck associated with the Genesis Flood
JOURNAL OF CREATION 30(2) 2016 || PAPERS

Skeptics familiar with the field of genetics claim the Creation/Flood/Babel model is unrealistic in terms of population genetics and demographics. To address these claims, we created a population modelling program designed to examine changes in allele frequency within ‘biblical’ populations. Our model included an artificial genome consisting of 100,000 alleles within 40 independent chromosome arms of variable length. We start with two individuals, set their alleles to a heterozygous state (to model ‘created diversity’), and allow children to be born according to a set of predetermined population parameters. We control the average number of recombination events per chromosome arm per generation and track all alleles in all individuals. At a set year, we can introduce a ‘Flood’ by reducing the population to a single couple with three sons. Wives are assigned to these sons either by choosing randomly from available females in the population or by allowing the parental couple to produce three sisters. Population sizes of 100–500 individuals caused extreme levels of genetic drift and fixation, as expected, but these effects were minimal in populations between 4,000 and 50,000. The Flood had a demonstrable effect on reducing heterozygosity (due to inbreeding), but average fixation rates were low for moderate to large population sizes (an average of 0.76% loss with random wives, 3.07% if the wives are sisters to the parental couple’s sons). After comparing to real-world allele frequency data, we conclude that the effective population size of humanity was at one point very small and that models with small antediluvian population sizes are more likely to reflect human history. The small early population size produced a significant amount of genetic drift in the original alleles and possibly led to a significant loss of created diversity. Thus, skeptical claims that biblical models are excluded by population genetics are unwarranted.

I have no idea what Ross is talking about. He seems to be conflating ancestral population size, effective population size, and the lower bound on the ancestral population size, which are three different things. I’ve only been in genetics for 20 years, but that 20 years is longer than we’ve had good genetic data for estimating any of those quantities. In that time, the estimate of the effective population size (which is what is most often calculated) has gone from 10,000 to about 15,000 – I guess you could call that a negative decrease. The earliest estimate of human ancestral effective population size based on any molecular data (in other words, based on any data) dates from a paper in 1972 by Haigh and Maynard Smith. They arrive at an estimate of less than 10,000 (although they assume the population was larger before that).

In my experience, Ross is rarely an accurate source of information about biology.

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Oh yeah – that was the paper where they compared their simulation with ‘real-world allele frequency data’, but failed to realize that the data they were comparing do not in any way reflect actual population allele frequencies. Their simulations look nothing like actual human allele frequency distributions.

ETA: I described the problems with the comparison in more detail here

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Since I was asked, I’ll offer a few overnight reflections:

  1. The article was two years old. Hugh has generally shown a willingness to alter his position in the light of new evidence.
  2. Hugh is first and foremost an astrophysicist. His command of other subjects is impressive, but not at the same level. Fuz Rana is really their go-to guy for biochemistry and genetics.
  3. “Predictions are hard, especially about the future”. Anyone’s predictions should be taken with a block of salt, no matter what position they’re coming from.
  4. While normal people acknowledge that there really is such a thing as settled science (e.g. circulation of blood, germ theory of disease), there’s also a lot that’s not. Too often we know this only in hindsight. Sometimes “settled science” gets unsettled. (see my new post on the opiate epidemic). I find paleogenetics interesting, but on the grand time scale it’s really in its infancy. I don’t know where it will lead.
  5. No one should be totally certain in their opinions. If you’re familiar with Dawkins 7 point scale, he says he’s a 6.9 out of 7.0 atheist. Well, I’m a theist 6.9 out of 7. Same for age of the earth. Yes, God could have made the earth look young. I just consider that wildly improbably and inconsistent with His revealed nature. Nor can I rule out that we’re living in a simulation, there are multiple quantum universes, or that I’m a disembodied Boltzman brain. The difference between impossible and wildly improbable is, in my opinion, moot and never worth arguing.
  6. A friend of mine, who is a molecular geneticist, believes that Adam and Eve were selected out of a human population, given the image of God, and passed it on to all of their descendents. Any remaining non-endowed humans could have died out or been extinguished by an extermination event such as a widespread flood. I think the term is “geneological” Adam & Eve. The position has some merit and would explain some other odd Genesis references. I simply don’t know.
  7. On a personal level of importance, the precise nature of how God created us is about a 3 on a scale of 1-10. I am passionate about the damaging effects of pride upon the life, health, and ministry of the church, and one field where I see the greatest damage is the AiG mentality. In terms of arrogance and confirmation bias and various related vices, they are no different than the most ardent atheists. So, I’m really more concerned with how people approach the subject than where they end up.

I would love to glimpse the future and see where paleogenetics is in 50 years. But I’m 63 and that isn’t going to happen.

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Thanks for your response! I should have been clear- he said the exact same thing just yesterday.

Also do you have an example of him correcting/tweaking his position with evidence?

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Good observations, Steve. Thanks for sharing, we can learn a lot from your approach. My lingering question is what number the data supports, and if the numbers quoted by Ross are accurate and in what context.

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Well, one just popped up this weekend on the RTB apologist group. It’s not specifically Hugh, but Fuz and Jeff both chimed in. They have argued in the past that the time interval between the late heavy bombardment and the earliest appearance of life was too short. Since astronomers/geologists are now thinking the LHB was much earlier than 3.8bya, they are acknowledging this and moving on.

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That’s good. This is a big deal since it’s been in presentations and books for decades. Specifically, the harshness of the LHB and window that was really small for life to arise (10 mya) was part of the RTB OoL model from 2001. They both also acknowledged that the LHB was not so sterile nearly 10 years later after all and that this left a few scars on their model. Yet I still see and hear material being produced (either at churches or universities) where the same old model that is crushing the ‘naturalistic model’ and the RTB model just gets stronger all the time. There seems to be a big gap between the two and I think Rana or Zweerink ought to write a well thought out article on this.

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