Latest Critique of Venema's Claims About Past Human Population Sizes

Faith & Science Conversation
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Ann Gauger posted a new article at Evolution News & Science Today critiquing Venema’s claims about the improbability of a single couple founding the modern human population.

Overall, my criticism of the latest article goes back to an analogy I previously used. Let’s say that a whale washed up on shore. Scientist A estimates the weight of the whale at 10,000 pounds using Method A. Scientist B estimates the weight of the whale at 4,000 pounds using Method B. Many more scientists estimate the weight of the whale using those previous methods and new methods, and their estimates come in at 3,000 to 10,000.

Someone critical of those findings points to the spread in those estimates and asks “Could the weight of the whale be 2 pounds?”. That seems a bit silly, doesn’t it? I think it is valid to point out that these methods aren’t accurate down to the single individual in an effective population size. However, what are the chances that several independent methods are all wrong by three orders of magnitude for population sizes over the last 200,000 years? As others have stated, it is so improbable as to be ignored.

On top of all of this, the effective population size is almost always much lower than the census population size which is the actual number of people in a population. The effective population size is the minimum number of individuals you would need to model a larger population. The effective population size for modern human populations can be orders of magnitude less than the actual population sizes. For example:

“Phase I of the HapMap project produced between 18 and 22 million SNP pairs in samples from four populations: Yoruba from Ibadan (YRI), Nigeria; Japanese from Tokyo (JPT); Han Chinese from Beijing (HCB); and residents from Utah with ancestry from northern and western Europe (CEU). For CEU, JPT, and HCB, the estimate of effective population size, adjusted for SNP ascertainment bias, was ∼3100, whereas the estimate for the YRI was ∼7500, consistent with the out-of-Africa theory of ancestral human population expansion and concurrent bottlenecks.”
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Obviously, there are more than 3,100 Han Chinese from Beijing. [edit: These population sizes may be referencing 200,000 to 10,000 years before present instead of modern populations, so ignore this last reference. I am keeping this section in since it was quoted by others.]

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You mean “census”, not consensus.

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Thanks for catching that. For some reason my brain says census and my fingers type consensus.

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First, I am not an expert on population genetics so my posts should not be taken as gospel and anyone should feel free to point out any errors.

The latest critique addresses parts of Venema’s argument that the previous critique did not. Specifically, Gauger and Buggs address the linkage disequilibrium evidence which uses the rate at which the genome gets shuffled by recombination events to estimate past population sizes. From the EN&ST article which cites Buggs:

“This study depends critically on knowing the recombination rate of the populations. Recombination rate is used both to calculate effective population size (from LD) and to estimate the time point that this is being measured for (from distance between loci). But the main method used to estimate the recombination rate by the authors is patterns of LD. Linkage disequilibrium patterns are also being used to calculate the effective population sizes given a known recombination rate. A degree of circular reasoning seems to be inevitable here. When the authors use a slightly different method to estimate recombination rate (which also relies upon measures of LD), all their estimates of Ne dropped by a mean of 27%. Thus, with the best will in the world, all we have here are ballpark figures for past effective population sizes. I am sure the authors of the study would not view their results as being of equivalent certainty to heliocentrism.”

So there are two things to unpack from that. First, they claim that recombination rates are determined from linkage disequilibrium (LD) data and then they are using that rate to measure population sizes from LD data. IOW, it is a circular argument. While I am not an expert and don’t know if these are truly independent measures, there is another way to find the recombination rate which is to directly measure that rate in sperm and eggs. As it turns out, the two are in strong agreement.

Recombination rate used by the paper Venema references: “For a segment length of 25 Mb and an effective population size of 2000, the chosen input parameters equate to a mutation rate of 10^−8 per nucleotide and a recombination rate of 0.01 per Mb.”
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Recombination rate observed in human gametes: “Following the procedure described by Coop and colleagues [11], we localized crossovers at high-resolution in 68 nuclear families with at least two children and examined variation in fine-scale recombination patterns among individuals. We observed an average of 41.7 (40.2–43.3 95%CI) and 27.7 (26.9–28.4 95%CI) recombination events among maternal and paternal transmissions, respectively, in close agreement with published estimates [4], [9]–[11], [19].”
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That looks like a pretty good match to me. Venema’s reference had 0.01 events per Mb which is 60 recombination events in a 6 billion base human genome. The observed rate in the other paper was 41.7 from mom and 27.7 from dad for a total of 69.4. 60 v. 69.4 is pretty darn good.

Next, Buggs claims that using a different estimate for the recombination rate reduces the effective population size. This isn’t the whole story.

"The second method, which estimates recombination rates between each pair of adjacent HapMap markers from a model-free method that detects recombination hotspots from LD (Clarke and Cardon 2005; Visscher and Hill 2006), changed the estimate of Ne between +33% and −45% with an average reduction of 27% (mean Ne = 1901) when compared with that obtained from the first method (results not shown in Tables). "
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27% is a mean reduction, but the model also shows increases in the effective population size in some instances. Buggs seems to imply that it always results in a reduction in the effective population size, but this isn’t the case.

In my opinion, these criticisms really miss the mark, but I am more than willing to change my mind if someone can demonstrate any errors that I have made.

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Hmmm. I have a feeling that I’m about to have my head on a platter, but …

As I read that paper, the ~3100 applies to the ancestral population. How does it have anything to do with the effective population size for modern Beijing?

Edit: I understand the difference between effective population and census population, if that helps.

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I think you are right about that. After further reading they are talking about population sizes over the last 200,000 to 10,000 years. Nonetheless, effective and census population size are two different things, but I do need to find a better reference for making that clear.

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The main problem is that the IDers want universal descent from two original humans (Adam and Eve), who were de novo, to fit in with fundamentalist theology, whereas even Bugg’s critique of Venema doesn’t get them that far. Bugg’s model has a possible bottleneck of two people, at some point in the human lineage, who descended from a previous population of many people (around 10,000), who were either human or pre-human. So it seems to me that the IDers are misrepresenting Bugg’s work. They’re giving people the impression it’s support for universal human descent from Adam and Eve as de novo humans, when it doesn’t really support that.

On the other hand, I believe that this is great support for a Biologos view.

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Bugg’s makes the assertion that you can start with two humans and then have rapid population growth which can produce the pattern of genetic variation that we see in modern populations. However, he never supports those claims with anything concrete.

The only point that has merit is his claim that Venema may have overstated the confidence that these population studies give us about past human populations. However, being 99% sure as compared to 99.99% sure of those results really doesn’t make for much of an argument against what Venema presented.

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I didn’t see him make the assertion that you can start with two humans who weren’t the product of an earlier, larger population.

Right.

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Conceptually, the effective population size is a single number that you can use to characterize the population – it’s the size an ideal population would have that would give the same value for some summary statistic describing genetic variation in the population. If the statistic you’re interested in is genetic diversity (or equivalently coalescence time), then the ancestral effective population size is the current effective population size for humans, since our diversity looks like that of a small population – we’re substantially less diverse than chimpanzees, for example. If you’re interested in some other measure (something having to do with rare alleles, say), you’ll be dealing with a very different effective population size.

If different applications yield very different effective population sizes, I tend to think the entire concept isn’t very useful for that population.

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I didn’t see that either, but that is kind of a secondary issue. If the evidence doesn’t support a two person founding population then you can’t even get to the question of where they came from.

As to that model, it would appear to me that Buggs tends to cherry pick items from papers. One of the pieces of evidence for a large human population is the amount of heterozygosity AND the amount of variation. Buggs tries to tackle these independently and in doing so cites papers that actually work against his conclusions.

For example:

“[P]opulation geneticists (M. Nei, T. Maruyama and R. Chakraborty 1975 Evolution, 29(1):1-10) showed that even a bottleneck of a single pair would not lead to massive decreases in genetic diversity, if followed by rapid population growth. When two individuals are taken at random from an existing large population, they will on average carry 75% of its heterozygosity (M. Slatkin and L. Excoffier 2012 Genetics 191:171–181). From a bottleneck of a single fertilised female, if population size doubles every generation, after many generations the population will have over half of the heterozygosity of the population before the bottleneck (Barton and Charlesworth 1984, Ann. Rev. Ecol. Syst. 15:133-64). If population growth is faster than this, the proportion of heterozygosity maintained will be higher.”

If we go to that Nei et al. 1975 paper we find this tidbit:

“If population size increases rapidly after going through a bottleneck, the reduction in average heterozygosity is rather small even if bottleneck size is extremely small. On the other hand, the loss of the average number of alleles per locus is profoundly affected by bottleneck size but not so much by the rate of population growth.”

That is a rather large problem for Buggs. He tries to cure this problem by claiming that rapid population growth will produce a lot of alleles, but the only problem is that this only produces very rare alleles that haven’t spread through the population like the ones we see in the current human population. This is from one of the papers that Buggs references in his attempt to support his A&E model.

“Singletons in studies of 20 to 60 individuals have a frequency on the order of 1% and are due to much older mutations than the singletons of 0.005% frequency in a sample of 10,000. In the latter sample, 80% of the variants were observed in fewer than 10 copies (<0.05%), with the vast majority of these being due to mutations that arose in the past 2500 years, according to the estimated model (18). In contrast, the majority of common SNPs with frequency greater than 5% have been segregating for several tens of thousands of years.”
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At least to me, it appears that Buggs is using a lot of smoke and mirrors in his argument.

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That seems to jive with what I have been reading, such as in this paper. Since everyone is born with mutations it only makes sense that you have to include everyone in the population in order to account for ALL genetic variation.

If a study wants to look at the history of population dynamics is it common to use a set value for the allele frequencies in a population, something like 1% or 5%?

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Yes, but if the evidence says that a two person founding population is possible, then it’s important to know whether that two person founding population had ancestors or not. For IDers that’s an important point; they don’t want an Adam and Eve who were the product of evolution, they want an Adam and Eve who had no ancestors at all.

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I think the idea is that if a 2-person bottleneck is argued for, then one can also argue for a specially-created pair who have the exact genetic variability as the 2-person bottleneck pair.

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@DennisVenema, good to see you on the boards now and then!

I’m even willing to consider a 2 person bottleneck with the maximum diversity that could theoretically be imagined for any 46 chromosomes! And we still have too little diversity to produce the diversity we see in the current human population.

To me, that’s a paradigm-buster! [[ And it would be great to see the specific math and allele counts that support this very impressive finding! ]]

That’s why I think the fundamentals of this diversity issue compels YECs to personally “evolve” to the one possible workaround that would fit both the YEC and BioLogos camp:

[1] That it took millions of years for God to create diverse humanity that we see today.

and

[2] That it took a day to “poof” a very special couple into existence, in order for them to
specifically steer the human species into exactly the direction God intended.

If a person has already affirmed that Jesus ascended into the heavens without benefit of a space suit, or that he had a supernatural relationship with a transcendant Universal Being … then, the miraculous creation of two humans is not “too much” … or “going half-way to Crazy Town” as one Evolutionist likes to say.

Naturally, all the mass and weight of the universe rests on the If in the above sentence.

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As soon as you invoke an undefined (and possibly all powerful) designer, then any outcome is possible. It all breaks down into solipsisms, Last Thursdayism, and other such philosophical navel gazing. Could God create a de novo A&E that would be indistinguishable from a human couple produced through evolution from pre-existing human populations? Yep, he sure could. Where do you go from there?

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A scary thought.

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@Jonathan_Burke

I think the Swami is right! I think @Swamidass can help us give the YECs their 2 humans with no ancestors… and nullify their opposition to Evolutionary scenarios by 25%…

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But this is my point; the science doesn’t support that. At least, that’s not what Bugg’s model supports.

That’s precisely why it’s a non-starter. If IDers want to claim a historical Adam and Eve who were created to give the same genetic impression as an Adam and Eve who were the product of evolution, they’ve lost. But I don’t think that’s what they’re arguing for. They’re arguing for a historical Adam and Eve who were the universal ancestors of all humans while having no ancestors themselves, and that’s not what Bugg’s model supports.

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That is what genealogical science supports. =)