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The following article was originally published here on March 5, 2018.
Dennis Venema is associate professor at Trinity Western University. His book Adam and the Genome is under active discussion here and over at BioLogos. The central question implied in the title of that book is: does our genome rule out Adam? Could humanity have had its origin in a first pair, or did it have to come from a population of at least several thousand?
This question has been addressed by numerous scientists in the past, ever since human genetic data began to roll in. And all of them, as far as I know, have said that yes, our genome rules out Adam. We are the product of common descent. We are descended from an ape-like population of at least several thousand. This we have heard before.
Now here’s where it gets interesting. There has been a debate going on over at BioLogos for a number of months that was triggered by Venema’s book. The debate is about whether there could have been a bottleneck of two at some time in the human past. This discussion was started when Richard Buggs, Senior Research Leader (Plant Health) at Royal Botanic Gardens Kew, and Reader in Evolutionary Genomics at Queen Mary, University of London, challenged Dennis Venema about what Venema wrote in Adam and the Genome. Venema had argued:
As our methodology becomes more sophisticated and more data are examined, we will likely further refine our estimates [of human population size] in the future. That said, we can be confident that finding evidence that we were created independently of other animals or that we descend from only two people just isn’t going to happen. Some ideas in science are so well supported that it is highly unlikely new evidence will substantially modify them, and these are among them. The sun is at the center of our solar system, humans evolved, and we evolved as a population.
Put most simply, DNA evidence indicates that humans descend from a large population because we, as a species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us. To date, every genetic analysis estimating ancestral population sizes has agreed that we descend from a population of thousands, not a single ancestral couple. Even though many of these methods are independent of each other, all methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last three million years or more — long before our lineage was even remotely close to what we would call “human.” Thus the hypothesis that humans descend solely from one ancestral couple has not yet found any experimental support — and it is therefore not one that geneticists view as viable. [Emphasis added.]
Then two new scientists entered the debate with Venema and Buggs. Remarkably, neither is an ID advocate, both affirm evolutionary theory, and both came to similar conclusions by different routes. A population geneticist named Dr. Steve Schaffner of the Broad Institute in Cambridge, Massachusetts, ran a simulation to determine whether a bottleneck of two individuals was possible. He found that, at dates older than 500,000 years ago, a bottleneck could not be ruled out. His analysis of allele frequencies could not distinguish between allele frequencies obtained after a bottleneck of two and those from current genetic data. Dr. Joshua Swamidass, assistant professor in the Department of Pathology and Immunology at Washington University in St. Louis, estimated the time to the most recent four alleles in the genome. An allele is a version of a gene. We all carry two copies of each gene (setting sex chromosomes aside), so a bottleneck of two individuals would have a maximum of four alleles per gene. His analysis likewise showed that the most recent time at which a bottleneck of two individuals, or four alleles, could have occurred was about 500,000 years ago. Both researchers used experimentally validated mutation rates in their models, and the precise details are worth looking at closely.
This is a big deal. The original claim that we had to come from a population of thousands is wrong, because there are dates past which we cannot tell if there was a bottleneck of two. The work of Schaffner and Swamidass has opened up the possibility of a first pair. It cannot be ruled out between about 500,000 years ago and 7 million years ago, when we supposedly split from chimps. If you want to read the discussion for yourself you can go here (you’ll have to go forward and backward, it’s a long discussion) or see Dr. Swamidass’s summary here .
This does not prove the existence of a first couple, but it shows how it could be possible. The claim that our population was never smaller than thousands is wrong. Nobody can claim a bottleneck of two could never have happened. These calculations come from the Schaffner and Swamidass, who have both argued against us many times in the past on questions of common descent and design. So this is a sea change for BioLogos, and if verified and published will cause turmoil.
The 500 thousand year date also does not rule out other dates based on other approaches and different assumptions. We have proposed an alternate model, to test the effect of a variety of variables, such as the effect of a structured population, migration, and primordial genetic diversity, on population statistics.
Another Challenge to a Bottleneck of Two
There is, however, another argument against a possible bottleneck. It has to do with genes that have many alleles (different versions of the gene), apparently too many to pass through a bottleneck of two. Many of the genes are involved in the immune system, and have as many as a thousand alleles per gene known at present. The reason for the incredible diversity is to be able to defend against the widest variety of diseases and parasites. The more diversity there is in the population, the greater the likelihood that the species will survive a new challenge.
Many of these human HLA (human leukocyte antigen) alleles are similar to alleles for the same gene in chimps and macaques (spider monkeys). When discovered, this was taken to mean that these similar alleles were inherited by common descent from the original population from which all three species came. The alleles were all present in that original population, it was theorized, and as each species diverged, each inherited a subset of alleles from the ancestral population. The subsets overlapped, meaning that alleles would be shared between species. It was postulated that the subset of alleles inherited by each species would have been too numerous to have come through a population bottleneck of two.
This hypothesis is called trans-species polymorphism (TSP), and especially in the 1990s, it was the central argument against the possibility of small bottlenecks. Francisco Ayala and Jan Klein were among the foremost proponents, and the HLA genes of the immune system were used as prime examples of TSP.
However, there are other possibilities that might explain the similarity between alleles across species: original diversity, meaning allelic differences present from the beginning as in our proposed model, or convergent evolution. When two sequences resemble one another but are not related by common descent, they are said to have evolved by convergent evolution. In this hypothesis, alleles resemble each other because they evolved the same sequence independently. Either explanation postulates that the alleles are not related by common descent.
Noting some methodological errors in Ayala’s papers, Swamidass decided to investigate. He said on the Peaceful Science discussion forum:
At the moment, the Ayala paper appears to be the only study which shows more than 4 allele lineages with trans-species variation. His analysis, however, did not estimate confidence nor did it use phylogenetics to determine lineages (it used sequence similarity instead). In 22 years, I cannot find a paper that replicates his finding with better methods (or any methods). Certainly, trans-species variation has been observed, but not more than 4 lineages, as far as I can tell. This is not enough evidence by which to make a confident claim against a single generation bottleneck. [Emphasis in the original.]
Dr. Swamidass wanted to determine if TSP was evidence of ancient lineages that had passed through multiple speciation events, or if it was the result of convergent evolution. He found a paper published in 2016 by Asli Vahdat and Andreas Wagner that looked for evidence of convergent evolution in the human genome. From their Abstract:
We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The structure of these networks varies widely among genes, indicating different patterns of variation despite a shared evolutionary history. We focus on those genes whose genotype networks show many cycles, which can indicate homoplasy, i.e., parallel or convergent evolution, on the sequence level. [Emphasis added.]
Let’s define what a cycle is. A cycle is formed when a haplotype network shows (multiple) parallel paths from one haplotype to another. In other words, instead of showing a straight-line pattern between haplotypes, representing common descent, a cycle appears as a square, hexagon or octagon of relationships, with nodes representing haplotypes and edges representing the mutations that connect nodes. From the authors:
Assume, for example, that genotype 1 [TG] is ancestral to the other genotypes, and different substitutions (A10T and A20G) produce genotypes 2 [TA] and 3 [AG] from it. Genotype 3 then experiences an additional A10T substitution that creates genotype 4 [AA]…
From genotype 2 [TA] it is also possible get to 4 [AA] with an A10T mutation. So there are 2 routes to get to the genotype [AA] and they are both present in the genotypes sampled. In the authors’ words:
[C]ycles require sequence changes that render the descendants of one (or more) genotypes more similar rather than less similar. In other words, cycles require some form of homoplasy, i.e., parallel or convergent evolution.
For 42 genes, the observed number of cycles is so large that it cannot be explained by either chance homoplasy or recombination. When analyzing possible explanations, we discovered evidence for positive selection in 21 of these genes and, in addition, a potential role for constrained variation and purifying selection. Balancing selection plays at most a small role. The 42 genes with excess cycles are enriched in functions related to immunity and response to pathogens. Genotype networks are representations of genetic variation data that can help understand unusual patterns of genomic variation. [Emphasis added.]
Just to repeat, many HLA genes showed signs of convergent evolution, as did other genes involved in immune recognition and response.
Says Dr. Swamidass about one of the HLA genes this study identified:
HLA-DRB1 is the most variable HLA gene. It is notable for having over 500 squares in the DNA of about merely 1,000 individuals, compared with an expected number of less than 10. That means if we had tried to put the DNA into a tree, we would see at least 500 mutations discordant with a phylogenetic tree. This is just a stunning result, because it means that HLA-DRB1 alleles are just not well described as a tree. The variation we see is evolving and re-evolving over and over again. Amazing. [Emphasis in the original.]
So TSP is not validated for these highly polymorphic genes, HLA-DRB1 in particular, and convergent evolution (or original diversity) is validated. I addressed, by the way, the question of HLA-DRB1’s polymorphism and TSP, and a first human pair, in the book Science and Human Origins (2012). That book was written after I discovered that Francisco Ayala’s argument against the possibility of a first pair based on HLA-DRB1 did not stand up. My hypothesis about a first pair was based on what I saw in papers about HLA-DRB1, most notably this and this, but the hypothesis was more suggested than demonstrated. I am glad to see that some of what I wrote has been substantiated.
So let me restate: the best explanation for the similarity among alleles is convergent evolution (or possibly original diversity), and not TSP. Finally, this analysis is strong evidence that TSP does not rule out a bottleneck of two.
To sum up, it’s very simple.
- A bottleneck of two that is older than 500,000 years ago cannot be ruled out. That does not mean such a bottleneck ever existed, but rather that the possibility cannot be excluded. Future models may change that number of 500,000 years, up or down.
- This is based on an analysis of the genetic data run by Drs. Schaffner and Swamidass, themselves evolutionary biologists and not ID supporters.
- In addition, the bottleneck hypothesis stood up to a test using TSP (trans-species polymorphism). The test showed TSP was due to convergent evolution. This was a surprise to Dr. Swamidass.
- A bottleneck of two, or a first pair at our origin older than 500,000 years, is possible.
- Evolutionary biologists, including Dennis Venema, can no longer say we had to come from a population of 10,000 at any time over the last 3 million years.
This whole debate has come as a surprise to many.
Image: Adam and Eve after the Expulsion from Paradise, by Paolo Veronese [Public domain], c. 1580-1588, via Wikimedia Commons.