Reports of Adam and Eve's demise greatly exaggerated?

Does Science Rule Out a First Human Pair? Geneticist Richard Buggs Says No
Ann Gauger

Dennis Venema, associate professor of biology at Trinity Western University, and Scot McKnight, professor of New Testament at Northern Seminary, have written a book,  Adam and the Genome: Reading Scripture after Genetic Science, that addresses the question of human origins. Venema defends the standard scientific narrative on neo-Darwinism and human origins, while McKnight attempts to reconcile Christian theology with the science. Because the book argues that science disproves the existence of a historical Adam and Eve, it is worth responding to in some detail.

One of the claims Venema makes in his book is that the effective population size of our last common ancestor with chimps has never been fewer than 10,000. In fact, he equates the certainty of that statement with our certainty about heliocentrism. That is an extreme claim that needs justification. Assuming no bottlenecks, this would exclude the possibility of an original human pair as the progenitors of the human race.

Effective population size is very hard to determine. In fact, in some situations the effective population size cannot be determined (On the Meaning and Existence of an  effective population size P. Sjödin, I. Kaj, S. Krone, M. Lascoux and M. Nordborg (2005) Genetics 169: 1061–1070). So any estimates concerning effective population size should be taken a bit skeptically.

You don’t have to take my word for it. Richard Buggs, a British biologist who has published over thirty articles on genetics in journals such as Nature, Current Biology, Evolution, and Philosophical Transactions of the Royal Society, wrote to Venema to lay out his concerns in May of this year. Venema failed to respond to Buggs’s email so Buggs  posted it online last week, and tweeted a link to it here. In his letter he comments on effective population size estimates:

As I am sure you know, effective population size is a measure of a population’s susceptibility to drift, rather than an attempt to measure census population size. I would be very hesitant to rely too heavily on any estimate of past effective population size.

Could we have begun with a population of 10,000 and then had a bottleneck of two? Obviously this estimate is relevant for human origins, since a bottleneck of two would indicate some sort of unique beginning. Venema says a bottleneck of two is impossible based on the levels of human genetic diversity present today.

If a species were formed through such an event [by a single ancestral breeding pair] or if a species were reduced in numbers to a single breeding pair at some point in its history, it would leave a telltale mark on its genome that would persist for hundreds of thousands of years — a severe reduction in genetic variability for the species as a whole.

Buggs responds:

It is easy to have misleading intuitions about the population genetic effects of a short, sudden bottleneck. For example, Ernst Mayr suggested that many species had passed through extreme bottlenecks in founder events. He argued that extreme loss of diversity in such events would promote evolutionary change. His intuition about loss of diversity in bottlenecks was wrong, though, and his argument lost much of its force when population 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.

This means that a single pair of individuals can carry a great deal of  heterozygosity  with them through a bottleneck, provided they come from an ancestral population with high diversity and undergo rapid population growth after the bottleneck. They will pass most of that diversity on to the population they found, so long as population grows rapidly.

Buggs goes on to discuss the relative genetic diversity of chimpanzees at 5.7 million SNPs (single nucleotide polymorphisms) and humans at 3.1 million (Prado-Martinez et al 2013 Nature). He makes the point that if a pair of chimpanzees were moved to an isolated region where rapid population growth was possible, the new population would have similar levels of genetic variability to modern humans.

He explains:

I am not stating these figures because existing populations of chimpanzee gave rise to modern humans, but simply to show that it is hard to see how overall levels of SNP diversity and heterozygosity in modern humans could exclude the possibility of a past bottleneck of two individuals.

On top of this, we need to add in the fact that explosive population growth in humans has allowed many new mutations to rapidly accumulate in human populations, accounting for many SNPs with low minor allele frequencies (A. Keinan and A. G. Clark (2012) Science 336 (6082): 740-743).

PSMC (pairwise sequentially Markovian coalescent) analysis is a method used by population geneticists to try to recover the history of human populations. Venema discusses it in his book. Unfortunately he cannot use it to prove that a sudden, short bottleneck never happened. In the original Li and Durbin 2011 paper describing PSMC analysis, the authors note that an instantaneous reduction in population size was not detected as such, but was instead “spread over several preceding tens of thousands of years in the PSMC reconstruction.” Continued work in  Beth Shapiro’s lab also indicates that the PSMC method cannot accurately reconstruct sharp bottlenecks.

Buggs sums up his problems with Venema’s analysis:

In general, I am concerned that the studies you cite did not set out to test the hypothesis that humans have passed through a single-couple bottleneck. They are simply trying to reconstruct the most probable past effective population sizes of humans given the standard assumptions of population genetic models. I personally would feel ill at ease claiming that they prove that a short sudden bottleneck is impossible.

 scientists have argued have argued against Venema’s position by disputing key assumptions, including the idea of common descent. Buggs’s argument is valid, though, whether or not common descent is true. In fact, he has told me he is assuming common ancestry, but arguing that we can still have come from a single couple as ancestors.

What is needed is a model that does not rely on the standard assumptions of population genetics. Recently Hössjer, Gauger, and Reeves have proposed such an alternative model. The model, when programmed, will be available for use by anyone to test the effects of various starting conditions, like population size, the degree of gene flow, recombination and mutation rates, mate choice effects, and ultimately the effects of selection. The outcomes of various scenarios can be tested and compared to summary statistics from modern populations, in order to determine which scenarios best explain current populations.

Finally, given Buggs’s critique, Venema’s claims that our starting population was at least 10,000, and that we could not have come from just two, seem unjustified. Certainly Venema cannot claim these are facts as sure as heliocentrism. He should at least acknowledge the facts above, and soften his claims. Further revision may be necessary following the results from Hössjer, Gauger, and Reeves’s model. We shall see.