A challenge to near neutral theory?

I came across this article in quanta recently regarding how a concept called background selection is posing a challenge to near neutral theory (at least the author claims it does so). It’s also related to human evolution.
The language is mostly accessible to non scientists.
I am attaching the link to the article and two papers cited in the article.

1 Like

This is not a challenge to near-neutral theory, because it is just another near neutral theory. I think this well within the range of views of mainstream science, and is not in conflict with the work I’ve explicated here. For simplicity, like Larry Moran at Sandwalk, I use “neutral theory” to refer to both “neutral theory” and “near-neutral theory.” You will not, also, that these article are careful not to be confused with “adaptationalism”, which is what Darwinism is usually mean to refer to.


Notice also that they are quoting very old work to support their claims,

To address this, one of Kimura’s students, Tomoko Ohta, now professor emeritus at Japan’s National Institute of Genetics, proposed the nearly neutral theory of molecular evolution in 1973.

Tomoko Ohta did foundational work showing the interaction between positive selection and neutral drift: neutral draft. That is an example of how selection indirectly affects a larger proportion of the genome, by influencing which neutral changes are fixed. Natural selection, for this reason, does at least indirectly influence a large part of the genome, but neutral processes are still far more important.


I was expecting response along those lines. And to be fair, the article acknowledges that these mutations are still neutral even if they are linked to mutations that are selected for.What intrigued me about the article was the following -

  1. a passing reference to how simulations/demographic studies can turn out wrong if this idea is true-

" According to Irina Arkhipova, a molecular evolutionary geneticist who studies the role of transposons at the Marine Biological Laboratory at the University of Chicago, “this portion of the genome is quintessentially neutral in Kimura’s sense,” even if some fraction of those transposons do affect the expression of genes. Because of this, neutral models applied to the nonfunctional regions of the genome can be used to infer the demographic history of human populations (and a variety of other organisms) quite accurately, Cornejo said.
Kern disagrees. “I’d argue we have no idea if we are accurately estimating human demographic history,” he wrote in an email. If you computationally simulate a population evolving neutrally, then methods for estimating demography will work; but introduce linked selection, and those methods fail.

A recent paper in eLife by Fanny Pouyet and her computational-geneticist colleagues at the University of Bern and the Swiss Institute of Bioinformatics pins down that number. “Up to 80-85 percent of the human genome is probably affected by background selection,” the authors wrote.

After they additionally accounted for biased changes in genes that recombination can introduce during DNA repair, they concluded that less than 5 percent of the human genome evolved by chance alone. As the editors of eLife noted in their summary of the paper, “This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection.”

So essentially, the challenge seems to be to the validity of current simulations in population genetics if i get the article correctly. Do you think it can have an impact on geneaological Adam?

1 Like

It should have no impact on genealogical Adam (not that most of the ideas here are particularly new). Genealogical Adam doesn’t depend on genetics at all, just on genealogical relationships and on human mating behavior. It also shouldn’t have any effect on the minimum time to a population bottleneck of size two.


Perhaps a more precise way to put it is that it does not have an effect we haven’t accounted for in the most recent analysis. We certainly relied on our understanding of non-neutral processes (e.g. balancing selection, neutral draft) to determine how to interpret the data. Neutrality is the most important model, but other factors can modify or overwhelm it. (note, neutral draft is neutral)

I’m sure @glipsnort knows this already. I’m just pointing this out so that no one is confused to think we did not consider the effect of non-neutral evolution.

1 Like