The embargo has now ended on the second, and far more important paper that I mentioned the other day. It is a product of work I've been doing with Bob Moyzis of UC Irvine, his former graduate student Eric Wang, now at Affymetrix, my friend Greg Cochran and Henry Harpending at the University of Utah.
Some readers may know I've been working on this project -- I've given presentations at meetings and at a number of universities about it. But otherwise I've been silent about it. In particular I have been systematically avoiding the topic of recent selection here on the weblog. It has been a great inconvenience to me, but the unhappy fact is that journals want new results, and blogging about something is at least perceived to reduce its news value. And of course, working with other people across the country entails a lot of respect for keeping discussions and results confidential until we have all signed off on everything.
Anyway, I'm hugely excited about this project, our current results, and what we will be doing next. Which means I have some pent-up writing to do! Over the next few days, this will be acceleration central -- I'll be laying out what these genomic data mean for recent human evolution, what kinds of genes we have been finding under selection, and exactly how these kinds of analyses are done.
I'll also be tracking press articles and blog reactions to the paper. PNAS is, if anything, consistently unpredictable about when they actually make papers available. If you want a preprint, please let me know. I'd also appreciate your links.
Also, if you've come here for the first time, welcome! I may get a lot of traffic for a few days, so I apologize if things are slow.
Here's a start: the abstract.
Recent acceleration of human adaptive evolution
John Hawks, Eric T. Wang, Gregory Cochran, Henry C. Harpending, and Robert K. Moyzis
Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would predict (i) site heterozygosity at least 10-fold lower than is observed in humans, (ii) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (iii) an implausibly high number of adaptive substitutions between humans and chimpanzees, and (iv) nearly 100 times the observed number of high-frequency linkage disequilibrium blocks. Larger populations generate more new selected mutations, and we show the consistency of the observed data with the historical pattern of human population growth. We consider human demographic growth to be linked with past changes in human cultures and ecologies. Both processes have contributed to the extraordinarily rapid recent genetic evolution of our species.
This is a bold assertion, and I will be putting out an FAQ later today that covers many of the questions I have been fielding from the press. There is a lot of technical detail in it, but we have accomplished essentially two things:
- An empirical age distribution for alleles under recent selection, which number in the thousands.
- A theoretical account of why these new alleles should have been increasing rapidly in numbers during the last 40,000 years.
It is a powerful paper because it shows why a rapid acceleration of our evolution is expected in theory, and it matches those expectations to real empirical data. It shows the absolute impossibility of a constant rate of selective change in humans, and that gives reality to our estimate of the amount of acceleration.
The last paragraph of the discussion:
It is sometimes claimed that the pace of human evolution should have slowed as cultural adaptation supplanted genetic adaptation. The high empirical number of recent adaptive variants would seem sufficient to refute this claim. It is important to note that the peak ages of new selected variants in our data do not reflect the highest intensity of selection, but merely our ability to detect selection. Due to the recent acceleration, many more new adaptive mutations should exist than have yet been ascertained, occurring at a faster and faster rate during historic times. Adaptive alleles with frequencies under 22% should then greatly outnumber those at higher frequencies. To the extent that new adaptive alleles continued to reflect demographic growth, the Neolithic and later periods would have experienced a rate of adaptive evolution more than 100 times higher than characterized most of human evolution. Cultural changes have reduced mortality rates, but variance in reproduction has continued to fuel genetic change. In our view, the rapid cultural evolution during the Late Pleistocene created vastly more opportunities for further genetic change, not fewer, as new avenues emerged for communication, social interactions, and creativity.
Over the next few days, I'll fill you in a bit about the course of this research -- how we got started, how it proceeded, and what parts of it remain exciting. Also, I'll try to give a flavor to what genomics means for anthropology -- what exactly is "anthropological genomics?" I think that there is an exciting frontier opening in the way we look at the past, and I hope to be able to show how some of it will work over the next few years.