Saturday, 30 October 2010

Did human evolution accelerate?

Modern humans changed little when they initially spread out of Africa and into the Middle East. Real change occurred farther north, when they entered seasonally varying environments that differed much more even in summer.

Three years ago, a research team led by John Hawks found that the rate of genetic change accelerated once ancestral humans had spread from Africa to the other continents. Over the past 40,000 years, natural selection seems to have altered at least 7% of our genome. And this process speeded up even more as agriculture replaced hunting and gathering over the past 10,000 years. The rate of genetic change then increased more than a hundred-fold (Hawks et al. 2007).

This finding, however, seems to be at odds with a recent Scientific American article by Jonathan Pritchard:

As early Homo sapiens spread out from Africa starting around 60,000 years ago, they encountered environmental challenges that they could not overcome with prehistoric technology.

Many scientists thus expected that surveys of our genomes would reveal considerable evidence of novel genetic mutations that have recently spread quickly through different populations by natural selection […]

But it turns out that although the genome contains some examples of very strong, rapid natural selection, most of the detectable natural selection appears to have occurred at a far slower pace than researchers had envisioned.
(Pritchard 2010)

Is there a fundamental disagreement here between Jonathan Pritchard and John Hawks? Perhaps not. Pritchard doesn’t actually deny that genetic change accelerated in ancestral humans. He simply states that its pace has been far slower than the one envisioned by “researchers.”

Curiously, he makes no reference to John Hawks. This is all the more curious because no one else matches the unnamed “many scientists” and “researchers.” Until three years ago, and even today, the conventional view has been that cultural evolution replaced genetic evolution in our species. Culture provided us with faster ways to adapt. Instead of changing our genes, we changed our environment by means of new technologies, modes of subsistence, forms of shelter, and so on.

That’s what I learned as an undergrad. If Pritchard wishes to argue against Hawks’ position, why not mention him by name? Why create a fictitious ‘conventional view’ that needs to be put in its place?

I see other weaknesses in this Scientific American article, particularly in the methodology behind its conclusion that human genetic evolution has been relatively slow. One is recognized by Pritchard himself. What matters is not the degree of change at a single gene, but rather the total change at all genes that influence a single trait:

A series of papers published in 2008, for example, identified more than 50 different genes that influence human height, and certainly many more remain to be found. For each of these, one allele increases average height by just three to five millimeters compared with the other allele.

When natural selection targets human height […] it may operate in large part by tweaking the allele frequencies of hundreds of different genes. If the “short” version of every height gene became just 10 percent more common, then most people in the population would quickly come to have more “short” alleles, and the population would be shorter overall.
(Pritchard 2010)

Another weakness is the impossibility of measuring the rate of genetic change directly:

It would be great if in our efforts to understand recent human evolution, we could obtain DNA samples from ancient remains and actually track the changes of favored alleles over time. (Pritchard 2010)

Because this approach is still in its infancy, Pritchard falls back on assumptions about when and where human populations have come into being. He assumes that Homo sapiens began to spread out of Africa some 60,000 years ago and then split into Europeans and East Asians some 20,000 to 30,000 years ago. These are the baselines he uses to calculate the rate of genetic change.

But these are high-end estimates. The ‘Out of Africa’ event is probably closer to 45,000 BP (1) and the best dating for the European/East Asian split is 20,000 BP (Laval et al. 2010) (2). Moreover, natural selection has not changed non-African humans at a constant rate since their ancestors left Africa. Those who remained within the tropical zone, such as Australian Aborigines, Papua-New Guineans, and Andaman Islanders, have changed surprisingly little. There has been much more evolution among those who spread out of the tropical zone and into temperate and arctic environments, beginning around 30,000 BP. Evolutionarily speaking, the key event was not when humans began to spread out of Africa. It was when they began to spread out of the Tropics (3).

So for many if not most traits, Pritchard is underestimating the rate of genetic change by a factor of two. Another source of error is his unspoken assumption that genetic change in Eurasia has never flowed back into Africa. By using Africa as a baseline for genetic change, he is excluding new Eurasian alleles that have displaced older ones even in Africa. Evidently, this error would lead to underestimation of the rate of genetic change both within and outside Africa.

Notes

1. Uranium dating suggests that modern humans entered the Middle East c. 46,500 BP (Schwarcz et al. 1979).

2. Maps of human prehistory typically show two lines of advance out of Africa: one turning left and into Europe and another turning right and into South Asia, Southeast Asia, and East Asia. The second line of advance did exist, but was not ancestral to present-day East Asians. It was instead ancestral to relic groups like the Andaman Islanders and the Semang, as well as Papua-New Guineans and Australian Aborigines.

East Asians, like the Inuit and Amerindians, have their origins in North Asia, as seen by their ‘Arctic’ physiognomy. These early North Asians in turn came from early Europeans, specifically the reindeer-hunting nomads who spread eastward through the steppe-tundra belt of northern Eurasia. In other words, Europeans and East Asians are not siblings who parted company in the Middle East some 45,000 years ago. The latter are instead ‘offspring’ of the former, the two groups having become reproductively isolated from each other at the height of the last ice age, c. 20,000 BP.

3. In sum, the ‘Out of Africa’ event did not occur when modern humans first ventured across the present-day Suez Canal. This is an arbitrary line based on current geopolitical realities. Ecologically speaking, the Middle East is part of Africa. Real adaptive change did not begin until modern humans had spread farther north and into environments with wide seasonal variations in temperature, vegetation, wildlife, and other resources.

References

Hawks, J., E.T. Wang, G.M. Cochran, H.C. Harpending, and R.K. Moyzis. (2007).
Recent acceleration of human adaptive evolution. Proceedings of the National Academy of Sciences (USA), 104, 20753-20758.

Laval, G., E. Patin, L.B. Barreiro, and L-Quintana-Murci. (2010). Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions, PloS ONE, 5(4), e10284

Pritchard, J.K. (2010). How we are evolving, Scientific American, October, pp. 41-47.

Schwarcz, H.P., B. Blackwell, P. Goldberg, and A.E. Marks. (1979). Uranium series dating of travertine from archaeological sites, Nahal Zin, Israel, Nature, 277, 558-560.

12 comments:

Insightful said...

Those who remained within the tropical zone, such as Australian Aborigines, Papua-New Guineans, and Andaman Islanders, have changed surprisingly little.

You forgot to mention the people from Fiji and the people of the Solomon islands as well. They have also changed very little right down to their hair texture is still African in trait...

Anonymous said...

That paper by Laval et Al appears to be here:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010284

Henry Harpending said...

Peter don't you suppose that getting summoned to DC and told to keep quiet has something to do with "suddenly" discovering that there hasn't been so much evolution after all.

Here is the summons I got, which I ignored:


Dear Dr. Harpending:

The National Human Genome Research Institute (NHGRI) is planning a
workshop to explore the ethical, legal, and social issues (ELSI) raised
by research on natural selection in humans. The impetus for this
meeting is the sense of a growing need for more thoughtful deliberation
by genomic researchers, ELSI researchers, science writers and science
editors regarding the societal issues raised by natural selection
research. The goals of the meeting will be to: 1) discuss the
scientific design and interpretation issues pertinent to this research
to determine whether a set of "best practices" can be identified for
investigators and peer reviewers in this area; 2) discuss the relevant
ethical issues and issues surrounding public understanding and reporting
of the findings of this research to assess what issues science editors
should consider when dealing with papers in this area; and 3) discuss
future directions for genomic and ELSI research related to natural
selection.

We would like to invite you to attend this workshop, which will be held
in Rockville, MD on October 28, 2008. NHGRI will cover your travel
expenses. An agenda for the workshop is attached. Please let us know
by COB on Monday, September 8, 2008 if you would like to participate in
the meeting, by replying to Chris Juenger (Juengerc@mail.nih.gov and
Jean McEwen (mcewenj@mail.nih.gov). Please do not hesitate to contact
either Chris or Jean if you have any questions.

Best regards,

Alan Guttmacher

Anonymous said...

That paper by Laval et Al

Although I do not have much substantive to say about this paper in general, I have to say that I find a paper which uses an equal representation of Danes and Chuvash to represent Europeans seems somewhat questionable ("47 European individuals represented by Danes (N = 23) and Chuvash from Russia (N = 24)"). Even though the East Asian component in Chuvash is perhaps only a quarter.

PRCalDude said...

Does anyone still read SciAm? The editors are all basically blank-slater doomer peak-oiler chicken-littles now. My dad finally canceled his subscription after 40 years.

Peter Frost said...

Insightful, Anon,

Thanks for the additional info!

Henry,

It's easier (and more acceptable) to control research through covert measures. Once the control becomes overt, it's a sign that covert measures are no longer working.

One might be able to control research in one country, but what about the others? This was one of Diamond's points in explaining why Europe succeeded and East Asia failed. In Europe, efforts to stifle the growth of secular, scientific knowledge were frustrated by Europe's fragmentation along political and religious lines.

Anon,

I agree. They should not have used Chuvash subjects. I'll see if I can get an answer via e-mail from the authors.

PRCaldude,

Scientific America has been dumbed down in recent years. It's no longer a first-tier journal.

Kiwiguy said...

***One might be able to control research in one country, but what about the others? This was one of Diamond's points in explaining why Europe succeeded and East Asia failed.***

The wheel has turned.

"Economist: ... with the delivery of 120 spanking new top-of-the-range Illumina sequencing machines. When they have all been installed the building will, so it is claimed, have more DNA-sequencing capacity than the whole of the United States.

... The building belongs to the BGI, once known as the Beijing Genomics Institute. Mr Wong manages the institute’s Hong Kong operation, but the institute itself is based over the border in the People’s Republic proper, in Shenzhen. The BGI itself is one part—arguably the leading one—of China’s effort to show that it can be the scientific peer of the West.
...
But the organisation is involved in even more controversial projects. It is about to embark on a search for the genetic underpinning of intelligence. Two thousand Chinese schoolchildren will have 2,000 of their protein-coding genes sampled, and the results correlated with their test scores at school. Though it will cover less than a tenth of the total number of protein-coding genes, it will be the largest-scale examination to date of the idea that differences between individuals’ intelligence scores are partly due to differences in their DNA.

Dr Yang is also candid about the possibility of the 1,000-genome project revealing systematic geographical differences in human genetics—or, to put it politically incorrectly, racial differences. The differences that have come to light so far are not in sensitive areas such as intelligence. But if his study of schoolchildren does find genes that help control intelligence, a comparison with the results of the 1,000-genome project will be only a mouse-click away."

http://infoproc.blogspot.com/2010/06/china-genomics-without-political.html

Kiwiguy said...

Jonathan Haidt's prediction:

"But now that we can examine partial genetic maps from thousands of people around the world, the old view is crumbling. Genetic evolution is not slow, and it certainly did not stop around 50,000 years ago, when people began leaving Africa and filling every continent save Antarctica. In fact, it now appears that the human diaspora greatly increased the pace of genetic change. When people exposed themselves to new climates, pathogens, diets, technologies, and social structures, they exposed their genes to new selection pressures. You don't need 50 millennia to get big changes. Some Russian fox breeders created what was essentially a new species of tame, doglike foxes in just 30 generations.

Over the next 10 years, therefore, we'll be hearing less about the Pleistocene and more about the Holocene—the 12,000 years since the beginning of agriculture. We've accepted findings that some ethnic groups adapted during the Holocene to digest milk as adults or to breathe more easily at high altitudes. But what will happen when findings come in about personality traits? Nearly all traits are heritable, and some traits surely paid off more handsomely in commercial cultures than in agricultural ones, or on peaceful islands than on raid-prone steppes. Such findings will be among the greatest threats to political correctness ever to emerge from the natural sciences."

Fast Evolution -
For the 10th-anniversary issue of The Chronicle Review, we asked scholars and illustrators to answer this question: What will be the defining idea of the coming decade, and why?

Tod said...

I have a feeling that we will be hearing a lot more about the period of evolution of humans up until "out of Africa" being the most important.


The old kind of selection stopped hundreds of years ago, what kind of selection is occurring now ?

Romek R. said...

One example of recent evolution is minimalization of people who like sex, but don't like children. Advancement of birth control methods allowed to have sex without children, so their needs are met, without leaving offspring or with few offspring. In past times people who were obsessed with sex were the ones to leave most descendants as a byproduct of doing sex. Today only people who consciously choose to have children reproduce at large level (there are various reasons - from emotions toward children to feelings of religious/partiotic-citizen obligations). Sex will of course survive in next generations with people who like both sex and children.

Anonymous said...

Today only people who consciously choose to have children reproduce at large level (there are various reasons - from emotions toward children to feelings of religious/partiotic-citizen obligations).

What about people who like/are obsessed by/can't control their impulse towards sex but are too stupid, lazy, irresponsible, low in future time-orientation, etc. to use birth control? Presumably they're reproducing just fine at high levels.

sykes.1 said...

Tod--
"The old kind of selection stopped hundreds of years ago, what kind of selection is occurring now ?"

I hope you don't mean natural/sexual/kin selection, because these are still operative.

The most obvious severe environmental change that has occurred recently is the movement of the great mass of humanity out of the countryside and into large metropolitan complexes. That alone should induce change. Beyond that, the requirement for high levels of literacy and numeracy is very much greater now than before. On the flip side, we now have large welfare states that allow unproductive classes to flourish.

I couldn't begin to guess the outcome. Well's Eloi/Morlock fantasy is not so fantastic.