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How WeEvolve
Feature by Benjamin Phelan / October 7, 2008
A growing number of scientists argue that human culture itself has become the foremost agent of biological change.
1)When the previous generation of life scientists was coming up through the academy, there was a widespread assumption, not always articulated by professors, that human evolution had all but stopped. It had certainly shaped our prehuman ancestors — Australopithecus, Paranthropus, and the rest of the ape-men and man-apes in our bushy lineage — but onceHomo sapiens developed agriculture and language, it was thought, we stopped changing. It was as though, having achieved its aim by the seventh day, evolution rested. “That was the stereotype that I learned,” says population geneticist and anthropologist Henry Harpending. “We showed up 45,000 years ago and haven’t changed since then.”
2)The idea makes a rough-and-ready kind of sense. Natural selection derives its power to transform from the survival of some and the demise of others, and from differential reproductive success. But we nurse our sick back to health, and mating is no longer a privilege that males beat each other senseless to secure. As a result, even the less fit get to pass on their genes. Promiscuity and sperm competition have given way to spiritual love; the fittest and the unfit are treated as equals, and equally flourish. With the advent of culture and our fine sensibilities, the assumption was, natural selection went by the board.
3)Moreover, evolution had never been observed in humans, except in a few odd cases, so the conclusion was drawn that it wasn’t happening. One can’t fault the logic. The most famous case of adaptive change in humans, that of sickle cell trait as an evolutionary response to malaria, seemed to prove the point that human evolution must be rare: Even in as dire and malaria-stricken an environment as West Africa, the only response evolution has been able to come up with is an imperfect defense that can cause serious health problems along with its solitary benefit. Selection pressures as strong as those brought about by endemic malaria are uncommon, and civilization was thought to wash out those less powerful.
4)But since the turn of the millennium, genomics has undergone a revolution. With the completion of such landmark studies as the Human Genome Project and the publication of HapMap, scientists finally have access to the particles of evolution. They can inspect vast stretches of DNA from people of all ethnicities, and the colossal amount of information suddenly available has spurred a revision of the old static picture that will render it unrecognizable. Harpending and a host of researchers have discovered in our DNA evidence that culture, far from halting evolution, appears to accelerate it.
5)John Hawks started out as a “fossil guy” studying under Milford Wolpoff, a paleoanthropologist who is the leading proponent of the faintly heretical multiregional theory of human evolution. Coming to genetics from such a background has perhaps given Hawks the stomach to wield unfashionable hypotheses. In December of last year, he, Harpending, and others published a paper whose central finding, that evolution in humans is observable and accelerating, would have been nonsensical to many geneticists 20 years ago. Up to 10 percent of the human genome appears to be evolving at the maximum rate, more quickly than ever before in human history.
6)“Seven percent is a minimum,” Hawks says. “It’s an amazing number,” and one that is difficult to square with the prevailing view of natural selection’s power. Because most mutations have a neutral effect on their carriers, making them neither fitter nor less fit, neither more fertile nor sterile, only slightly different, those changes are invisible to natural selection. They spread or don’t spread through a population by chance, in a process called genetic drift, which is often thought of as the agent of more change than natural selection. But the changes that Hawks detected, if he is correct, are too consistent from person to person, from nationality to nationality, to have been caused by genetic drift alone.
7)By looking at the data from HapMap, a massive survey of the genetic differences between selected populations from around the world, Hawks identified gene variants, or alleles, that were present in many people’s DNA, but not in everyone’s. These alleles seemed to be moving, over time, through populations in a way that matched mathematical predictions of what natural selection should look like on the genomic level. And though Hawks doesn’t know why possession of the new alleles should be advantageous, he doesn’t need to know. The signature that natural selection inscribes on the genome is legible even when the import of the message is unclear.
8)HapMap can reveal where natural selection has occurred thanks to the tendency of DNA “neighborhoods” to be inherited in blocks that do not change much, if at all, from parent to offspring. When an organism reproduces, adjacent DNA sticks together and is passed on as a unit to the offspring. Such sections of linked DNA are called haplotypes; HapMap is a directory of them. A given haplotype is nearly identical among family members, but populations that have had recent contact with each other, such as the French and the Spanish, or the Cherokee and the Inuit, also tend to share it.
9)One of the characteristics of this linkage is that it is strong over short distances on a chromosome and weak over long distances. This is because mutations are rare but equally likely at every location, so they happen less often in a small region of DNA than in a large region. Over many generations, mutations nibble away at the edges of haplotypes and poke holes in their interiors, and the routine reshuffling of nucleotides, called recombination, can move linked sections of DNA far from one another, thereby breaking the linkage. Thus, the length of a haplotype roughly indicates its age, as does the amount of variation within it. Since mutations and recombination occur at a predictable rate, by comparing haplotypes from two populations, one can determine their degree of relatedness and thus estimate how long ago they diverged. So, for example, the San of southern Africa and the Han Chinese, would tend not to share haplotypes because their populations diverged long ago, and those they did share would be short or contain a great deal of variation.
10)Because haplotypes are similar from population to population, differences are easy to spot; a variation on a familiar haplotype background is like a smear of red paint on a white wall. If one looks at a haplotype in 100 individuals, and 90 of them are identical but 10 show the exact same variation, the odds are vanishingly small that random processes generated the same mutation 10 different times. Such a site is a candidate for one undergoing natural selection, because only a mutation that confers some kind of advantage will be propagated reliably through the population.
11)If the trait under selection produces a significant enough adaptive advantage, the allele responsible for the trait will rise in frequency so quickly that it will drag a long haplotype along with it before recombination and mutation can break it down to a short haplotype. So a rare allele on a long haplotype is an indication of strong and recent selection.
12)Hawks’s analysis of the HapMap data yielded many such candidate sites, but some of his colleagues were unimpressed. “They didn’t like the idea,” he says. An anonymous reviewer of his paper claimed not to think that natural selection could possibly be important in recent evolution, “so much so that they said positive selection happens rarely, if ever.”
13)An oft-cited example of evolution in historic times is the spread of the mutation that allows humans to digest milk in adulthood. It seems to have arisen around 8,000 years ago and has since spread to all parts of the world, though there are still plenty of us without it: One in 50 Swedes and nine out of 10 Asian Americans lack the mutation. The lactose intolerant are, at least in this respect, as the first Homo sapiens were.
14)“There are five versions of the lactase drinking gene, so five different populations have mutations that let them drink milk,” says Hawks. Because of this, many mutations conferring the same benefit are unlikely to have become common by genetic drift, but Hawks knows of practicing geneticists who find the idea that natural selection was the agent of their propagation to be preposterous. He’s incredulous at what he sees as such scientists’ fundamental misprision of the field’s core principle. “This is Darwin’s field,” he says. “Darwin talks about evolution, and Darwinism is about natural selection. But these people don’t believe in natural selection — except way back when, when chimps and humans were the same.”
15)By Hawks’s own description, his research “depends on a view of evolution that’s dominated by natural selection. When I look at the evolutionary processes leading to humans I’m thinking, what’s the adaptive change that’s happening? What are the constraints on our adaptation?” One of those, he says, “is demography.”
16)By invoking ancient demography via the anthropological record, Hawks believes he has identified what has been driving all the adaptive evolution he detected: an explosion in the global human population roughly coincident with the agricultural revolution of some 10,000 years ago. We invented agriculture, started eating different food, and began dwelling in cities. Our numbers swelled, our world changed, and our DNA is still catching up.
17)Spencer Wells, director of the Genographic Project, an attempt to reconstruct human migration patterns by sampling DNA from the world’s populations, has studied humanity’s transition to agriculture extensively. Hawks’s result was no surprise to him.
18)“The biggest change in our lifestyle as a species has happened in the past 10,000 years,” Wells says. “We spent most of the past million or so years of evolution living as hunter-gatherers, hunting game on the African savannas, or gathering shellfish on the coast, gradually moving out to Eurasia. Then, suddenly, in the past 10,000 years, we become a species that settles down. The diversity of food sources drops precipitously from over 100 in the hunter-gatherer diet to fewer than 10 in the average agricultural diet. And then, of course, you build up the population densities and disease takes off.”
19)Such changes to environment, diet, and disease load are classic agents of natural selection. The three acting in concert could certainly accelerate evolution. But it might seem odd that a larger population is required to produce a faster rate of evolution, especially if you happen to be American.
20)The early and mid-20th century witnessed a tension between two interpretations of evolutionary theory. Sewall Wright, an American, argued that for rapid evolution to occur, what was required was a small, semi-isolated population through which a mutation could spread quickly, even by genetic drift. Thereafter, that population could migrate and spread the allele in other populations. R.A. Fisher, a Brit, argued that, in fact, a large population was required, because only a large population can produce large numbers of mutations. Because most mutations are neutral, he reasoned, it takes a large number of mutations to produce one beneficial allele. American biologists were most influenced by Wright, but Fisher’s work is where Hawks and Harpending find their support.
21)Fisher developed a mathematical model of how beneficial mutations should move through a population toward fixation, the point at which all members of a species have the allele. The shape of the curve is characterized by slow dispersion at first, because the mutation initially exists in only one member of the species. It takes a long time for a new allele to reach an appreciable frequency in a population, but at a certain point the growth rate becomes much steeper; many carriers bear many offspring, and the gene becomes widespread. But during the last leg of the push toward fixation, the rate decreases and begins to resemble a curve approaching an asymptote.
22)When anthropologists analyzed caches of ancient Eurasian skeletons, they found evidence that Fisher’s model was correct. In the DNA of a group of 5,000-year-old skeletons from Germany, they discovered no trace of the lactase allele, even though it had originated a good 3,000 years beforehand. Similar tests done on 3,000-year-old skeletons from Ukraine showed a 30 percent frequency of the allele. In the modern populations of both locales, the frequency is around 90 percent.
23)“This is the curve that Fisher predicted,” says Hawks. “The frequency [of the lactase allele] that we have at different times fits this curve. This means that the maximum rate of change in frequency of this gene was within the past 3,000 years, even though the gene originated 8,000 years ago.”
24)Seeing the mathematical model he was using borne out in data other than his own was encouraging to Hawks: Many of the alleles he’d identified as being under selection seem to show a similar trajectory toward fixation.
25)“My attitude about recent human evolution comes straight out of mathematics,” he says. “I can say, this is population growth, and these are the effects it should have. And as long as I keep observing data that’s consistent with that idea, I think it’s a strong model…. Once you can connect history with genes, you can build up knowledge from the standpoint of anthropology, then let the biochemists work out what each gene does.”
26)Being able to understand the purpose of a given gene, however, is perhaps the main challenge facing the current generation. Hawks doesn’t know what function the genes he identified as evolving perform, but such information isn’t important for his purposes. He is content with linking demographic history with mathematics and gene surveys and hypothesizing natural selection based on the confluence of those streams of evidence. A biochemist, though, might balk at saying that a gene is under selection without knowing what the gene actually does.
27)“Human genetics made a major leap forward at the turn of the millennium,” says Pardis Sabeti, an evolutionary geneticist at MIT’s Broad Institute who has done a great deal of work on methods for assessing genomic surveys like HapMap, the first draft of which was published in 2005. HapMap is a leaner and in some ways more powerful version of the Human Genome Project, as it compiles only those regions of the human genome — less than 1 percent — that have the potential to differ from person to person. In comparing different populations’ genetic information, it’s possible to tease out patterns of gene inheritance, how certain genes correlate with certain diseases, and even the likely geographic origin of some mutations.
28)One of the methods that Sabeti has developed to identify selection is to search for rare alleles on long haplotypes, which is useful for identifying selection in the past 30,000 years or so. Using the long haplotype test on HapMap data, Sabeti was able to find what appears to be a signature for recent natural selection on genes that are associated with resistance to lassa, a hemorrhagic fever that’s endemic to parts of central and western Africa. She is perhaps more cautious than Hawks in her conclusions, though; they are in different fields and have different standards of proof.
29)“I’m a little guarded on the findings for lassa, because the question is, is the finding real?” she says. “The strongest signal of selection we’ve detected in a West African population is on a gene called Large, which has been biologically linked to lassa.” Lassa is a poorly understood and infrequently studied pathogen, she says, so there was not much literature to consult about genes possibly associated with it. However, a microbiologist named Stefan Kunz had demonstrated that if Large is deleted from a mouse’s DNA, lassa is unable to infect it.
30)“That was exciting, because otherwise we’d look at the gene and say ‘I don’t know what it does,’ and that would have been the end of it. But now we could see a link,” she says. “But when you look at selection you never believe your results completely because it’s circumstantial. We have basic evidence that it seems to be evolving and we can link it to this disease, but we don’t have a real biological link.”
31)The molecular record, for all its overwhelming garrulousness, its babel of A’s, C’s, G’s, and T’s, is ambiguous. But the fossilized skulls of our ape lineage seem to tell a clear story, with respect to one trait, anyway. The past few million years have witnessed a steady, plodding increase in the volume of the human lineage’s brains and, presumably, the sophistication of their contents. High intelligence is to great apes as the wing is to birds.
32)But where are we in that process? Is intelligence still being selected for? Parsimony and uniformitarianism would compel one to answer yes; things in the present are, by and large, as they were in the past. But the way evolution works, whereby mutations arise in one person and slowly spread throughout a population, makes such a question difficult to frame, for if intelligence is still under selection, that could mean that some populations at this very moment are slightly smarter than others — that, perhaps, even certain ethnicities are slightly smarter than others. In the West, speculation on the subject almost automatically tars the speculator as a eugenicist or a racialist.