March 07, 2006
HapMap Yields Evidence Of Recent Human Evolution

Using data from the International HapMap project (HapMap stands for Haplotype Map of genetic variations) researchers find evidence for recent changes in the frequencies of genes in different human populations.

By scanning the entire human genome in search of genetic variations that may signal recent evolution, University of Chicago researchers found more than 700 genetic variants that may be targets of recent natural positive selection during the past 10,000 years of human evolution.

In one of the first comprehensive genome scans for selection, the researchers found widespread evidence of evolution in all of the populations studied. Their results are published and freely available online in the open-access journal PLoS Biology.

The data analyzed here were collected by the International HapMap Project and consist of genetic data from 209 unrelated individuals who are grouped into three distinct populations: 89 East Asians, 60 Europeans and 60 Yorubans from Nigeria. The researchers found roughly the same number of signals of positive selection within each population. They also found that each population shares about one fifth of the signals with one or both of the other groups.

"This approach allows us to take a broad prospective to see what kinds of biological systems are undergoing adaptation," said Jonathan Pritchard, professor of human genetics and corresponding author of the paper. "There have been a lot of recent changes--the advent of agriculture, shifts in diet, new habitats, climatic conditions--over the past 10,000 years, and we're using these data to look for those signals of very recent adaptation."

Among the more than 700 signals the team found were previously known sites of recent adaptation, such as the salt-sensitive hypertension gene and the lactase gene--the strongest signal in the genome hunt. The lactase mutation, which enables the digestion of milk to continue into adulthood, appeared in approximately 90 percent of Europeans.

"Presumably," Pritchard said, "a few thousand years from now, if selection pressure remains the same, everyone will have [the selected mutation]."

Classifying all the genes by their biological functions, the researchers listed the top 16 categories that had the strongest signals, including olfaction (the sense of smell), reproduction-related processes and carbohydrate metabolism, which includes the lactase gene.

Other processes that show signals of selection include genes related to metabolism of foreign compounds, brain development and morphology. For example, the researchers found five genes involved in skin pigmentation that show evidence of positive selection in Europeans. "Only one of these five signals was known before," Pritchard said. The authors also found signals of reproductive selection and sexual competition in all three populations.

"Many of the signals, however, seem to be more specific to modern human adaptation," he said, "like skin pigmentation, which may respond to changes in habitat, or metabolism genes, like lactase, which may respond to changes in agriculture."

From the text of the journal article: They found several brain genes under selective pressure.

Recent articles have proposed that genes involved in brain development and function may have been important targets of selection in recent human evolution [8,9]. While we do not find evidence for selection in the two genes reported in those studies (MCPH1 and ASPM), we do find signals in two other microcephaly genes, namely, CDK5RAP2 in Yoruba, and CENPJ in Europeans and East Asians [46]. Though there is not an overall enrichment for neurological genes in our gene ontology analysis, several other important brain genes also have signals of selection, including the primary inhibitory neurotransmitter GABRA4, an Alzheimer's susceptibility gene PSEN1, and SYT1 in Yoruba; the serotonin transporter SLC6A4 in Europeans and East Asians; and the dystrophin binding gene SNTG1 in all populations.

It is possible some genes with influence on brain function were missed in their analysis because the genes have as yet unidentified roles in influencing cognitive function. A couple of other factors suggest these results are far from comprehensive. First, they looked at only 800,000 single nucleotide polymorphisms (SNPs). Well, the human race has more than that. Also, and perhaps more importantly, they looked only at SNPs. Yet another type of genetic variation called large copy variations have fairly recently been found to create suprisingly large amounts of genetic variation between humans. So this latest result with such a small sample size of humans and a subset of all human genetic variations understates the extent of recent evolution in humans.

Regarding their lack of evidence for the recent evolution of MCPH1 and ASPM see my previous post Brain Gene Allele Frequences Show Brain Still Evolving. Also see my post PDYN Brain Gene Modified During Primate Evolution.

Human evolution did not stop tens of thousands of years ago. We are more different from each other due to genetic factors than left-liberal political ideologues would have you believe. We are still evolving and adapting to local environments. Starting some time in the next 20 or 30 years our rate of genetic change is going to accelerate by orders of magnitude and subpopulations of homo sapiens will diverge even more radically than human racial groups have diverged so far.

Share |      Randall Parker, 2006 March 07 10:28 PM  Brain Evolution


Comments
Mox said at March 7, 2006 11:16 PM:

"Starting some time in the next 20 or 30 years our rate of genetic change is going to accelerate by orders of magnitude and subpopulations of homo sapiens will diverge even more radically than human racial groups have diverged so far."

Care to explain your reasoning behind this prediction?

Mthson said at March 8, 2006 4:33 AM:

Does that estimate refer to both germline engineering (embryos) and gene therapy (adults)?

Bob Badour said at March 8, 2006 6:28 AM:

Mox,

Randall has lots of articles and posts that explain the coming advancing rate of human evolution. With increasingly better tools, we will be able to identify and select genetic traits for our offspring with greater ease.

We will influence the genes of our offspring through: more informed mate selection, selection of sperm and ova, introduction of genes into the germline etc.

Since not everyone values the same traits, subpopulations will choose different traits with increasing regularity. One can see this already where some cultures practice sex selection quite regularly while it would never occur to people in other cultures to do so.

Bob Badour said at March 8, 2006 6:31 AM:

Randall,

How much of the 20% common adaptation do you suppose might have been driven by disease? Influenza has only been around for a few hundred years and I expect it has had significant selective pressure during that time.

Jake said at March 8, 2006 7:36 AM:

The end of discrimination against women in America 40 years ago, meant that intelligent men and women were aggregated together in college and at work. The resulting marriages have probably produced even more intelligent and talented offspring.

That means that less intelligent men were left with less intelligent women to marry and the resulting offspring were less intelligent.

Can this stratification of our society by intelligence and talent and the resulting offspring be called evolution?

Randall Parker said at March 8, 2006 8:24 AM:

Mox,

As I've repeatedly argued here, first people will use DNA sequence information to choose mates, egg donors, and sperm donors (with the latter probably having the biggest impact). They will also use DNA sequence information to do more extensive selection of IVF fertilized eggs (Pre-Implantation Genetic Diagnosis or PIGD or PGD). That step requires cheap DNA sequencing technology. I figure the price breakthrough on DNA sequencing will happen within 10 years. Then sperm banks and egg donors will offer DNA sequence information and the information will become available to interpret it.

The number of medically useful known genetic variations that have tests available for them is already around 1000. That number will go up by a couple of orders of magnitude in the next decade.

Then next people will do genetic engineering to embryos to give them desired changes in genetic sequences. I figure that happens within 20 years, maybe sooner, maybe later, but certainly within 30 years. Gene therapy techniques are being developed for lots of medical purposes. Some of those techniques will turn out to be useful on embryos as well. I bet they first get used in animal breeding within 10 to 20 years.

Genetic engineering to embryos will speed up changes in the human genome to a point where in the 21th century the human genome will change more than it has in the last 100,000 years.

Mark Amerman said at March 8, 2006 3:37 PM:

Jake,

I suspect if you look closely at the rate of reproduction of
your cognitive elite, or as you describe them:

"...resulting marriages [that] have probably produced even more
intelligent and talented offspring"

you'll discover it's below replacement. Or maybe I should
rephrase that. It's isn't the marriages that are below
replacement but if we include all the similar people who
don't marry and have children, then the group as a whole
is below replacement.

So that from an evolutionary perspective what we are seeing,
assuming the trend continues, is a group of characteristics
rapidly being purged from the population.

gcochran said at March 8, 2006 5:25 PM:


" Can this stratification of our society by intelligence and talent and the resulting offspring be called evolution? "

If it doesn't affect fertiltiy, the answer would be no - assortative mating does not by itself change gene frequencies.

Happy Bunny said at March 8, 2006 5:26 PM:

I still think that this is the problem with these kind of studies...sure, we may have found ways that we are adapting, and improving as humans, but that still doesn't mean that evolution is true. We are still humans, and we have not evolved into a different life form, neither have we seen any other animal jump to another animal.

Bob Badour said at March 8, 2006 7:06 PM:

Happy Bunny,

Are chimps and bonobos the same species?

Allan L said at March 14, 2006 2:49 AM:

Regarding the first comment, by Mox, asking why genetic change is going to accelerate:

It will increase because genetic maladaption will become an anachronism in a technically sophisticated society which ensures equal survival for almost all genetic configurations. All will survive and all will be equally fecund (as in China), and with no negative genetic pressure, diversity will increase unless the State disallows particular genes or configurations.

Seth Erebos said at May 22, 2008 3:36 PM:

I think that's wrong also. Because when you ask someone what is intelligent, whether it's common sense, mathemetical or science inclined, artistic and creative, politically. There's to much factors pushing people in the areas of intelligence that one only one type can lead. Also though intelligence is sexy on a person, who's not to say that I don't want someone who's like me and who's analytical or all about school and just want to become a mom. So sorry Jake I don't agree with your theory, but it's quite interesting.

Seth Erebos said at May 22, 2008 3:43 PM:

I think that's wrong also. Because when you ask someone what is intelligent, whether it's common sense, mathemetical or science inclined, artistic and creative, politically. There's to much factors pushing people in the areas of intelligence that one only one type can lead. Also though intelligence is sexy on a person, who's not to say that I don't want someone who's like me and who's analytical or all about school and just want to become a mom. So sorry Jake I don't agree with your theory, but it's quite interesting.

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