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September 08, 2005

Brain Gene Allele Frequences Show Brain Still Evolving
Bruce Lahn and colleagues at the University of Chicago continue their ground-breaking
research on the evolution of human intelligence with their finding that two genes
involved in cognition have been under strong selective pressure since humans left
Africa.

The gene Microcephalin (MCPH1) regulates brain size and has evolved under strong
positive selection in the human evolutionary lineage. We show that one genetic variant
of Microcephalin in modern humans, which arose ~37,000 years ago, increased in
frequency too rapidly to be compatible with neutral drift. This indicates that it has
spread under strong positive selection, although the exact nature of the selection is
unknown. The finding that an important brain gene has continued to evolve adaptively
in anatomically modern humans suggests the ongoing evolutionary plasticity of the
human brain. It also makes Microcephalin an attractive candidate locus for studying the
genetics of human variation in brain-related phenotypes.

A popular myth holds that evolution takes hundreds of thousands or millions of years to
produce significant differences in a species. But even 1000 years is enough time in
human evolution to produce large changes in allele frequencies. Heck, just look at the
different rates of growth of various human population in the 20th century. At the
beginning of the century white Europeans were about 25% of the world's population and
last I read they were at 10% (or was it even lower?) and dropping. That caused big
changes in the frequencies of a large number of alleles (places where DNA sequences
differ between people).

Think about the times when these alleles started increasing in frequency in Lahn's
reports. One he estimates started sweeping approximately 37,000 years ago. Another
started sweeping approximately 5,800 years ago. Note they might both be much older.
But those dates appear to be the dates when they really started spreading. They have
both spread far in some human populations and yet not in others. This has big
implications. Many other alleles for other traits (e.g. the ability to make lactase while an
adult or red hair) obviously have spread in some populations on time scales in the
thousands of years. But some people didn't want to believe that this could or did happen
for brain gene alleles. Well, yes, it did.

I've coined a term to describe people who argue that the brain hasn't changed much
since humans left Africa: Neo-Cartesian Dualists. Why that term? Well, Cartesian
Dualism was the idea that the mind somehow existed independent of the brain. The
modern Neo-Cartesian Dualism basically holds (not that I think its believers all really
understand this implication of their myth) that the genes for coding the brain exist
independent of any Darwinian selective force. The brain genes exist in a sort of magical
realm where either natural selection can't reach or natural selection magically operates
equally on all humans. But this could only be the case if a supernatural entity intervened
to make it so. Reality does not work that way.
From the Howard Hughes Medical Institute press release.

Howard Hughes Medical Institute researchers who have analyzed sequence variations in
two genes that regulate brain size in human populations have found evidence that the
human brain is still evolving.

They speculate that if the human species continues to survive, the human brain may
continue to evolve, driven by the pressures of natural selection. Their data suggest that
major variants in these genes arose at roughly the same times as the origin of culture in
human populations as well as the advent of agriculture and written language.

The research team, which was led by Bruce T. Lahn, a Howard Hughes Medical
Institute investigator at the University of Chicago, published its findings in two articles
in the September 9, 2005, issue of the journal Science.

Their analyses focused on detecting sequence changes in two genes - Microcephalin and
“abnormal spindle-like microcephaly associated” (ASPM) - across different human
populations. In humans, mutations in either of these genes can render the gene
nonfunctional and cause microcephaly - a clinical syndrome in which the brain develops
to a much smaller size than normal.

In earlier studies of non-human primates and humans, Lahn and his colleagues
determined that both Microcephalin and ASPM showed significant changes under the
pressure of natural selection during the making of the human species. “Our earlier
studies showed that Microcephalin showed evidence of accelerated evolution along the
entire primate lineage leading to humans, for the entire thirty to thirty-five million years
that we sampled,” he said. “However, it seemed to have evolved slightly slower later
on. By contrast, ASPM has evolved most rapidly in the last six million years of hominid
evolution, after the divergence of humans and chimpanzees.”

Here is the most important part:

The researchers first sequenced the two genes in an ethnically diverse selection of about
90 individuals. The researchers also sequenced the genes in the chimpanzee, to
determine the “ancestral” state of polymorphisms in the genes and to assess the extent
of human-chimpanzee divergence.

In each gene, the researchers found distinctive sets of polymorphisms, which are
sequence differences between different individuals. Blocks of linked polymorphisms are
called haplotypes, whereby each haplotype is, in essence, a distinct genetic variant of
the gene. They found that they could further break the haplotypes down into related
variants called haplogroups. Their analysis indicated that for each of the two genes, one
haplogroup occurs at a frequency far higher than that expected by chance, indicating
that natural selection has driven up the frequency of the haplogroup. They referred to
the high-frequency haplogroup as haplogroup D.

When the researchers compared the ethnic groups in their sample for haplogroup
D of ASPM, they found that it occurs more frequently in European and related
populations, including Iberians, Basques, Russians, North Africans, Middle
Easterners and South Asians. That haplogroup was found at a lower incidence in
East Asians, sub-Saharan Africans and New World Indians. For Microcephalin,
the researchers found that haplogroup D is more abundant in populations outside
of Africa than in populations from sub-Saharan Africa.

Selective pressures on brain genes continued after humans migrated from Africa. The
size of those selective pressures was not the same in populations that moved to various
different parts of the world. Natural selection did not stop operating on brain genes once
humanity developed into distinct races. The implications of this result are profound.

The ASPM haplogroup D spread started perhaps about 5,800 years ago (and that
is an estimate around some range) and its emergence coincided with the spread of
agriculture and the emergence of culturally modern humans!

To produce more informative statistical data on the frequency of haplotype D among

population groups, the researchers applied their methods to a larger population sample
of more than one thousand people. That analysis also showed the same distribution of
haplogroups.

Their statistical analysis indicated that the Microcephalin haplogroup D appeared about
37,000 years ago, and the ASPM haplogroup D appeared about 5,800 years ago - both
well after the emergence of modern humans about 200,000 years ago. “In the case of
Microcephalin, the origin of the new variant coincides with the emergence of culturally
modern humans,” said Lahn. “And the ASPM new variant originated at a time that
coincides with the spread of agriculture, settled cities, and the first record of written
language. So, a major question is whether the coincidence between the genetic
evolution that we see and the cultural evolution of humans was causative, or did they
synergize with each other?”

Lahn said that the geographic origin and circumstances surrounding the spread of the
haplogroups can only be surmised at this point. “One can make guesses, but our study
doesn't reveal how these positively selected variants arrived," he said. "They may have
arisen in Europe or the Middle East and spread more readily east and west due to
human migrations, as opposed to south to Africa because of geographic barriers.
Or, they could have arisen in Africa, and increased in frequency once early
humans migrated out of Africa.”
While the roles of Microcephalin and ASPM in regulating brain size suggest that
the selective pressure on the new variants may relate to cognition, Lahn
emphasized that this possibility remains speculative. “What we can say is that our
findings provide evidence that the human brain, the most important organ that
distinguishes our species, is evolutionarily plastic,” he said. Finding evidence of
selection in two such genes is mutually reinforcing, he pointed out. “Finding this effect
in one gene could be anecdotal, but finding it in two genes would make it a trend. Here
we have two microcephaly genes that show evidence of selection in the evolutionary
history of the human species and that also show evidence of ongoing selection in
humans.”

I've been expecting the left-liberal inequality taboo to die by 2015. But declines in the
cost of DNA sequencing combined with research results such as that reported above
make me more optimistic. The taboo might have only about 5 more years to run.
Also see my previous posts "Many Genes Changed To Make Human Ancestors
Progressively Smarter", "Researchers Find Key Gene For Evolution Of Human
Intelligence", "Human Brain Size Regulating Gene To Be Inserted Into Mice", and
"Genetic Causes Of Infidelity Found In Twins Study".

Update: Nicholas Wade of the New York Times provides more details on the frequency
of each allele in different human populations.

They report that with microcephalin, a new allele arose about 37,000 years ago,
although it could have appeared as early as 60,000 or as late as 14,000 years ago. Some
70 percent or more of people in most European and East Asian populations carry
this allele of the gene, as do 100 percent of those in three South American Indian
populations, but the allele is much rarer in most sub-Saharan Africans.

With the other gene, ASPM, a new allele emerged some time between 14,100 and 500
years ago, the researchers favoring a mid-way date of 5,800 years. The allele has
attained a frequency of about 50 percent in populations of the Middle East and
Europe, is less common in East Asia, and found at low frequency in some sub-
Saharan Africa peoples.

The handwriting is on the wall. The evidence about human genetic differences in
cognition found in psychometric research increasingly is getting buttressed by results
from biological research. The discovery of more alleles that affect cognitive ability
combined with DNA sequence comparisons will, within a few years time, lead to the
collapse of the most damaging myth of our era.