Posted: Wed 06 Dec 2006 11:07 Post subject: Potential "Smart" gene in Eurasians rare in Africans?
Would probably be the ghastly subtext of Dr. Bruce T. Lahn's headlining research published a month ago..
Quote:
Could Interbreeding Between Humans and Neanderthals Have Led to an Enhanced Human Brain?
Might mating between an ancient human and a Neanderthal - perhaps occurring in only a single instance - have introduced a gene variant into the human population that enhanced human brain function? That question is at the heart of a new study by researchers at the Howard Hughes Medical Institute and the University of Chicago.
The new research, which was published online during the week of November 6, 2006, in the early edition of the Proceedings of the National Academy of Sciences (PNAS), suggests that human evolution was not just a matter of spontaneous advantageous mutations arising within the human lineage. Human evolution may also have been influenced by interbreeding with other Homo species, which introduced gene variants, known as alleles, that are beneficial to human reproductive fitness, said the study's senior author Bruce T. Lahn, a Howard Hughes Medical Institute researcher at the University of Chicago.
The scientists said they have developed the most robust genetic evidence to date that suggests humans and Neanderthals interbred when they existed together thousands of years ago. The interbreeding hypothesis contrasts with at least one prominent theory that posits that no interbreeding occurred when the two species encountered one another.
Lahn collaborated on the studies with Patrick D. Evans, Nitzan Mekel-Bobrov, Eric J. Vallender and Richard R. Hudson, all of the University of Chicago.
In their studies, Lahn and his colleagues performed a detailed statistical analysis of the DNA sequence structure of the gene microcephalin, which is known to play a role in regulating brain size in humans. Mutations in the human gene cause development of a much smaller brain, a condition called microcephaly.
Earlier studies by Lahn's group yielded evidence that the microcephalin gene has two distinct classes of alleles. One class, called the D alleles, is comprised of a group of alleles with rather similar DNA sequences. The other class is called the non-D alleles. Lahn and colleagues previously showed that all modern copies of the D alleles arose from a single progenitor copy about 37,000 years ago, which then increased in frequency rapidly and are now present in about 70 percent of the world's population. This rapid rise in frequency indicates that the D alleles underwent positive selection in the recent history of humans. This means that these alleles conferred a fitness advantage on those who possessed one of them such that these people had slightly higher reproductive success than people who didn't possess the alleles, said Lahn.
The estimate that all modern copies of the D alleles descended from a single progenitor copy about 37,000 years ago is based on the measurement of sequence difference between different copies of the D alleles. As a copy of a gene is passed from one generation to the next, mutations are introduced at a steady rate, such that a certain number of generations later, the descendent copies of the gene would on average vary from one another in DNA sequence by a certain amount. The greater the number of the generations, the more DNA sequence difference there would be between two descendent copies, said Lahn. The amount of sequence difference between different copies of a gene can therefore be used to estimate the amount of evolutionary time that has elapsed since the two copies descended from their common progenitor.
In the new studies reported in PNAS, the researchers performed detailed sequence comparisons between the D alleles and the non-D alleles of microcephalin. The scientists determined that these two classes of alleles have likely evolved in two separate lineages for about 1.1 million years — with the non-D alleles having evolved in the Homo sapiens lineage and the D alleles having evolved in an archaic, and now extinct, Homo lineage. Then, about 37,000 years ago, a copy of the D allele crossed from the archaic Homo lineage into humans, possibly by interbreeding between members of the two populations. This copy subsequently spread in humans from a single copy when it first crossed into humans to an allele that is now present in an estimated 70 percent of the population worldwide today.
The estimate of 1.1 million years that separates the two lineages is based on the amount of sequence difference between the D and the non-D alleles. Although the identity of this archaic Homo lineage is yet to be determined, the researchers argue that a likely candidate is the Neanderthals. The 1.1 million year separation between humans and this archaic Homo species is roughly consistent with previous estimates of the amount of evolutionary time separating the Homo sapiens lineage and the Neanderthal lineage, said Lahn. Furthermore, the time of introgression of the D allele into humans — about 37,000 years ago — is when humans and Neanderthals coexisted in many parts of the world.
Lahn said the group's data suggest that the interbreeding was unlikely to be a thorough genetic mixing, but rather a rare - and perhaps even a single — event that introduced the ancestral D allele previously present in this other Homo species into the human line.
“By no means do these findings constitute definitive proof that a Neanderthal was the source of the original copy of the D allele,” said Lahn. “However, our evidence shows that it is one of the best candidates. The timeline - including the introgression of the allele into humans 37,000 years ago and its origin in a lineage that separated with the human line 1.1 million years ago — agrees with the contact between, and the evolutionary history of, Neanderthals and humans.
“And a third line of evidence, albeit weaker, is that the D alleles are much more prevalent in Eurasia and lower in sub-Saharan Africa, which is consistent with an origin in the former area. And we know that Neanderthals evolved outside of Africa,” said Lahn.
Lahn also said that although the disruption of the microcephalin gene in humans leads to smaller brains, the role of the D alleles in brain evolution remains unknown. “The D alleles may not even change brain size; they may only make the brain a bit more efficient if it indeed affects brain function,” he said. “For example, someone inheriting the D allele may have only a slightly more efficient brain on average. While that enhancement might confer only a subtle evolutionary advantage on that person, when that effect is propagated over a thousand generations of natural selection, the result will be to drive the D alleles to a very high prevalence.”
Lahn and his colleagues believe that other genes might well show similar telltale signs of an origin in archaic Homo lineages such as Neanderthals. They are currently using their analytical tool to search for evidence of that origin for other genes in the human genome.
Such findings may have broader implications for understanding human evolution than just revealing the possibility of human-Neanderthal interbreeding, he said. “In addition to being perhaps the most robust genetic evidence for introgression of genes from archaic Homo species into humans, I think this finding demonstrates that the evolution of our species has been profoundly impacted by gene flow from our relative species,” said Lahn.
“Finding evidence of mixing is not all that surprising. But our study demonstrates the possibility that interbreeding contributed advantageous variants into the human gene pool that subsequently spread. This implies that the evolution of human biology has been affected by the contribution of advantageous genetic variants from archaic relatives that we have replaced or even killed off,” he said.
Until now, said Lahn, the scientific debate over genetic exchange between humans and other Homo species has led to two prominent competing theories. One holds that anatomically modern humans replaced archaic species, with no interbreeding. And the other states that extensive interbreeding did take place and that modern humans evolved from that interbreeding in many regions of the world.
Genetic and fossil evidence for the latter “multiregional” theory has been inconclusive, said Lahn, so that theory has been largely discredited. However, he said, the newer evidence of gene exchange — as well as other genetic evidence that might follow — could give rise to a more moderate version holding that some genetic exchange did take place. Furthermore, it will become increasingly appreciated that such genetic exchange might have made our species much more fit.
Bruce Lahn Courts More Controversy
November 13, 2006
This past summer, Bruce Lahn, a human geneticist at the University of Chicago announced that he was abandoning his research on ancient DNA and human intelligence. He had reported findings in September of 2005 that suggested there had been recent evolution in the brains of people native to Europe, Asia and Americas. Unfortunately, he did not have evidence that the brain of Sub-Saharan Africans had undergone the same transition. He effectively stumbled into the same hole that the authors of The Bell Curve had dug over a decade before--the very same ditch also held the decaying career of one Lawrence Summers, now the ex-president of Harvard.
Identity politics don't mix with intelligence research.
Lahn is notably somewhat more cautious this time around. In one article he mentioned haplogroup D may simply make it easier for childbirth. However, if I remember correctly, when he first announced his findings on the brain genes he correlated certain allele emergence with the emergence of "cave art" and other specific supposed cultural earmarks of advanced civilization -- clearly indicating his thoughts on the adaptive role the allele played in the technological development of some populations.
Sounds like Eugenicist hogwash. If this intelligence thing were true then Neanderthals would have had to have been All over Asia. They were only found in Europe and the Near East.
Sounds like Eugenicist hogwash. If this intelligence thing were true then Neanderthals would have had to have been All over Asia. They were only found in Europe and the Near East.
I agree, although I would quibble with the usage of "Eugenicist."
The fact is that Europe was inaccessible when our species (H. sapiens) first appeared in Africa. It was geographically isolated by thousands of miles of desert. Hence, H. neanderthalensis had a good 400 ky to adapt to their environment. Then, when the climate changed 35-40 kya and Europe again became reachable, our species moved into Europe. Despite that fact that we were (and still are) strongly adapted to tropical steppes and patchy forests (and strongly maladapted to Europe's subarctic climate of the era), the Neandertals went extinct within 10 ky of our arrival.
It is hard to define "intelligence" objectively. But any definition that includes the tendency, after 400 ky of adaptation, to become extinct immediately upon being placed into competition with a maladapted newcomer species seems fishy to me.
Still, I would dearly love to read the original study (not the garbled newspaper accounts). Does anyone have a link to it?
Doesn't seem that Neanderthal lost to a maladapted newcomer, but that the change in environment and loss of forests were better suited for the newcomers.
the change in environment and loss of forests were better suited for the newcomers.
I think that the linked-to article conflates two issues. First, the neandertal adaptation to cold (versus our adaptation to tropics) and loss of their favored habitat consequent to the ending of the ice ages. Second, their inability to adapt to rapid climate change.
The first is a non-issue. The peak of the last ice-age was 16 kya, about 10-15 kya after the neandertals became extinct. We thrived as the glaciers peaked. The neandertals had all died long before the climate reached its coldest level.
The second is accurate. The climate did not get gradually colder until the peak 16kya and then get warm again. Instead, the Pleistocene in Europe (and everywhere else) was a period of rapid and dramatic climate change. Several decades of glaciers followed by several decades of broiling desert followed by several decades of humid tropics followed by several decades of glaciers again in rapid succession, over and over. Forests, steppes, deserts and swamps came and went many times. It was during this period, when a phenomenal ability to react and change your lifestyle virtually overnight was the only guarantee of survival, that neandertal became extinct and we conquered the planet.
Let me again thank JamalFSU for providing the original of this report. I shall publish my own comments in a few days. For now, I want to take advantage of the article as a test/demonstration of the critical thinking associated with science-as-process.
Specifically, I ask everyone reading these words to: (1) Read the message titled Introduction to Science-As-Process in the "Anti-Racialism FAQs" forum. Especially read the three paragraphs dealing with conclusions versus findings. (2) Apply the message's advice to the article in question.
Here are some definitions for those of you who need help with the jargon.
Alleles, haplotypes, haplogroups -- The microcephalin gene (which if broken causes a lethal failure of the brain to develop) comes in several fully functioning variants (alleles, haplotypes) in normal people. One group (haplogroup) of variants, called "non-D," appeared in 54 of the 178 chromosomes tested. The other group of variants, called "D," appeared in 124 of the 178 chromosomes tested.
Coalescence -- The non-D variants have a wide range of internal mini-variation (long coalescence) consistent with an age of 900-1200 kya. The D variants, which appeared in 124 of the 178 chromosomes tested, are so different from non-D and yet so similar to each other (short coalescence) that they either came into our species from recent (37-530 kya) hybridization with another species, or they have co-existed side-by-side with non-D within our lineage's DNA for 1100 kya or more.
Frequency -- If the remarkably homogenous (indicating an age of 37-530 kya) D variant was found in just one or two percent of the population, it would have been shrugged off as just one more oddity in our DNA. But it appeared in most of the chromosomes tested. This leads to two questions. If "D" came from recent (37-530 kya) hybridization with another species, it must have spread like wildfire through our species. This means that it must be adaptive in some way. But if it has been in our species all along, then why does it show so little internal variation?
Balancing -- The most common mechanism whereby a gene variant can exist indefinitely in a stable form side-by-side with another variant is if individuals who have one copy of each variant (heterozygotes) are better adapted than those who have both of either (homozygotes). Such "balancing selection" is very common in our species, and hundreds of such cases are known. The one most frequently discussed here in OneDropRule is the HbS hemoglobin variant. Those with two original hemoglobin genes die of malaria. Those with two HbS die of sickle-cell. Those with one of each flourish in mosquito-infested settlements.
Isolation, bottleneck, rejoining -- The second most common mechanism whereby a gene variant can exist indefinitely in a stable form side-by-side with another variant is if each of the variants became prevalent within two isolated populations. It is well known that when a population becomes isolated its genome gradually "drifts" to diverge from its parent population. If the isolated population then goes through a near-extinction, the reduction in number of individuals wipes out most variants of every gene. This produces an artificially short coalescence and gives the illusion that the variant is recent when, in fact, it is ancient but is simply the only survivor from among many sibling variants. When the isolated population then rejoins the mainstream, its variant looks strangely different and yet of recent origin. But this is not due to hybridization with another species, but simply to a rejoining of a population once isolated by, say, several ky of glaciers or deserts.
Armed with the above explanation of the jargon, you should now try to list each of the conclusions implied by the report's abstract regarding advantageous gene variants, neandertals, intelligence, and so forth. Then, you should try to list each of the raw data findings reported by the study. From which specific neandertal fossil specimen was DNA extracted? How was the D variant's adaptive benefit identified and measured? How was its benefit shown to relate to intelligence? Precisely what was the measured difference in distribution of D in Eurasia versus sub-Saharan Africa? Finally, you should compare the findings with the conclusions to see how smoothly the latter springs from the former.
This is merely an exercise and it will not be graded <grin>. I just thought it would be a fun way to demonstrate science-as-process. I will post my own remarks in a few days to give y'all a chance to post your own observations.
The goal of the report was evidently to falsify the current consensus hypothesis that H. sapiens was not interfertile with H. neanderthalensis. The report implies that mating between H. sapiens and H. neanderthalensis introduced a gene variant into the sapiens population that enhanced human brain function.
The eight elements of this conclusion are:
1. Most H. sapiens DNA today has variant D.
2. D has little internal variation.
3. D is adaptively beneficial.
4. D enhances brain function.
5. H. neanderthalensis DNA also had D
6. H. sapiens lacked D before 37 kya.
7. H. sapiens met H. neanderthalensis around 37 kya.
8. D is rare outside of the habitat range of H. neanderthalensis.
Let us see how each element of the conclusion is supported by a finding.
1. Most H. sapiens DNA today has D. -- True. This fact was shown in the findings.
2. D has little internal variation. -- True. This fact was shown in the findings.
3. D is adaptively beneficial. -- False. No finding showed this. This conclusion was solely based on points 1 and 2. There are other likely explanations for the short coalescence of D. The two most obvious are balancing and isolation.
4. D enhances brain function. -- False. No finding showed this. This conclusion was based solely on D being found within a gene which, when broken, prevents normal brain development. But no difference in brain function has ever been found between D and non-D.
5. H. neanderthalensis DNA also contained D. -- False. No neandertal DNA was ever tested, much less any D found in it. As the third paragraph of the right column of page 5 admits: "It would be of great interest to sequence the microcephalin locus in Neanderthals...."
6. H. sapiens lacked D before 37 kya. -- False. No finding showed this. According to the findings, the computed age of D (based on its lack of internal variation, and assuming no balancing nor isolation) falls WITHIN A RANGE of 37 kya to 530 kya. Taking the range's midpoint means that, even if D came into our lineage from another species, it came long before H. sapiens first appeared in Africa.
7. H. sapiens met H. neanderthalensis around 37 kya. -- True. No finding in the report showed this, but it is a well-known fact.
8. D is rare outside of the habitat range of H. neanderthalensis. -- False. No finding showed this. Indeed, no data on relative phylogeography of D was presented. It was just a bald assertion. Nevertheless, the strange dichotomous wording of the assertion ("Eurasia" versus "sub-Saharan Africa") makes one suspect that D is prevalent in the Far East. This is far outside the neandertal’s range, and so if it came from post-Diaspora inter-species mating, it must have come from H. erectus.
Let us summarize. Only two findings were presented: (1) D is prevalent and (2) D has little internal variation. This means (assuming no balancing nor isolation) that D first appeared sometime between 530 kya (long before our species was born) and 37 ky (when we were had left Africa and were colonizing the planet). That is all. Nothing about intelligence. Nothing about neandertals.
The first thing I noticed about the article was the misspelling of Homo neanderthalensis (correct) as Homo neanderthalis (incorrect); a silly goof that proofreaders should have caught. The second thing was wonderment at how PNAS could have accepted such a report. It is merely a set of assertions unsupported by the report's own findings. One fact explains both oddities.
The PNAS editorial board is a conservative group of established scholars who tend to prefer confirmation of previous knowledge to ground-breaking discoveries. Until a few decades ago, neandertal was thought to be a subspecies of H. sapiens, and the ancestor of the Caucasoid "race." Similarly, it was thought that each of the other modern "races" (Mongoloid, Congoid, Capoid, Australoid) also descended from its own ancient subspecies. At that time, neandertal's formal name was Homo sapiens neanderthalis. But when modern bio-races were discarded and neandertal found to be a distinct species, it received its present name, Homo neanderthalensis. The suffix changed, indicating species rather than bio-race.
I believe that the misspelling was a freudian slip, recalling the days when neandertal was seen as the brainy ancestor of White folks only. Similarly, the article's tissue of unsubstantiated conclusions passed review because it reaffirmed beliefs that were taught many years ago. Perhaps Jaime was right. "Eugenicist hogwash" may well be the best description.
Joined: 05 Apr 2006 {Posts: 300 } Location: Chatsworth, CA
Posted: Wed 13 Dec 2006 05:46 Post subject:
I read some stories on Lahn's research earlier this year. The impression the stories gave was that Lahn had found a gene that caused larger brain size, and that this gene was largely absent from sub Saharan Africa, but common in Europe.
Then it was revealed that the gene in question was common among the peoples of New Guinea, but rare among the peoples of China and Japan. Most lay readers, including me, decided the microencephalin-IQ-race linkage was silly at that point.
You've taken this a step further by essentially debunking most of the claims. My understanding is that neo eugenicists like Phillippe Rushton and Steve Sailer are looking for a kind of holy grail of population genetics that will prove once and for all the mental inferiority of peoples of sub saharan ancestry.
From my POV, the theoretical basis of Rushton et al is wrong. They would have us believe that the intelligence provided less survival value in the harsh, widely varied environments of Africa than in other parts of the world.
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