Did human IQ rise because of hybridization with the Neanderthal man?

Europeans and East Asians have statistically larger brains and higher measured IQ than sub-Sahara Africans. They also have Neanderthal mixture. It is not a new idea to suggest that the bigger brain was a result of an ingression of some alleles from the Neanderthal, but such theories have not found support from scientific studies. All non-African populations have Neanderthal mixture, but not all have equally high measured IQs. This fact can maybe be partially explained by mixture with Denisovas and early hominids (maybe with East Asian Homo Erectus) and by later migrations from Africa, but the inability of scientists in finding possible IQ-raising alleles that could have come from Neanderthals is a problem to such theories. Yet, there are some reasons to investigate this idea further.

Rather than raising IQ, Neanderthal genes in humans seem to influence skin, hair and the immune system. Earlier studies have shown that Neanderthals and modern humans had different genes for red hair, that modern Caucasians got their light skin relatively recently from South-Siberia or Caucasian invaders, that Early European Hunter Gatherers (Cro-Magnons) had dark skins but blue eyes, and that Caucasian and East Asian light skin color is caused by different genes. Based on these results it seemed that mixture with the Neanderthal man cannot be connected with the light skin color or red/blond hair, but later studies have found that mixture with the Neanderthal man did provide humans with new alleles, which later mutated to the present ones determining skin and hair color.

An interesting finding by Michael Danneman and Janet Kelso in [1] was that Brits with red hair color have least often a Neanderthal allele for hair color genes. This confirms the earlier result that red hair color of humans is indeed not by genes that are inherited from the Neanderthal man. Indeed, red haired Neanderthals were a minority. Black haired Brits had slightly more Neanderthal alleles than blonds. Those, who have dark olive skin and who never tan in sun had a bit more often Neanderthal alleles than those, who tan easily and have very light complexion. The Neanderthal allele causing inability to tan in sun was present in 66% of Europeans. With skin color, both blonds and darker skin Brits had often Neanderthal alleles, but in different genes. This seems to indicate that Neanderthals had variable skin colors and the same was true with hair colors. These researchers found four behavior types affected by Neanderthal gene: chronotype (morning/evening person), loneliness/isolation, frequency of disinterest and smoking status.

In this post I will investigate the possibility that the higher genetic IQ of East Asians and Caucasians compared with Sub-Saharan Africans has originated from mixture with the Neanderthal man. Let me explain why I consider this possibility. It is a minority view. The politically correct IQ researchers still deny the genetic basis of IQ, but even race realists, like late Henry Harpending or Richard Lynn, prefer to think that human populations have evolved by natural selection since the departure from Africa some 80.000 years ago and the largest changes have been since the start of agriculture 10.000 years ago. This position is very logical: after the invention of agriculture, human population grew fast and most Caucasians, the same with other agricultural populations, have lived after the start of agriculture. The same is true in East Asia. The fact that the same is true also for South Asians, whose measured IQ is not as high, does not present major problems, since one can explain the increase of IQ by colder weather or any of the four other main theories, none suggesting Neanderthal mixture as the cause.

The oldest Cro-Magnon, or Western European Hunter Gatherer (WHG) skulls are 37,000 years old. Non-African humans diverged maybe 50,000 years ago. One can estimate how many humans have lived in Europe between 50,000 ybp (years before present= and 37,000 ybp. It is about 40 times less than how many have lived in Europe from 37,000 ybp to the present time. More new mutations are created in larger populations. Therefore almost all of the development must have happened after 37.000 ybp rather than in the time from 50.000 ybp to 37.000 ybp. If European IQ had risen because of random mutations and natural selection, we would expect that modern Europeans must have much higher IQ than Cro-Magnon, but this does not agree with the cranial capacity of WHG, which is larger, not smaller, than that of present day Europeans.

The oldest known Cro-Magnon skulls have cranial capacities about 1600 cc. According an old rule of thumb from Deniker, the brain weight in grams is about 0.87 times the cranial capacity in cc, so the brain of Cro-Magnon weighted about 1392 g. In 50.000 ybp Europeans and aboriginal Australians and other non-African populations were the same population with the same IQ. As aboriginal Australian today have a measured IQ of 61 and because of a small population size cannot have had many IQ increasing mutations, the IQ of Europeans in 50.000 ybp most probably was about 60. Aboriginal Australians have much smaller brain size that Cro-Magnons, 1199 g versus estimated 1392 g. The bigger brained Cro-Magnons probably were more intelligent.

Or were they? There is a positive correlation between brain size and IQ, but Cro-Magnons had archaic skulls, they could have been less intelligent than modern people despite having a large brain. But let us initially assume that they were indeed as intelligent as what the brain size indicates. The Cro-Magnon cranial capacity is only slightly higher than that of Eskimos (1588 cc) and Eskimos have average IQ of 91. Eskimo cranial capacity is larger than the European average, but not larger than in Northern Europe, where people also have large heads. Estimating from the cranial capacity difference, we get 96 as the IQ of Cro-Magnon people. The problem is how from 50.000 ybp to 37.000 ybp the European IQ grew from 60 to 96 and from 37.000 ybp to the present time only from 96 to 100. The reason is not mixture, since Northern Europeans have mainly descended from WHG and Eastern European Hunter Gatherer (EHG), which had a similar cranial capacity as WHG.

The problem is actually worse than that. We must assume that if IQ increased because of random mutations and natural selection, it still grew from 37.000 ybp to 15.000 ybp, when the environment changed and the population started growing. Estimating in a linear way, Cro-Magnons would have reached the IQ of 154 in 15.000 ybp and after that IQ has been dropping to 100. This does not sound reasonable. Indeed, there must be some mechanism, which limits human IQ, because modern human populations differ quite little in IQ. No population with IQ anywhere near to 154 has survived, ipso, there never existed such smart populations. Something must be wrong with the assumptions.

One possibility is that Cro-Magnons were not so intelligent, but why did they have so large cranial capacities? The other possibility is that it is incorrect to assume that from 50.000 ybp to 37.000 ybp the main reason for the increase of the brain, and consequent increase of IQ, was random mutations and natural selection. It could have been caused by a mechanism, which once was and then stopped, such as hybridization with the Neanderthal man. The Neanderthal man had cranial capacity of about 1500 cc, comparable with modern Europeans, and the species become extinct 30.000 years ago. There are only few Neanderthal genes in human brains, but some Neanderthal genes influence behavioral traits as [1] showed.

I could not find any scientific article, which investigated the problem of whether Neanderthal mixture could be the cause of the larger brain in Cro-Magnons, I found only less formal suggestions to this theory, but there are studies of genes which influence the brain size. The problem with these studies is that many genes have been suggested and later other studies reject them.

Humans have certain duplicated genes, which are believed to have made the human brains larger than those of hominids: SRGAP2A, SRGAP2B, SRGAP2C, SRGAP2D. That is, humans have four not identical copies of the SRGAP2 gene in chromosome 1. These duplicates may have given humans the language capabilities. The last duplicate, SRGAP2D, emerged about 1 million years ago.

There are four known genes that regulate the brain size and can cause microcephaly (a condition where the brain is exceptionally small): MCPH1, CDK5RAP2, CENPJ, and ASPM. A new ASPM allele was born maybe 5,800 ybp and it made a selective sweep in Europe, also in New Guinea: about half of Europeans and 58% of New Guineans have this gene. About half penetration points out towards the case that heterozygotes, those with one new and one ancestral allele of ASPM, have some selective advantage. It has been tested that the new allele does not raise IQ, so the selective advantage is something else. The new ASPM allele is missing from China, but instead it has been found that Chinese have a new DAB1 allele. This allele has some cognitive relevance and it may have a similar evolutionary advantage as the new ASPM allele elsewhere.

Not only ASP, but also CDK5RAP2, CENPJ and MCPH1 had a rapid evolution under strong positive selection. MCPH1 is only in females, CDK5RAP2 is only in males. A new allele, D haplotype, of MCPH1 is rare in sub-Saharan Africa. The allele appeared some 37,000 ybp and initially it seemed to be strongly correlated with IQ, but this hope died when a new study was published. Nowadays it is thought that the allele does not increase IQ, but may boost the immunology system, which may raise IQ by fighting viral illnesses. While geneticist Bruce Lahn is said to have suggested that Neanderthals gave Eurasians a gene on MCPH1 for larger and more developed brains, so far decoded Neanderthal genomes did not have MCPH1 D haplotype.

According to [2] the genes ASPM, CDK5RAP2, BRCA1, MCPH1 are not associated with general cognition, reading or language, and that they have long time ago reached stabilizing selection meaning that they are not becoming more common. The list contains three of the first four genes causing microcephaly.

Article [2] does not mention CENPJ, but we can assume that also the spreading of CENPJ is stabilized and the gene is not associated with cognitive improvements. The article mentions a brain size regulating gene, BRC1, which according to the study also does not cause cognitive improvements. The BRCA1 gene is the breast cancer susceptibility gene: some alleles of BRCA1 can cause breast and ovarian cancer. The association of BRCA1 with the brain size is so far supported by mice studies only. Some alleles of BRCA1 lead to death of mice by destroying their brains. Ashkenazi Jewish population has a higher rate of breast cancer caused by mutations in the BRCA1, notably 185delAG, or in the BRCA2 gene. There is a theory that higher Ashkenazi Jewish IQ would be caused by genetic disease genes such as the sphingolipid pathway genes, but this theory has not been verified. The more natural explanation for Ashkenazi intelligence is selective immigration to the USA, England and Canada. There is no reason to expect that humans would have got IQ-raising allele of the BRCA1 gene from Neanderthals, or that it would be responsible for IQ differences.

There many more genes implicated in the development of microcephaly: WDR62, CEP152, STIL, CEP135, ZNF335, PHC1, CDK6, TRMT10A and CASC5. With the exception of CASC5 they have not been positively strongly selected and consequently they are poor candidate genes for new IQ-raisin alleles that possibly were obtained from Neanderthals.

East Asians have more mutations in CASC5 that Europeans or Africans and it has been proposed as the reason why East Asians have in average larger brains than Europeans. Indeed, some alleles of this gene seem to cause larger amount of grey material in the brain. Apparently CASC5 is human specific. Neanderthals or Denisovas did not have the gene and humans could not have obtained new alleles by breeding with them. There is some 40.000 years for East Asians to have created new alleles of this gene and as a result have maybe 40 g heavier brains that Europeans and some 5 IQ points higher intelligence.

There are some other genes, which have been linked to brain size: HARE5, Beta-catein, IL3 and KATNB1 but none of them seems suitable for our purposes. They probably were important earlier in the growth of the brain of hominids. KATNB1 determines the brain size of fish.

This leaves us with only two newly found genes regulating brain size: ARHGAP11B and CASC5. Could humans have obtained new alleles of these genes from breeding with Neanderthals or Denisovas? ARHGAP11B increases the number of stem cells specific to the neocortex. This gene was present in Neanderthals and Denisovas and is present in all humans. It is also a duplication gene: it is a partial duplication of a very ancient gene ARHGAP11A. ARHGAP11A partial duplication arose some 5 million years ago creating ARHGAP11B, but the original version of this gene did not increase brain size. This ability developed more recently, but still before humans, Neanderthals and Denisovans separated. If there was gene ingression from Neanderthals to modern humans around 40-30.000 years ago and it caused the human brain to grow, it could have been some Neanderthal alleles of ARHGAP11B.

In addition to genes influencing the brain size, there are also genes, which have been associated with human intelligence. Eupedia lists the following IQ genes ADRB2, CHRM2, DNTBP1, BDNF, SNAP25, FADS2, ANKK1, DISC1, SIRT1 and their IQ-influencing alleles, but [3] says it all already in the title of the paper: “Most reported genetic associations with general intelligence are probably false positives”. At the moment there is the fashion to find IQ genes, more precisely, SNPs, by GWAS studies. [4] gives two tables copied here (without asking for permission, but this is just a blog), one from the 1000 Genomes and the second from ALFRED projects. Apart from Piffer’s nice, but I guess not so well verified, conclusion from 1000 Genomes that Finns have the highest polygenic score in Europe, the characteristic feature is that the first project found 9 IQ-raising SNPs and the second found 7, but only two SNPs are in both lists.

* AFR: African; AMR: American; ASN: Asian; EUR: European; ASW: African ancestry in SW USA;LWK: Luhya, Kenya; YRI: Yoruba, Nigeria; CLM: Colombian; MXL: Mexican ancestry from LA, California; PUR: Puerto Ricans from Puerto Rica; CHB: Han Chinese in Bejing, China; CHS: Southern Han Chinese; JPT: Japanese in Tokyo, Japan; CEU: Utah Residents with Northern and Western European Ancestry; FIN: Finnish in Finland; GBR: British in England and Scotland; IBS: Iberian population in Spain; TSI: Tuscany in Italy.

The top three SNPs from the 1000 Genomes project are: rs932013 A, rs11584700 G, rs4851266 T, but each has a very minor effect on IQ. Another study has found still another IQ-raising gene, HMGA2. C-allele of this gene is linked to a smaller intracranial volume and lower IQ. HMGA2 C lowers IQ by 1.29 points, the largest so far. For homozygotes on the C-allele the drop is 2.6 points. In total, 74 regions influencing IQ have so far been found by these GWAS studies but they explain less than 5% of variation in IQ scores.

Genes involved in many diseases, such as Alzhemer’s disease and schizophrenia have alleles, which have been proposed as influencing IQ. They include APOE, BDNF, CHRM2 and CTSD, but later studies have not confirmed a link to intelligence.

Did we get anywhere by studying IQ-gene research?

Not really. So far I have in this post only restated my earlier observation that there is a problem with the brain size of Cro-Magnon, it grew too fast and then stopped growing, and pointed out that possibly mixture with the Neanderthal could explain it, which I already did in an earlier post. As the only new contribution I suggested that the first gene to check be ARHGAP11B.

No, I have to do better than that. There should be some contribution, why else anybody would care to read these? Let’s think more.

What do we agree?

• Searching for IQ genes has so far found only genes with minor contribution to IQ, but the studies have been extensive. Let us accept the proposal, that there are no genes that directly contribute to IQ in a major or even moderate way. All contributions are small.
• Yet we agree that IQ is largely heritable, 80% by twin studies. This means that the IQs of identical twins are very similar, but it does not necessarily mean that heritable IQ differences between people are caused by very different genetic IQs. That is, there are other traits identical twins have in common, like behavior patters, such as reading books, not giving up easily, being curious, and so on. They can have genetic basis and they may contribute to the twins developing higher or lower IQ than other people in the population. Still the direct genetic differences in IQ may be much smaller than the observed differences. That is, if we close all these people in the cellar for from the birth to 25 years, how much will their IQs differ? It is not environment which makes the difference, but the internal largely genetic drive how to behave in the environment.
• There are differences in measured IQ between human populations, races, and these differences have genetic basis. The populations have genetic differences. This does not necessarily mean that the inherited IQ differs so much between the populations. It can be that the genetic behavior differences cause that one population develops its intelligence more than another.
• Brain size correlates with IQ. There are also large brain size differences, as in microcephaly. In most of those cases there are also large IQ differences, but not always. 15% of people with microcephaly have normal intelligence. They may also have higher than normal IQ. People with half of their brains removed may have normal intelligence. This means that IQ is not only determined by the brain size. It can mean that loss of brain volume can be compensated by using the brain better.
• There are different races. Some have not mixed with the Neanderthal, while some have mixed with Neanderthal, Denisova and an unknown archaic species, suspected to be East Asian Homo Erectus. They have slightly different brain sizes and IQ.
• East Asians have a bit higher IQ than Europeans. They have slightly larger brains, which can be explained with new alleles of a human only gene CASC5, which has been shown to increase the grey material in the brain.

Summarizing from this, we do not need another explanation for the East Asian – European IQ differences, 6) will do. We also can explain why some Asian people do not have high IQ, they either have mixture with Denisovas (nobody knows what their brain size was) or archaic hominids, or they have been mixed with sub-Saharan Africans, as is the case in the Middle East. We will try to explain the IQ difference to sub-Saharan Africans by the lack of Neanderthal mixture, by gene alleles which increase the brain size. The candidates are MCPH1 D haplotype and some unstudied allele of ARHGAP11B.

Sub-Saharan brain is smaller than European, but has also had time to increase. Let us assume that 50.000 ybp the brain weight was 1199 g as in aboriginal Australians, Europeans and Asians got a boost from Neanderthal around 50.000 ybp by ingression of an allele, which increased the brain size. They bred with Neanderthal and Denisova also, but that did not any more increase their brain size. All populations, European, Asian and sub-Saharan African, had human specific IQ-increasing mutations during the last 50.000 years, but their effect on the brain size was small with the exception of some East Asian alleles of CASC5. Their direct effect on the average IQ was also small.

What is left is how to account for large heritable IQ-differences between individuals inside a population, and for this we will propose that it is not caused by genes, which directly raise IQ, but by genes, which modify behavior so that the individual behaves in a way, which increases IQ. Such ways include studying, thinking, solving problems.

What kind of personality traits could lead an individual to develop his IQ? Introversion is one such trait. It is heritable. Cold weather may have spread genes causing introversion, and humans could have even obtained new alleles from Neanderthals. There are some studies of Neanderthal trains. As mentioned, [1] identified four behavior types affected by Neanderthal gene: chronotype, loneliness/isolation, frequency of disinterest and smoking status. Additionally, the risk of schizophrenia and depression is affected by Neanderthal mixture and it is often stated that autism may have something to do with Neanderthal genes.

There is a theory claiming that early humans, including the Neanderthal man, did not have schizophrenia. The mental illness emerged in humans after the split between humans and the Neanderthal man. Certain loci in the human brain developed differently and as a side effect created schizophrenia. In these loci there is large difference between human and Neanderthal gene expression. Normally, what would be expected is that a very different gene from another species would not work. We would expect that if a human inherits a Neanderthal gene from one parent and a human gene from the other parent, the Neanderthal gene cannot be expressed. If so, then a single modified human gene can create a phenotype trait, which would be masked by a normal human gene in individuals with two human genes. This is the case with many Neanderthal genes, but not with the schizophrenia gene. There is a special gene, ADAMTSL3. The Neanderthal allele does code proteins in humans and codes them differently than the human allele. The Neanderthal allele offers some protection to schizophrenia and increases the height.

The effect of Neanderthal mixture in schizophrenia cannot be verified simply by comparing the incidence of schizophrenia in sub-Saharan Africans, Caucasians and East Asians because there are many environmental causes contributing to this illness. Statistics shows contradictory results. On one hand, mortality from schizophrenia in East Asia, Southeast Asia and Oceania is 0.5 per 100.000, in Caucasian countries 0.2 and in Sub-Saharan Africa 0.1, which may support the Neanderthal hypothesis, but on the other hand people in UK of African-Caribbean origin have nearly four times higher incidences of schizophrenia than the rest of the population, mostly Whites. Yet other studies have found the life-time incidence of schizophrenia in sub-Saharan Africans to be 4.7/1000, which is similar to the rate in developing countries and on the upper range of developed countries. Refugees in Sweden were found to have four times higher schizophrenia rate than Swedes, most probably indicating traumatic experiences. Environmental effects mask the possible differences in genetic risk.

There is a popular, but not scientifically verified, theory that autistic spectrum diseases could be caused by Neanderthal mixture. Also with autism spectrum diseases, statistics shows contradictory results for ethnic differences in the rates of the disorders. In the USA autism spectrum diseases are according to one study most often diagnosed in White, then in Hispanic and least often in Black children, but other studies show that autism with intellectual disability affects most Black, then Hispanic and then White. For autism spectrum diseases to be connected with Neanderthal mixture, we would expect them to be still more common in East Asians. In one study Japan indeed had the highest incidence of autism, followed by Northern European countries and Canada, but the results can be better explained by autism being more common in developed countries, probably because it is more often diagnosed. Again, no clear connection to Neanderthal mixture can be detected from statistics.

I did not find any gene study connecting autistic spectrum diseases to Neanderthal genes in humans. The theory seems to be only speculation. It is natural to think that e.g. eidetic memory would be a trait inherited from another species with a very different way of thinking, but no proof can be offered.

Let us forget schizophrenia and autism, but introversion and maybe some other personality traits may be factors in higher intelligence. Gene mutations for personality are largely responsible for IQ differences inside a population, while the genetic IQ differences caused by IQ-genes are rather small, explaining only less than 5 % of variation in IQ scores.

These alleles of personality genes were human, not obtained from Neanderthals, since there is a range of IQs in all populations, although we do not know if variation of IQ scores actually is the same in all populations. The standard deviation is fixed to be the same in all populations, but there is little reliable data to say if it actually is the same.

Why then, if these personality traits were present in all human populations, some populations developed higher IQs? It may be so that natural selection preferred introversion and maybe intuition in colder climates and therefore personality distributions become different in different areas. Personality distributions are different.

So let us say, I cannot today create a better theory. This contribution has to do. Of course some people say that introversion is not associated with higher IQ, but East-Asians are more introvert and very high IQ people are considerably more introvert, so it depends. One can look for some other mental factors that humans may have inherited from other hominids, so far I only could find those four traits.

 

References:

[1] Michael Dannemann and Janet Kelso, The Contribution of Neanderthals to Phenotypic Variation in Modern Humans, http://www.cell.com/ajhg/pdf/S0002-9297(17)30379-8.pdf

[2] Timothy C. Bates et al., “Recently-derived variants of brain-size genes ASPM, MCPH1, CDK5RAP and BRCA1 not associated with general cognition, reading or language’, http://www.sciencedirect.com/science/article/pii/S0160289608000421

[3] CF. Chabris et al.: “Most reported genetic associations with general intelligence are probably false positives”. Psychol Sci. 2012.

https://www.ncbi.nlm.nih.gov/pubmed/23012269

[4] Davide Piffer: Factor Analysis of Population Allele Frequencies as a Simple, Novel Method of Detecting Signals of Recent Polygenic Selection: The Example of Educational Attainment and IQ. https://lesacreduprintemps19.files.wordpress.com/2014/01/factor-analysis-of-population-allele-frequencies-as-a-simple-novel-method-of-detecting-signals-of-recent-polygenic-selection-copy.pdf