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NEW EVIDENCE FOR THE DECREASE OF THE GENOTYPIC INTELLIGENCE DURING HOLOCENE: A RECENT STUDY OF DAVID HILL

David Hill republished, in 5 june 2017, an extremly interesting revised study in bioRxiv:

In Table 3 page 21, David Hill presents the variance of intelligence and education explained by minor alleles with different frequencies, that demonstrates different genetic architectures for the two complex traits, despite many authors use educational attainment as a proxy for intelligence.

The most interesting fact is that MAF 0.001-0.01 account for 44% of genotypic IQ and only for 33% of genotypic EDU. The MAF 0.001-0.01 have arose between 25,000 and 5,500 years ago (Zwick, 2001). There are much more MAF 0.001-0.01 that decrease than increase IQ and EDU. The very high percentage of variance explained by both of them could indicate a relaxed selection on the two traits since Last Glacial Maximum, and a relatively weaker selection on genotypic IQ than on genotypic EDU. This decrease of the selection parallels the decrease of brain size last 25,000 years (Ruff, 1997).

Another very interesting fact is that MAF 0.1-0.2 account for significantly less variance of IQ than all other MAF. MAF 0.1-0.2 arose between 325,000 and 200,000 years ago (Zwick, 2001), and their uniformly distribution in humans suggests this period was the period with the strongest selection on intelligence in humans. This is the period of emergence of Homo Sapiens. Also, brain size increased at 1450 cmc, larger than today brains. The penultimate place in explaining differences of IQ is occupied by MAF 0.01-0.1 (that arose between 200,000 and 25,000 years ago (Zwick, 2001)) suggesting during this period the selection on intelligence also was strong, and purifying selection uniformised the distribution of these MAF in humans.

Also, these MAF 0.01-0.1 and MAF 0.4-0.5 (that arose between 550,000 and 475,000 years ago (Zwick, 2001)) account for significantly less variance of EDU than all other MAF, suggesting between 200,000 and 25,000 years ago and between 550,000 and 475,000 years ago the selection for EDU was stronger than during other periods. Upper Palaeolithic selection on EDU is in line with the results of Racimo (2017), that found selection in East Asians before Holocene. Also, around 500,000 years ago emerged archaic humans, and brain sizes expanded from 900 cmc to 1300 cmc. Between 200,000 and 25,000 years ago there was strong selection on both EDU and IQ. During this period the brain size of humans peaked at 1600 cmc.

The lower decrease of selection on EDU than on IQ during Holocene could be explained if we admit that there are two types of variants that favor high-EDU: the first are shared variants that favor high-IQ, and the second are variants that favor high (self-)domestication of humans. Many of variants that favor high domestication favor low-IQ too. During Holocene variants that favor high-IQ decreased, and variants that favor low-IQ but high domestication increased. By this way, genotypic IQ decreased more than genotypic EDU during Holocene.

Concerning MAF younger than MAF studied by the article of David Hill, an older paper estimated that 81.4% of the rare protein-altering SNVs found in Americans with European origins originated in the last 5,000 years, and 14.4% of these SNVs are deleterious. 91.2% of the deleterious alleles originated in the last 5,000 years (Fu et al., 2013).

Although, Spain (2015) found fewer rare SNP in exome of people with very high IQ. Also, the IQ of superpopulations in 1000 GENOMES parallel the proportion of individuals that carry uncommon minor SNP (MAF frequency lower than 5%) in genes (Rao, 2017).

Probably future studies of David Hill will produce even stronger proofs for the decrease of genotypic intelligence since Palaeolithic period.

REFERENCES

Fu, W., O’Connor, T.D., Jun, G., Kang, H.M., Abecasis, G., Leal, S.M.,… & Akey, J.M. (2013). Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493: 216-220.

Hill, D.W. et al. (2017) Genomic analysis of family data reveals additional genetic effects on intelligence and personality. bioRxiv http://dx.doi.org/10.1101/106203

Racimo, F. et al (2017) Detecting polygenic adaptation in admixture graphs. bioRxiv doi: http://dx.doi.org/10.1101/146043

Rao, A.R. & Nelson, S.F. (2017) Calculating the statistical significance of rare variants causal for Mendelian and complex disorders. bioRxiv doi: http://dx.doi.org/10.1101/103218

Ruff, C.B., Trinkaus, E. & Holliday, T.V. (1997). Body mass and encephalisation in
Pleistocene Homo. Nature 387: 173-176.

Spain, S.L., Pedroso, I., Kadeva, N., Miller, M.B., Plomin, R. & Simpson, M.A. (2015). A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Molecular Psychiatry 21: 1145-1151.

Zwick, M.E. et al (2001) Genetic Variation Analysis of Neuropsychiatric Traits. in Methods in Genomic Neuroscience Chin, H.R., Moldin, S.O. (editors) CRC Press LLC

 

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THE GENOTYPIC INTELLIGENCE OF EUROPEANS DECREASED SINCE BRONZE AGE (III)

Between the 70 de novo mutations (DNM) 1.4% are in exome, 1% are nonsynonymous and 0.4% are synonymous. For 70 de novo SNP (and 5 de novo indels), an individual will have 75×1.4%=1.05 total de novo mutations in exome, 75×1%=0,75 de novo nonsynonymous mutations, and 0,30 de novo synonymous mutations.
The percentages of nonsynonymous, synonymous and total SNP in exome between total SNP in genome are around: 0.28%, 0,32% and 0,6% respectively (very slightly higher in non-Africans than in Africans), significantly lower than percentages of de novo mutations (1000 GENOMES, 2015). At an accumulation rate of 70 SNP per generation, the oldest SNP of human genome have at least 1.5 millions years.
It means 74% of de novo nonsynonymous mutations, 20% of de novo synonymous mutations and 47% of all de novo mutations in exome were eliminated each generation by natural selection. But it means that at least 47% of de novo mutations in exome (in one DNA base by two!) are deleterious enough to be eliminated by selection. At this strength of selection pressure on exome, only 53% of individuals in each generation could reproduce, and this individuals must have 4 surviving offspring to maintain the actual number of population. Clark & Hamilton (2006) found between 2.2 and 3.2 surviving children for all economic and social classes in pre-Industrial England, and this is far to strength of selection that operated during last 1.5 millions years.
Also, al least 8.2% of the human genome sequence is functionally significant and selectively constrained (Rands, 2014). Hence, each individual will have, on average, 8.2% x 75 =6.1 deleterious DNM.
According with The Omnigenic Theory of Boyle, Li & Pritchard (2017), it means that 35% of people could have one de novo mutation detrimental for intelligence in the exome, because 15,000 genes (75% of all genes) are expressed in the brain. Although, Spain (2015) found fewer rare SNP in exome of people with very high IQ. Also, the IQ of superpopulations in 1000 GENOMES parallel the proportion of individuals that carry uncommon minor SNP (MAF frequency lower than 5%) in genes (Rao, 2017). Furthermore, according to Omnigenic Theory, all humans have 6 IQ-decreasing DMN in non-coding genome. This signify that polygenic score on IQ/EDU must increase to maintain the genotypic IQ/EDU at the actual level, and even POLY IQ/EDU can increase and genotypic IQ/EDU can decrease, despite selection for high-IQ.
During 100 generations, the accumulation of the IQ-decreasing DMN in non-coding genome will be 600 SNP. If the average effect of an IQ-decreasing DMN equates the average effect of an IQ-increased SNP found by GWAS, the POLY IQ must increase with 600 SNP after 100 generations to maintain the actual level of genotypic IQ. If POLY IQ/EDU contains 30,000 SNP, this signifies a 2% increase of POLY IQ/EDU.
Woodley & Piffer (2017) found a 2% increase of POLY EDU during 114 generations, since Bronze Age.
REFERENCES

 

Boyle, E.A. et al (2017) An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell 169(7): 1177-1186 DOI: http://dx.doi.org/10.1016/j.cell.2017.05.038

Clark, G. & Hamilton, G. (2006) Survival of the Richest: The Malthusian Mechanism in Pre-Industrial England. The Journal of Economic History 66(3): 1-30

Rands, C.M. et al (2014) 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage. PLoS Genet 10(7): e1004525. doi:10.1371/journal.pgen.1004525

Rao, A.R. & Nelson, S.F. (2017) Calculating the statistical significance of rare variants causal for Mendelian and complex disorders. bioRxiv doi: http://dx.doi.org/10.1101/103218

Spain, S.L., Pedroso, I., Kadeva, N., Miller, M.B., Plomin, R. & Simpson, M.A. (2015). A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Molecular Psychiatry 21: 1145-1151.

Woodley, M.A. et al. (2017) Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes. bioRxiv http://dx.doi.org/10.1101/109678

 

THE EASTERN ASIAN CRO-MAGNON THAT LIVED DURING THE LAST GLACIAL MAXIMUM WAS THE MOST INTELLIGENT HUMAN

Davide Piffer published the polygenic scores resulted from 15 leading SNP found by the most recent GWAS on intelligence (Sniekers, 2017):  http://rpubs.com/Daxide/279148

These scores suggest no significant increase of the intelligence of Western Eurasians since Out of Africa. Today differences in intelligence between Africans and Europeans are due rather of a higher decrease of intelligence of Africans than Europeans since Out of Africa.

The POLY IQ of super-populations from 1000 GENOMES are: AFR-0.4714, SAS-0.4439, EUR-0.4627, EAS-0.5129, AMR-0.4515.

All of these 15 SNP increase the intelligence of Europeans. It is expected fewer of them increase the intelligence of SAS, even fewer of EAS and the fewest of AFR, because genetic distances and times since divergence between these populations.

We can suppose that in the moment of Out of Africa, the Africans and the future non-Africans have roughly the same polygenic scores on these 15 SNP. We can suppose the polygenic score increase during last 60,000 years in all populations. If non-Africans ancestors are also the ancestors of LWK (today LWK have the lowest polygenic score of today Africans: 0.4567), the increase of the polygenic score in EUR is only 0.01 higher than the increase of LWK during last 60,000 years. But if the ancestors of the non-Africans are not the ancestors of LWK, the frequency of these 15 variants increased more in Africans than in Europeans since the Out of Africa, because all the other today Africans (excepting LWK) have higher polygenic scores than the average of Europeans. Also, the frequency increased more in Africans than in South Asians. This results are in line with polygenic scores on EDU, obtained with the 74 SNP found by the GWAS of Okbay (2016): ASW have the same score with IBS and TSI, and higher score than CEU and GBR. Also, CEU have lower score than all Africans, excepting LWK. (The GWAS on EDU find not only IQ-increasing SNP, but also SNP that favor „domestication”, and these common variants spread due of civilization. For example, peoples that entered faster in Neolithic and complex civilization, like IBS and TSI, have 0.01-0.02 higher scores on EDU-SNP and 0.02 lower scores on IQ-SNP than peoples that had latter entrance in sedentary civilizations, like CEU, GBR, FIN.)

Althought, Racimo (2017) found selection on polygenic score on educational attainment only for EAS, and not for other populations or super-populations of 1000 GENOMES, and this selection in EAS produced before 10,000 years ago. If there was not positive selection on EDU, the genotypic EDU decreased due of the increase of rare variants detrimental to EDU, produced by de novo mutations. It is necessary a positive selection on a complex trait (and an increase of polygenic score) to maintain this trait at the actual level. Hence, the result of Racimo (2017) demonstrates that genotypic EDU decreased in all populations during Holocene, and decreased in all (super)populations excepting EAS between Out of Africa and Holocene. But it is probable there were some periods of selection on EDU in Europeans during last 60,000 years, because all GWAS did not find any common SNP that decreases barely 1 or to 2 IQ points the genotypic EDU, hence the IQ-decreasing SNP did not reach the frequency of common polymorphism in Europeans. The alternation of periods of positive selection and periods of negative selection could explain too the fact, noticed by Piffer (2016), that there are 45% ancestral alleles between IQ-increasing SNP found by the GWAS of Okbay (2016). During periods of selection against high intelligence, IQ-decreasing variants could reach the frequency of common polymorphism. Also, EUR have fewer IQ-increasing ancestral alleles than EAS, and this fact could be due of the spread of IQ-decreasing derived alleles during longer (or stronger) periods of negative selection on IQ in EUR than in EAS.

Although, the selection against high-IQ did not produce only after Industrial Revolution. De la Croix (2017) found Upper class (presumed also the most intelligent social class) had the lowest fertility in pre-industrial England.

It would be very strange a higher increase of the frequency of some neutral alleles in Africans, and a lower increase of the same beneficial alleles in Europeans during 2,000 generations. It is more probable these 15 SNP (and the other IQ-increasing SNP) were under a soft selection in Europeans, and partially in other populations, the most of last 60,000 years. It is more probable too these IQ-increasing common SNP were selected against in all the populations (mostly in Europeans, South Asians and Native Americans) during some periods that favored selection against high-intelligence: Neolithic transition, entrance in complex civilizations and Industrial Revolution. This selection against high intelligence decreased the polygenic scores more in Europeans, South Asians and Amerindians than in Africans, because many of these alleles are not related to intelligence in Africans and are not influenced by the selection against high-IQ. During periods of soft selection for high-IQ, like in European Metal Ages and Medieval Age (Woodley & Piffer, 2017), the polygenic score could increase even if genotypic intelligence remains constant or even decreases, because the detrimental effect of de novo mutations is partially compensated by the increase of polygenic score, and only partially compensated by elimination of deleterious de novo mutations and other rare alleles. The frequency of these common SNP could increase even if the selection on intelligence is zero, due of pleiotropy of some of them, and of selection on other complex traits.

Even if not all these 15 SNP increase the IQ of East Asians, their polygenic score is 0.05 higher than in Europeans. This is in line with all polygenic scores on educational attainment, resulting after the counts of SNP found by the GWAS of Rietveld (2013), Davies (2016) and Okbay (2016). All of these counts found 0.05 higher POLY EDU of East Asians than of Europeans and other Eurasians. Probable many (or even mostly) of the IQ-increasing mutations in linkage with SNP found by different GWAS are older than the divergence of Europeans and East Asians, and these mutations increase the intelligence of both populations. The 0.05 higher polygenic score of all East Asians (in 1000 GENOMES and in ALFRED too) than Europeans demonstrates a strong selection on intelligence of East Asians. It is near zero probability that the same very strong selection pressure operated on Eastern Siberian hunter-gatherers and on Vietnamese and Han farmers during Holocene. It is more probable this high selection on intelligence operated before Holocene, before the separation of different populations of East Asians, but after the split of Native Americans, that have 0.06 lower polygenic score than East Asians, and that diverged from East Asians 23,000 years ago (Raghavan, 2015). Also, Northern East Asians have higher POLY IQ than Southern East Asians, due of the dilution of Northern Han Chinese during Southward migration. But Japanese have the highest POLY IQ of EAS, even higher than Northern Han Chinese, and it means the increase of the strong selection on IQ of East Asians produced before the divergence of Jomons, estimated 22,000-23,000 years ago (Kanazawa-Kiriyama, 2017). The most probable this strong selection on intelligence of East Asians produced during Last Glacial Maximum.

After this high increase of the genotypic intelligence of East Asians, the selection pressure relaxed and probably their intelligence decreased during Holocene, due of warmer climate and of civilizations, mostly by accumulation of IQ-decreasing rare variants.

The Eastern Asian Cro-Magnon living during Last Glacial Maximum had the highest genotypic intelligence of all humans ever living on the Earth.

Finally, I would like to draw attention to some proof, which I find indisputable,
of the superiority of Palaeolithic man to modern man in terms of visual-spatial
intelligence and memory. A study that analyzed how accurately quadrupedal
walking was rendered in 1000 works of art from the Palaeolithic and modern times
found an error rate of 46.2% in Palaeolithic artists, of 83.5% in artists before 1887,
and of 57.9% in artists after 1887, the year when Eadweard Muybridge published
a series of 20,000 photographs investigating the stages of animal locomotion
(Horvath et al., 2012). Furthermore, Cro-Magnons had an error rate even lower
than the rate of those illustrating animal anatomy books, of 63.6%, and they were
very close to the error rate of taxidermists of natural history museums, of 41.1-
43.1% (Horvath et al., 2009).

The loss of (visuo-spatial) intelligence of modern man compared to Paleolithic man should not surprise us. Today, untrained and even trained adult man has a working memory for numbers lower than that of a young trained chimpanzee (Inoue, 2007; Matsuzawa, 2009; Cook, 2010). Also, chimpanzee choice rates in competitive games match equilibrium game theory predictions. Chimpanzee’s choices are close to the equilibrium predictions and are more responsive than human choices to past history and to payoff changes (Martin, 2014). Also, baboons but not modern humans break cognitive set in a visuo-motor task, indicating greater mental flexibility (Pope, 2015). Furthermore, Koko the gorilla, at 43 to 65 month, scored between 85.2 and 91.7 IQ points on the Stanford-Binet intelligence test (Patterson, 1993), surpassing many living humans who already benefited by Lynn-Flynn effect at that time, in 1975-1976.

 

REFERENCES

Cook, Peter & Wilson, Margaret (2010) Do young chimpanzees have extraordinary working memory?Psychonomic Bulletin & Review 17(4): 599-600

Davies, G., Marioni, R.E., Liewald, D.C., Hill, W.D., Hagenaars, S.P.,… & Deary, I.J. (2016). Genome-wide association study of cognitive functions and educational attainment
in UK Biobank (N=112,151). Molecular Psychiatry 1-10.

De la Croix, D. et al (2017) “Decessit sine prole” – Childlessness, Celibacy, and Survival of the Richest in Pre-Industrial England. CEPR Discussion Paper No. DP11752. Available at SSRN: https://ssrn.com/abstract=2896042

Horvath, G., Csapo, A., Nyeste, A., Gerics, B., Csorba, G. et al. (2009). Erroneous quadruped walking depictions in natural history museums. Current Biology 19: 61-62.

Horvath, G., Farkas, E., Boncz, I., Blaho, M. & Kriska, G. (2012). Cavemen were better at depicting quadruped walking than modern artists: Erroneous walking illustrations in the fine arts from prehistory to today. PLoS ONE 7(12): e49786

Inoue, Sana & Matsuzawa, Tetsuro (2007) Working memory of numerals in chimpanzees. Current Biology 17(23): 1004-1005

Kanazawa-Kyryiama, H. (2017) A partial nuclear genome of the Jomons who lived
3000 years ago in Fukushima, Japan. Journal of Human Genetics 62: 213–221

Martin, Cristopher F. et al (2014) Chimpanzee choice rates in competitive games match equilibrium game theory predictions. Scientific Reports 4: 5182 doi: 10.1038/srep05182

Matsuzawa, Tetsuro (2009) Symbolic representation of number in chimpanzees. Current Opinion in Neurobiology 19: 92–98

Okbay, A., Beauchamp, J.P., Fontana, M.A., Lee, J.J., Pers, T.H., Rietveld, C., & Benjamin, D.J. (2016). Genome-wide association study identifies 74 loci associated with educational attainment. Nature 533: 539-542.

Patterson, Francine & Gordon, Wendy (1993) The Case for the Personhood of Gorillas.In Paola Cavalieri& Peter Singer (eds.) The Great Ape Project. New York: St. Martin’s Griffin, pp. 58-77

Piffer, D. (2017)  2017 Intelligence GWAS: Group-level polygenic scores http://rpubs.com/Daxide/279148

Pope, Sarah M. et al (2015) Baboons (Papio papio), but not humans, break cognitive set in a visuomotor task. Animal Cognition 18:1339–1346

Raghavan, M. (2015) Genomic evidence for the Pleistocene and recent population history of Native Americans. Science Vol. 349, Issue 6250, aab3884 DOI: 10.1126/science.aab3884

Racimo, F. et al (2017) Detecting polygenic adaptation in admixture graphs. bioRxiv doi: http://dx.doi.org/10.1101/146043

Rietveld, C.A., Medland, S.E., Derringer, J., Yang, J., Esko, T., & Koellinger, P.D. (2013). GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science 340: 1467-1471.

Sniekers, S. et al (2017) Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence. Nature Genetics doi:10.1038/ng.3869

Woodley, M.A. et al. (2017) Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes. bioRxiv http://dx.doi.org/10.1101/109678

THE GENOTYPIC INTELLIGENCE OF EUROPEANS DECREASED SINCE BRONZE AGE (II)

Woodley & Piffer (2017) found an increase of nearly 0.02 (from 0.4521 to 0.4717) of polygenic score on EDU since 3,500 years ago.
Counting the SNP discovered by the GWAS on IQ of Sniekers (2017), Davide Piffer (2017) found (http://rpubs.com/Daxide/279148) the lowest polygenic score between Europeans for Iberians (0.4535) and Tuscans (0.4579). Britsh score (0.4654) nearly 0.01 higher, and Utah-Whites (0.4747) score nearly 0.02 (exactly the increase of POLY EDU since Bronze Age, from 0.45 to 0.47) higher than the average of Iberians and Tuscans. But the polygenic count based on GWAS on EDU of Okbay (2016) found 0.01 higher scores for Iberians (0.513) and Tuscans (0.513) than for Utah-Whites (0.503) and British (0.506). Also, the count based on SNP discovered by the GWAS on EDU of Davies (2016) found 0.02 and 0.01 higher polygenic scores for Iberians (512) and Tuscans (0.501), respectively, than for Utah-Whites (0.493). It means Iberians and Tuscans could have 0.03 at 0.04 more common SNP related to EDU, but not to IQ, than Utah-Whites.
These 0.03-0.04 SNP are probably variants that favored the (auto)domestication of humans. The variants that favor domestication could have higher frequencies in Iberians and Tuscans because the higher Neolithic ancestry of these peoples than more Northern peoples, and because their faster entrance in a complex civilization.
Also, it is possible the common variants related to domestication increased even more than 0.02 since Bronze Age, but common SNP related on IQ could decrease during last 3,500 years.

EVIDENCE FOR 13,000 YEARS OF RELAXED SELECTION (ON INTELLIGENCE) IN WEST EURASIANS

Harris & Pritchard (2016) found an increased 5′-TCC-3′ to 5′-TTC-3′ mutation rate in Europeans from about 15,000 to 2,000 years ago.
Mathieson & Reich (2017) confirmed this increase for all West Eurasians. The highest increase for this type of mutation was found in a 7,000 years old European farmer, and it was found also in a 8,000 years old European hunter-gatherer, but this effect is not strongly driven by ancestry (farmer/hunter-gatherer) or by latitude, but is predicted by longitude (increasing east to west). This is in line with the increase of the mutation rate in sexual populations during range expansion found by Cobben & Kubisch (2014) and with the relaxed selection on the wave front of expansion found by Peischl (2016) in French Canadians, 6-9 generations ago. Also, Clark & Hamilton (2007) found higher fertility of Lower Class than Upper Class in French Canadians.
We know Near Easterner hunter-gatherers migrated in Europe 13,000 years ago, followed by Anatolian Neolithic farmers 9,000 years ago, and Steppe pastoralists 5,000 years ago. The relaxed selection on the front waves of these migrations could lead to a relaxed selection pressure that could favor not only the accumulation of mutations, but the increase of the mutation rate too. This is in line with the gradient east to west of the increase of the mutation rate.
 
Also, Mallick (2016) demonstrated an accumulation of mutations 5% higher in non-Africans than in Africans since the Out of Africa. The highest accumulation in Eurasians was found in West Eurasians. Most of this accumulation could produce after Last Glacial Maximum. The warming of the climate and a more sedentary life-style in Near East could relax the selection in this region. This is evidence of more permanent settlements and even of farming in Near East since 13,000 (Wilcox, 2012), 19,000 (Ramsey, 2016) and even 23,000 years ago (Snir, 2015). Also, the expansion of Near Easterners in Eurasia was not „Malthusian”, but rather resembled with the expansion of French Canadians. Furthermore, the decrease of human body size since Upper Palaeolithic is in line with the increase of the mutation rate, that is negatively correlated with the body size in mammals (Martin & Palumbi, 1993). Also, the mutation rate in mammals is higher in warmer climates (Gillman, 2009).
 
The evidence of a relaxed „general” selection is not a direct proof for a decrease of selection on intelligence. But a strong selection on intelligence could not lead to an increase of the mutation rate during 13,000 years (15,000 – 2,000 years ago), because the mutational target on intelligence is enormous. Probably genotypic intelligence decreased during this period in West Eurasia, and this is in line with Cold Winters Theory of Richard Lynn.
 
REFERENCES
Clark, G. & Hamilton, G. (2007) ECONOMIC STATUS AND REPRODUCTIVE SUCCESS IN NEW FRANCE. https://econ.ucalgary.ca/sites/econ.ucalgary.ca/files/seminars/clark%20and%20hamilton%20new%20france%202.pdf
Cobben, M.M.P. & Kubisch, A. (2014) The evolution of mutation rate in sexual populations during range expansion. bioRxiv doi: http://dx.doi.org/10.1101/008979
Gillman, L.N., et al (2009). Latitude, elevation and the tempo of molecular evolution in mammals. Proceedings of the Royal Society B 276: 3353-3359
Harris, K. & Pritchard, J.K. (2016) Rapid evolution of the human mutation spectrum. bioRxiv doi: http://dx.doi.org/10.1101/084343
Mallick, S. et al (2016) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538(7624): 201-206. doi: 10.1038/nature18964
Martin, A.P. & Palumbi, S.R. (1993) Body size, metabolic rate, generation time and the molecular clock. PNAS 90(9): 4087–4091
Mathieson, I. & Reich, D. (2017) Differences in the rare variant spectrum among human populations. PLoS Genet 13(2): e1006581. doi:10.1371/journal.pgen.1006581
Peischl, S. et al (2016) Relaxed selection during a recent human expansion. bioRxiv doi: http://dx.doi.org/10.1101/064691
Ramsey, M.N. et al (2016) Risk, Reliability and Resilience: Phytolith Evidence for Alternative ‘Neolithization’ Pathways at Kharaneh IV in the Azraq Basin, Jordan. PLoS ONE 11(10): e0164081. doi:10.1371/journal.pone.0164081
Snir, A. et al (2015) The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming. PLoS ONE 10(7): e0131422. doi:10.1371/journal.pone.0131422
Wilcox, G. (2012) Pre-Domestic Cultivation during the Late Pleistocene and Early Holocene in the Northern Levant. in Biodiversity in Agriculture: Domestication, Evolution, and Sustainability, editors Gepts, P. et al. Cambridge University Press

THE GENOTYPIC INTELLIGENCE OF EUROPEANS DECREASED SINCE BRONZE AGE (I)

UPDATE 03.05.2017

Michael Woodley & Davide Piffer (2017) published in bioRxiv a very interesting study, comparing polygenic scores on educational attainment of today and Bronze Age samples. They demonstrated a positive selection on intelligence, but they believe they demonstrated the increase of the genotypic intelligence of Europeans since Bronze Age. Their results rather demonstrate a decrease of the genotypic intelligence during last 4,000 years.

The most powerful GWAS on educational attainment (Okbay, 2016) found 74 common SNP that favor high-IQ (equating the educational attainment with the intelligence). The average effect of each of these SNP is 0.02% of variance and 0.02 SD of educational attainment (Okbay, 2016, Extended Data Figure 2). But 1 SD of EA equates with 3.8 IQ points (Kong, 2017), hence the effect of each SNP is 0.02 x 3.8 = 0.076 IQ points. In aggregate, these 74 SNPs explain 0.43% of the variation in educational attainment (Okbay, 2016).

Woodley & Piffer used a polygenic score using 130 common SNP resulted from the same GWAS (Okbay, 2016). They found a polygenic score of 3,298.5 : (3,298.5 + 3,997.5) = 45.21% for Bronze Age samples and 61666 : (61,666 + 69,114) = 47.15% for today Europeans. We can assume that for only 74 SNP Woodley & Piffer could find the same values of polygenic scores of today Europeans (47.15%) and Bronze Age Eurasians (45.21%). It means an average difference (47.15 – 45.21)% x 74 = 1.44 more IQ-increasing SNP in each today sample, equating with 1.44 x 0.076 = 0.11 IQ points.

Jointly, the variance explained by the 74 SNP is 0.43%, but the variance explained by all the common SNP is 15.6% (Hill, 2017). We can assume that polygenic score increased with (47.15% – 45.21%) = 1.94% for all IQ-increasing common SNP of entire genome. In this case, the average total increase of the genotypic IQ due of common SNP since Bronze Age is (15.6% : 0.43%) x 0.11 IQ points = 3.99 IQ points.

It means the selection pressure on intelligence was strong enough to increase the frequency of common SNP that favor high-IQ with the  the equivalent of 3.99 IQ points.

But common SNP account for 15.6 : (15.6 + 28.1) = 35.67% and rare variants account for 64.33% of genotypic IQ (Hill, 2017). It means the same selection pressure that increased the IQ with 3.99 points on common polymorphism SNP will increase the IQ on rare variants with (64.33% : 35.67%) x 3.99 IQ points = 7.20 IQ points. The total increase of the genotypic IQ will be 3.99 + 7.20 = 11.19 IQ points. In fact, since Bronze Age, the selection eliminated IQ-decreasing common SNP and IQ-decreasing rare variants that equate with 11.19 IQ points.

The average age of Bronze Age samples is 3,440 years, equating with 3,440 : 30 = 114.66 generations. Hence, the selection eliminated IQ-decreasing (common and rare) variants of 11.16 : 114.66 = 0.098 IQ points by generation.

If the average decrease of genotypic intelligence by de novo mutations is higher than 0.098 IQ points by generation, the genotypic IQ of Europeans decreased since Bronze Age.

If we estimate a decrease of 8 IQ points of the genotypic intelligence, due of dysgenic fertility after the demographic transition (started 8 generations ago), the selection could eliminate IQ-decreasing (common and rare) variants (11.6 + 8) : (114.66 – 8) = 0.184 IQ points by generation before the demographic transition. If the average decrease of genotypic IQ by de novo mutations was higher than 0.184 IQ points by generation, the genotypic intelligence of Europeans decreased even before the demographic transition.

PS. The polygenic scores for 9 SNP and 11 SNP are 5% higher for today Europeans than for Bronze Age Europeans. If we assume that for all IQ-increasing common SNP the increase is of 5%, the selection eliminated IQ-decreasing (common and rare) variants equating with (5% : 1.94%) x 0.098 = 0.253 IQ points by generation since Bronze Age, and equating with (5% : 1.94%) x 0.184 = 0.474 IQ points by generation (before Industrial Revolution).

PPS. (26.05.2017) Prevalence of ADHD is 7%. Heritability of ADHD is 75%, hence sporadic cases are 85% of all cases. 36% of sporadic cases of ADHD are due of de novo mutations (Kim, 2017). Paternal age higher than 45 years increases 13 fold the risk for ADHD (D’Onofrio, 2014). The prevalence of ADHD due of de novo mutations is 0.07 x 0.85 x 0.36 = 0.0214

A meta-analysis (Frazier, 2004) found 7 at 11 points lower than average IQ of those with ADHD. In all psychiatric diseases, cases due of de novo mutations have the lowest IQ. We can consider those with ADHD by de novo mutations have at least 11 points lower IQ than average.
The generational lost of genotypic intelligence due of ADHD by de novo mutations is 0.0215 x 11 = 0.236 IQ points.
Also, people with ADHD have higher fertility than average (Weiss, 1985; Williams, 2006).
Even only the generational loss of IQ (0.236 points) due of de novo mutations producing ADHD overcompensated the positive selection on intelligence between Bronze Age and Industrial Revolution found by Woodley & Piffer, that had a strength of 0.184 IQ points by generation.
PPPS. (11.08.2017) Mullins (2017) found a higher fertility (0.15) than average of those with a high POLY_ADHD, and confirms the higher fertility of those with ADHD found by Weiss (1985) and Williams (2006). Probably carriers of rare variants and de novo mutations that favor ADHD have higher fertility too. But the prevalence of ADHD is 7%, and it means the selection for ADHD is much older than 200 years, and acted before the Industrial Revolution too. Sniekers (2017) found a genetic correlation of -0.27 between IQ and ADHD, that confirms the lower IQ than average of those with ADHD found by Frazier (2004).
Also, POLY_MDD positively correlates (0.04) with fertility (Mullins, 2017) and negatively correlates (-0.11) with IQ (Sniekers, 2017).
Furthermore, Mullins (2017) found lower fertility (-0.25) of healthy carriers of high POLY_ASD, and POLY_ASD is positively correlated (0.21) with IQ (Sniekers, 2017). But the true fertility is even lower if we count the carriers of high POLY_ASD and of the disorder too.
Also, Mullins (2017) did not find selection for or against POLY_SCZ and POLY_BD in healthy carriers. But, in fact, there is a selection against POLY_SCZ/BD, because those that have these disorders have lower fertility than average. The decrease of POLY_SCZ was found by Kong (2017). But it is possible de novo mutations that favor SCZ overcompensate the decrease of POLY_SCZ in modern Europeans.

 

 

REFERENCES

D’Onofrio, B.M. et al. (2014) Paternal age at childbearing and offspring psychiatric and academic morbidity. JAMA Psychiatry. 2014 Apr;71(4):432-8. doi: 10.1001/jamapsychiatry.2013.4525.
Frazier, T.W. et al. (2014) Meta-Analysis of Intellectual and Neuropsychological Test Performance in Attention-Deficit/Hyperactivity Disorder. Neuropsychology, 18(3), 543-555. http://dx.doi.org/10.1037/0894-4105.18.3.543
Hill, D.W. et al. (2017) Genomic analysis of family data reveals additional genetic effects on intelligence and personality. bioRxiv http://dx.doi.org/10.1101/106203
Kim, D.S. et al. (2017) Sequencing of sporadic Attention-Deficit Hyperactivity Disorder (ADHD) identifies novel and potentially pathogenic de novo variants and excludes overlap with genes associated with autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet. 174(4):381-389. doi: 10.1002/ajmg.b.32527.
Kong, A. et al. (2017) Selection against variants in the genome associated with educational attainment. PNAS 114(5): E727-E732. doi: 10.1073/pnas.1612113114.
Mullins, N. et al. (2017) Reproductive fitness and genetic risk of psychiatric
disorders in the general population. NATURE COMMUNICATIONS | 8:15833 | DOI: 10.1038/ncomms15833.
Okbay, A. et al. (2016). Genome-wide association study identifies 74 loci associated with educational attainment. Nature 533: 539-542.
Sniekers, S. et al (2017) Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence. Nature Genetics doi:10.1038/ng.3869
Weiss, G. et al. (1985) Psychiatric status of hyperactives as adults: a controlled prospective 15-year follow-up of 63 hyperactive children. J. Am. Acad. Child Psychiatry 24: 211–220.
Williams, J. & Taylor, E. (2006) The evolution of hyperactivity, impulsivity and cognitive diversity. J. R. Soc. Interface 3: 399–413 doi:10.1098/rsif.2005.010
Woodley, M.A. et al. (2017) Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes. bioRxiv http://dx.doi.org/10.1101/109678

THE TASMANIAN MODEL – THE DEGENERATION OF HUMAN INTELLIGENCE

When they started colonizing Tasmania, at the beginning of the 19th century, the British came to the conclusion that the inhabitants of that island were the least developed human community on Earth. The Tasmanian aborigines were incapable of mastering fire, they did not manufacture bone tools, they did not possess specialized stone tools, they did not use composite tools (e.g. axes with handles), they did not have boomerangs, spear launchers, shields, nor did they chop trees or engage in mural painting. Although they were living especially in coastal regions, the Tasmanians were incapable of fishing. Although they were living in a region with rather cold winters, they were not capable of sowing their own clothes – they could only cover their bodies with animal skins. Although they were members of the Homo Sapiens species, the material part of their civilization was inferior to the one achieved by the Homo Neanderthalensis and perhaps even by Homo Erectus (a species which most likely had already managed to master fire).

 

However, the British were not mistaken. The Tasmanian population was not the most evolved but the most degenerated in the entire world. The Tasmanian once had a superior material civilization, which included all of the achievements mentioned above, but which they lost in only a few thousand years.

 

The aborigines arrived in Tasmania at least 35,000-40,000 years ago, following a migration from Africa, along the Southern coast of Asia. At the time Tasmania was connected to Australia and only after the end of the last Ice Age did it become an island, as a consequence of a large part of the icecap melting and a rise in the water level. At the beginning of British colonization, the Tasmanian had been isolated from the rest of the world for more than 10,000 years. This was a period when they evolved on their own, without outside influence. The Tasmanian never actually suffered any British influence, as they were quickly exterminated.

 

Nobody provides a satisfying explanation for the degeneration of the Tasmanian civilization and that is because everything within human-related sciences is altered by various ideological filters.

’Scientists’ of political correctness (a new Inquisition of science) normally argue that the Tasmanian were too few to support civilization – even a Paleolithic-type one. It is estimated that the Tasmanian population amounted to 3,000-15,000 members. However, the Neanderthal population was of the same size, whose civilization not only did not degenerate over hundreds of thousands of years, but also continually evolved. In addition, contacts between human Neanderthal groups were not as frequent, as the area they covered was much larger than the one covered by Tasmanians. Hence, the small size of the population cannot be a serious argument for losing a certain level of civilization unless coupled with the distribution of intelligence according to the Gaussian curve. For a certain average IQ, it is necessary for a population to have a certain size in order to possess sufficient members with a sufficiently high level of intelligence in order to preserve the achievements of that civilization. For an average IQ of 60 (this was the measured IQ for Australian aborigines), the Tasmanians were too few to preserve their civilization. With an IQ which was probably much higher, the Neanderthals, although with a population not larger than the Tasmanian, had enough members to continually perfect their civilization. Nonetheless, the ’scientists’ of political correctness prefer to ignore the only plausible explanation for the degeneration of Tasmanian civilization and of any other civilization: the decrease of the IQ as a consequence of a decrease in the pressure of selection.

 

Racist scientists will not be particularly fond of this thesis either. If they accepted the genetic degradation of intelligence for the Tasmanian, they would then be forced to accept the same for other races which they see as being forever superior – something which would blow away the very foundations of their ideology.

 

Nature however does not take ideological whims into account. The decline of human intelligence has been ongoing for tens of thousands of years everywhere around the world. The cause is always the same: a lower level of natural selection.

 

As all other humans, except for the ones in Sub-Saharan Africa, the Tasmanians were not pure Homo Sapiens but hybrids. In their genome, around 4% were Neanderthal genes and equally around 4% were the genes of the Denisova hominin– the same proportions as for Melanesians and Australians  This is already proof of the fact that at the peak of the Ice Age Tasmanian ancestors had reached sufficiently Northern latitudes to require a high level of intelligence.

 

The genetic degeneration of Tasmanian intelligence did not begin only once they were isolated on the island, but long before that. On the one hand, moving towards the South and living in the equatorial and tropical climate decreased the pressure of selection: humans required fewer calories in an environment which could provide more. On the other hand, hunting was (and especially so in Australia) much easier than in Asia while predators, human’s natural competition, were also more rudimentary and less intelligent. Moreover, as the region was not inhabited by other humans until this first migration, there was no human competition either. It is obvious that the humans who migrated to Tasmania were subject to a much lower pressure of selection than the humans who migrated towards Northern Eurasia. The fact is reflected by the current difference in IQ levels: the British Australian population has an IQ of 100 while the aborigines have an IQ of 60.

 

A similar phenomenon, although not of the same amplitude and duration, explains the IQ decrease for American natives. They originate in a Siberian population, of which probably only a few tens of thousands of members penetrated into America, about 11,000 years ago. They did so over the Behring Strait which at the time was no covered by waters but was a strip of land covered by ice. These humans were so intelligent and efficient that in approximately 1,000 years they managed to colonize the entire continent and exterminate 80% of the North American megafauna and 85% of the South American one. In the same millennium they managed to reach a population of millions of people. The price to be paid for this spectacular expansion was a decrease of the IQ (but not as dramatic as the one in Tasmania and Australia). Having a more numerous population with a higher IQ (today it stands at 87), the American natives not only did not lose the achievements of the civilization which they brought with them on the new continent; along with the end of the Ice Age, they managed to build much more complex civilizations, similar to the Eurasians: they invented agriculture, domesticated animals, processed metals, developed urban agglomerations and even empires, they gained scientific knowledge, etc. This additional development of civilization led to an additional decrease of the IQ. Following contact with European colonists, the IQ dropped even further – first through the decimation of American native elites and then by way of an accelerated reduction in the pressure of selection due to the Industrial Revolution.

 

Returning to the loss of Tasmanian civilization, the phenomenon which occurred on the little island illustrates the direction that the entire world is heading towards. The fall of civilizations consists of a loss of certain achievements (material or cultural). The Egyptians were no longer capable of building pyramids. The Greeks invented democracy but lost it. The world after the fall of the Roman Empire was no longer capable for a very long time of creating buildings that were similar to those of Roman engineers. In addition, as regards philosophy, science and art, the medieval world did not manage for very long to catch up with the ancient one. At all times and places, the fall of civilizations was due to the loss of IQ. The recovery of lost achievements always occurred only as a result of significant technological progress. Technological progress worked as prosthesis to replace the increasingly weaker minds of the ever larger share of the population. For instance, the general decline of IQ in the world leads to the consequence that fewer and fewer people are capable of solving simple arithmetic operations. But the invention of the calculator and its widespread use has enabled these people to reach correct results.

 

The genetic degradation of intelligence is, however, an inevitable phenomenon which is irreversible, global, whose beginnings can be found during the Upper Paleolithic and which will once day lead us all to the same situation as that of Tasmanians.