Thursday, November 06, 2014

The genetics of intelligence - early results

Refer to text below to understand this
A somewhat overlooked paper: "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" available here.

This is how Peter Frost summarises the paper.
"We know that human intellectual capacity has risen through small incremental changes at very many genes, probably hundreds if not thousands. Have these changes been the same in all populations?

"Davide Piffer (2013) has tried to answer this question by using a small subset of these genes. He began with seven SNPs whose different alleles are associated with differences in performance on PISA or IQ tests. Then, for fifty human populations, he looked up the prevalence of each allele that seems to increase performance. Finally, for each population, he calculated the average prevalence of these alleles at all seven genes.

"The average prevalence was 39% among East Asians, 36% among Europeans, 32% among Amerindians, 24% among Melanesians and Papuan-New Guineans, and 16% among sub-Saharan Africans. The lowest scores were among San Bushmen (6%) and Mbuti Pygmies (5%). A related finding is that all but one of the alleles are specific to humans and not shared with ancestral primates.

"Yes, he was using a small subset of genes that influence intellectual capacity. But you don't need a big number to get the big picture. If you dip your hand into a barrel of differently colored jelly beans, the colors you see in your hand will match well enough what's in the barrel. In any case, if the same trend holds up with a subset of 50 or so genes, it will be hard to say it's all due to chance."
The alleles which Piffer frequency-analysed differentially code for things like:
"... the regulation of neuronal morphology in neurons, including hippocampal neurons and developing brains"

"... neuronal excitability, synaptic plasticity and feedback regulation of acetylcholine release."
Ten or so SNPs don't determine very much of a person's intelligence, which depends upon the actions of hundreds or thousands of genes as well as environmental effects. But even a small sample - if representative and correlated - can be quite predictive, as Piffer explains.
"As the effect size of each SNP is typically very low (around 0.1%), even 10 SNPs would not account for more than 1% of the variance in IQ or educational attainment scores across populations. The likely explanation for why the effect size for the 10 SNPs at a cross population level detected in this study is so high (around 80%), is that the alleles are not randomly distributed across human races, so that the combined frequency of a few alleles predicts the frequencies of many other alleles affecting the same phenotype. This inflates the correlation with the phenotype well beyond anything that would be explainable by the modest effect sizes of the examined SNPs.

"This is nothing more than the principle applied to psychometric instruments, such as IQ tests or personality scales, where a handful of items produce a reliable score, precisely because these items represent an underlying, latent factor and are thus correlated among each other. Even reliable psychometric scales are usually composed of around 10 items, equal to the number of SNPs examined in the present study, which in turn showed good internal reliability (Cronbach’s α= 0.84).

"A model based on random evolution or genetic drift alone cannot account for such a pattern."
The particular SNPs used in the study are listed in the tables at the back of the paper. I was naturally interested in checking which of these SNPs are analysed by 23andMe. It turns out that about half are. So in the graphic above you see the 'good for intelligence' SNPs in the first column, the gene name (where available) in the second and the chromosome it's on (from 23andMe) in the third. The fourth column is the specific nucleotide which marks this as a 'good-for-intelligence' allele, and the fifth is the database where the source-data came from (refer to the paper for details). The final column is my own genotype at these alleles, as downloaded from 23andMe.

Here is an Excel workbook for you to try yourself. Hint: download your 23andMe results and load into an Excel spreadsheet; then search on the rs SNP identifiers.

There are sixteen alleles (2 x 8) which are both 'good' and available from 23andMe. Of these 16, you will see that I have 7 'good' ones, so my personal 'frequency' is 7/16 = 0.44. This sounds terrible, but in fact the European average frequency for these 'good alleles' is 35.5% and the East Asian (Chinese, Japanese) average frequency is 39.1. This number of alleles is too small to be a good estimator of anyone's overall IQ though.

The message of Piffer's paper is that, as humans radiated out of Africa, a rising tide of natural selection drove novel alleles coding for increased intelligence to higher and higher population frequencies. This emerges clearly from the  SNPs analysed in the paper, and is by hypothesis true for the rest too. It appears that selection for higher intelligence has been more, rather than less, intense over the last 10,000 years - possibly reflecting the cognitive demands of agrarian, pastoral and yet more complex modern civilisations.

More to come, undoubtedly as the larger scale GWAS studies begin to deliver.