Holocene selection for variants associated with cognitive ability: Comparing ancient & modern genome

[Petalpusher]

Abstract: Human populations living in Eurasia during the Holocene experienced significant evolutionary change. It has been predicted that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favoured via directional selection genetic variants associated with higher general cognitive ability (GCA). Population expansion and replacement has also been proposed as an important source of GCA gene-frequency change during this time period. To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4,557 to 1,208 years of age) with a sample of 503 modern European genomes, using three different cognitive polygenic scores. Significant differences favouring the modern genomes were found for all three polygenic scores (Odds Ratio=0.92, p=0.037; 0.81, p=0.001 and 0.81, p=0.02). Furthermore, a significant increase in positive allele count over 3,249 years was found using a sample of 66 ancient genomes (r=0.217, p one-tailed=0.04). These observations are consistent with the expectation that GCA rose during the Holocene.

Late Bronze Age European and Central Asian gene pools resemble present-day Eurasian genetic structure (17). Indeed, with values of Fst ranging from 0.00 to 0.08, the genetic distances between present-day European 1000 Genomes samples and the Ancient samples indicate little to modest levels of genetic differentiation (little differentiation corresponds to an Fst range of 0 to 0.05, and modest to an Fst range of 0.05 to 0.15 [41]). These values are lower than the distance between present-day Europeans and East Asians (F st =0.11) (17). Despite this the two ancient genomes belonging to the Siberian Okunevo culture (RISE515 and RISE516) were somewhat of an outlier, exhibiting modest differentiation relative to the EUR sample when compared with the other genomes in the sample (average F st =0.074 vs. 0.016 for the remainder of the sample). Their removal reduced the genetic differentiation between the two samples, yielding 99 ancient genomes, sourced from sites located in present-day Armenia (8.08%), Czech Republic (6.06%), Denmark (6.06%), Estonia (1.01%), Germany (10.1%), Hungary (10.1%), Italy (3.03%), Kazakhstan (1.01%), Lithuania (1.01%), Montenegro (2.02%), Poland (7.07%), Russia (36.36%) and Sweden (8.08%).


Changes in allele frequencies can also occur via population expansion and replacement, perhaps driven in part by the relative advantage in conflict conferred upon populations by GCA. Consistent with this, as a possible result of the Neolithic revolution and during the Bronze Age in Europe, three Y-chromosomal haplogroups (R1a, R1b, I1), which are associated with farming or pastoralist cultures, came to mostly replace the formerly dominant hunter-gatherer lineages (associated predominantly with haplogroups G2a and I2) (32). Ancient farming societies in particular are associated with higher social complexity and the use of more complex tools (11); furthermore the contemporary distribution of these three haplogroups is positively associated with the variation in cognitive ability among contemporary European nations (32). The major population movements occurred in the period between 3.5 and 7.3 kybp, however, as noted in (17), westward migration of populations associated with haplogroup R1a continued from the Pontic-Steppe region between 5 and 1.4 kybp.


G2a is the main early farmer lineage of Neolithic Western, Central and Southern Europe, and it arrived in Europe with early Neolithic farmers from Anatolia.

I2 is the main hunter-gatherer lineage of Mesolithic Western, Central and Southern Europe.

R1a and R1b appear to be the main hunter-gatherer lineages of Mesolithic and Neolithic Eastern Europe (keep in mind that the Neolithic in much of Eastern Europe was defined by the presence of pottery, not necessarily any type of farming).

At some point hunter-gatherers native to Western, Central and Southern Europe carrying I2 were acculturated into farming societies, and so I2 rose in frequency in farmer populations at the expense of G2a.

Then, during the Eneolithic/Copper Age, foragers on the Eastern European steppe carrying R1a and R1b mixed with pastoralists from the fringes of the steppe, like the North Caucasus, and became steppe pastoralists.

These steppe pastoralists with Eastern European forager-derived R1a and R1b then expanded rapidly and moved en masse into the rest of Europe, largely replacing the farmer G2a and I2 lineages there.


http://www.biorxiv.org/content/biorx...09678.full.pdf

http://www.biorxiv.org/content/early/2017/02/20/109678

[Lucas]

Where in this linked paper is something about Y-DNA of farmers and hunters?

EDIT: It's Davidsky comment...

[Petalpusher]

Where in this linked paper is something about Y-DNA of farmers and hunters?

It's in the Eurogenes article, not in the paper. I forgot to remove that part, but afterall useful for those not too familiar with all the Y-dna stuff.

http://eurogenes.blogspot.fr/2017/02...ur-bronze.html

[Lucas]

G2a is the main early farmer lineage of Neolithic Western, Central and Southern Europe, and it arrived in Europe with early Neolithic farmers from Anatolia.

I2 is the main hunter-gatherer lineage of Mesolithic Western, Central and Southern Europe.

R1a and R1b appear to be the main hunter-gatherer lineages of Mesolithic and Neolithic Eastern Europe (keep in mind that the Neolithic in much of Eastern Europe was defined by the presence of pottery, not necessarily any type of farming).

At some point hunter-gatherers native to Western, Central and Southern Europe carrying I2 were acculturated into farming societies, and so I2 rose in frequency in farmer populations at the expense of G2a.

Then, during the Eneolithic/Copper Age, foragers on the Eastern European steppe carrying R1a and R1b mixed with pastoralists from the fringes of the steppe, like the North Caucasus, and became steppe pastoralists.

These steppe pastoralists with Eastern European forager-derived R1a and R1b then expanded rapidly and moved en masse into the rest of Europe, largely replacing the farmer G2a and I2 lineages there.

It's inline with this http://www.theapricity.com/forum/sho...o&goto=newpost

[XenophobicPrussian]

The allele counts from the paper:

1. Nine linked hits(9 SNPs):

Ancient - 177 positive, 273 negative
Modern - 4017 positive, 5037 negative

2. Pooled analysis(Okbay et al, 2016, 130 SNPs):

Ancient - 3298.5/3997.5
Modern - 61666/69114

3. Significant hits(Davies et al, 2016, 9 SNPs):

Ancient - 268.5/282.5
Modern - 5960/5106

Did the math, we're either 14.9%, 7.3%, or 21.7% smarter than our bronze age ancestors.

Putting it in terms of IQ, assuming San IQ is the base homo sapien IQ(I'm using the San because they lack nearly all these intelligence SNPs and have the least of any human group, even Bantus have a lot more, the San still have some but very little), which I'm going to put at 67 as a genotypic IQ(taking actual San IQ results of 54, then adding the difference between what Richard Lynn calculated to be West African genotypic IQ at 80, calculated by removing the supposed Euro admixture IQ from African Americans and IQ tests on well off mainland SSAs) and actual average West African IQ results, which is 67(meaning SSA lack of early baby/infant nutrition lowers SSA IQ by 13 points), and also assuming the IQ of the modern European sample is 100, we get a result for the ancient Europeans at 95.1, 97.6, 93.1 IQ.

That correlates with Han Chinese IQ vs modern East Asian herding nomads and HGs who are basically still a bronze age or iron age culture, 105 vs 100(Mongolian), 100(Yakut), 99.8(Xibo), 96.5(Evenki).

Although, this sort of stuff should obviously be taken with a grain of salt, intelligence SNPs are nowhere near close to being fully mapped out, and different SNPs will have different greater/lesser values on it, not all of them will be equal. Shame they also didn't break down the allele frequency by different ancient groups.

Pretty cool, nonetheless.