Holocene Selection for Variants Associated With General Cognitive Ability: Comparing Ancient and Modern Genomes

Abstract

Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes (F st = 0.013), using three different cognitive polygenic scores (130 SNP, 9 SNP and 11 SNP). Significant differences favoring the modern genomes were found for all three polygenic scores (odds ratios = 0.92, p = 001; .81, p = 037; and .81, p = .02 respectively). These polygenic scores also outperformed the majority of scores assembled from random SNPs generated via a Monte Carlo model (between 76.4% and 84.6%). Furthermore, an indication of increasing positive allele count over 3.25 kyr was found using a subsample of 66 ancient genomes (r = 0.22, p one-tailed = .04). These observations are consistent with the expectation that GCA rose during the Holocene.

Global Ancestry and Cognitive Ability

“…If recent selection favored IQ-promoting variants and purged IQ-reducing variants, the more recent polymorphisms will be IQ-promoting, which will result in bias in favor of the discovery population. There is some evidence of an increase in PGS over time [97]. Of course, the reverse would be true, if recent selection disfavored high IQ alleles.…”

Biogeographic Ancestry, Cognitive Ability and Socioeconomic Outcomes

“…The study of highly polygenic selection via changes in frequencies of many alleles (soft sweeps) in humans has advanced recently due to the availability of large-scale, powerful computer clusters and large genomic datasets. A number of recent studies based on genomic data have found evidence of recent polygenic selection in humans over time [29,30] and space [31][32][33][34]. These findings indicate selection for, e.g., height [31], body mass [32], cognitive ability [33], educational attainment [34,35], and schizophrenia [36].…”

Genomic ancestry, cognitive ability, and socioeconomic outcomes

“…Furthermore, it has been shown that the Neanderthal admixture % in modern Eurasians has been decreasing over time, consistent with polygenic selection against whatever traits Neanderthal ancestry has higher polygenic scores for (Gregory et al, 2017;Simonti et al, 2016). Especially notable among the studies mentioned is that some of them found evidence of recent selection for educational attainment (Beauchamp, 2016;Kong et al, 2017;Woodley et al, 2017), which is highly genetically correlated with cognitive ability and often used as a proxy in genomic studies (Hill, Davies, McIntosh, Gale, & Deary, 2017;Marioni et al, 2014;Rietveld et al, 2014;Zabaneh et al, 2017). Taken together, these facts suggest the possibility that selection for cognitive ability has not been equal for all groups in recent history (e.g.…”

“…Despite this, soft sweeps are considered by some researchers to be the dominant mode of adaptation in humans (Schrider & Kern, 2017). A number of recent studies based on genomic data have found evidence of recent polygenic selection in humans (Berg, Zhang, & Coop, 2017;Joshi et al, 2015;Mathieson et al, 2015;Woodley, Younuskunju, Balan, & Piffer, 2017), including selection that differed by population such that populations would, over time, acquire different average polygenic scores for the traits (Berg et al, 2017;Joshi et al, 2015;Piffer, 2015;Robinson et al, 2015;Turchin et al, 2012). One example of this is the study by Robinsen et al (2015), which examined differences in height and BMI among 14 European national populations and found that some of the observed national differences in height and 5 A variety of times are used for this trait including skin color, skin tone, skin brightness, skin lightness.…”