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Abstract
Characterizing the natural selection of complex traits is important for understanding human evolution and both biological and pathological mechanisms. We leveraged genome-wide summary statistics for 870 polygenic traits and attempted to quantify signals of selection on traits of different forms in European ancestry across four periods in human history and evolution. We found that 88% of these traits underwent polygenic change in the past 2,000-3,000 years. Recent selection was associated with ancient selection signals in the same trait. Traits related to pigmentation, body measurement and nutritional intake exhibited strong selection signals across different time scales. Our findings are limited by our use of exclusively European data and the use of genome-wide association study data, which identify associations between genetic variants and phenotypes that may not be causal. In sum, we provide an overview of signals of selection on human polygenic traits and their characteristics across human evolution, based on a European subset of human genetic diversity. These findings could serve as a foundation for further populational and medical genetic studies.
Highlights
The genetic architecture of present-day human is shaped by the profound selection pressures in the long history[1]
Divided by category (Figure 2A and 2B), we found that 52% (23/44) of impedance traits (IMP) like height (Zncm=8.09, Zncf=4.91) and body mass index (BMI) (Zncm=7.11, Zncf=4.79) were causally related to male's number of children
We analyzed the essential characteristics of selection pressure, such as its prevalence and strength, its uneven distribution among time points and trait categories, as well as its association with genetic architectures
Summary
By filtration in traitDB12 database and literature research (Method), we collected the GWAS summary statistics of 870 polygenic traits with adequate power, 738 of which were carried out primarily in the UK Biobank. Most heritable traits underwent significant polygenic adaptation in the past 2000 years we extended our analysis to the recent history (past 2000-3000 years) Selection pressure at this time scale was measured by the Spearman correlation between SNPtrait association p-value and trait-increasing Singleton Density Score (tSDS), termed ρSDS, as applied by Field et al.[17] (Method). R2 for ρSDS prediction was 0.76 on non-disease traits but dropped to 0.47 when applied on polygenic diseases (p by jackknife =9.95×10-5, Table S9 and Method) This result suggested that selection pressure at Neolithic and the present time was profoundly altered and deviated from ancient selection pressure, and the deviation was more profound for polygenic diseases. For all functional genomics annotation, the most significant relation was found between CpG and ASMCavg (tCpG=-8.5, Figure 6D)
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