Detection of human adaptation during the past 2000 years

Abstract

Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

10 Years of GWAS Discovery: Biology, Function, and Translation

“…74,77 This chimes with the view of T2D as a largely post-reproductive trait and is consistent with a failure to detect compelling empirical evidence that T2D risk alleles have been subject to marked purifying selection. 78,79 In keeping with the age of these common risk alleles (which predates the diaspora of modern humans out of Africa), most common variant associations for T2D are replicated across major ethnic groups. 75,80 However, as increasingly diverse populations are genotyped and sequenced, more ethnic-specific alleles 82 From GWAS to Biology.…”

Tracing the peopling of the world through genomics

“…The best characterized example of polygenic adaptation in humans is selection for an adaptive increase in the height of northern Europeans 135 , a smaller increase in the height of Europeans compared to non-Europeans 136 and a decrease in the height in Sardinians 137 . Selection for height may have had small effects on loci across most of the human genome 138 . Polygenic adaptation may also have influenced a variety of other morphological traits, including increases in size of the head and body of infants in northern Europe 138 .…”

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

“…Furthermore, we used the recently published singleton density score (SDS) 11 , which detects very recent changes in allele frequencies from contemporary genome sequences. Publicly available SNP level SDS scores calculated from the UK10K…”