Paleolithic Gene Duplications Primed Adaptive Evolution of Human Amylase Locus Upon Agriculture

Abstract

Starch digestion is a cornerstone of human nutrition. The amylase enzyme, which digests starch, plays a key role in starch metabolism. Indeed, the copy number of the human amylase gene has been associated with metabolic diseases and adaptation to agricultural diets. Previous studies suggested that duplications of the salivary amylase gene are of recent origin. In the course of characterizing 51 distinct amylase haplotypes across 98 individuals employing long-read DNA sequencing and optical mapping methods, we detected four 31mers linked to duplication of the amylase locus. Analyses with these 31mers suggest that the first duplication of the amylase locus occurred more than 700,000 years ago before the split between modern humans and Neanderthals. After the original duplication events, amplification of theAMY1genes likely occurred via nonallelic homologous recombination in a manner that consistently results in an odd number of copies per chromosome. These findings suggest that amylase haplotypes may have been primed for bursts of natural-selection associated duplications that coincided with the incorporation of starch into human diets.

Emergence of saliva protein genes in the secretory calcium-binding phosphoprotein (SCPP) locus and accelerated evolution in primates

“…Since the expansion and diversification of saliva-related SCPP genes took place along with the diversification of the primate lineage, occupancy of different dietary niches, and exposure to different pathogenic challenges, we propose that this third expansion of genes within the SCPP locus could have been driven by primate species-specific selective pressures. Indeed, dietary change has been discussed as a major adaptive pressure in primates [44][45][46][47]. Despite the scarcity of clear functional data for saliva-related SCPP proteins, several lines of evidence support the hypothesis that saliva-related SCPP genes have evolved to accommodate the diverse dietary needs of primates, shaping taste perception [48,49] and physical properties of saliva [50].…”