2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2025
Abstrakt

Davide Bolognini, Alma Halgren, Runyang Nicolas Lou, Alessandro Raveane, Joana L. Rocha, Andrea Guarracino, Nicole Soranzo, Chen-Shan Chin, Erik Garrison, Peter H. Sudmant. Recurrent evolution and selection shape structural diversity at the amylase locus. Nature, 634(8034):617-625. 2024.

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Abstract:

The adoption of agriculture triggered a rapid shift towards starch-rich diets in 
human populations(1). Amylase genes facilitate starch digestion, and increased 
amylase copy number has been observed in some modern human populations with 
high-starch intake(2), although evidence of recent selection is lacking(3,4). 
Here, using 94 long-read haplotype-resolved assemblies and short-read data from 
approximately 5,600 contemporary and ancient humans, we resolve the diversity and 
evolutionary history of structural variation at the amylase locus. We find that 
amylase genes have higher copy numbers in agricultural populations than in 
fishing, hunting and pastoral populations. We identify 28 distinct amylase 
structural architectures and demonstrate that nearly identical structures have 
arisen recurrently on different haplotype backgrounds throughout recent human 
history. AMY1 and AMY2A genes each underwent multiple duplication/deletion events 
with mutation rates up to more than 10,000-fold the single-nucleotide 
polymorphism mutation rate, whereas AMY2B gene duplications share a single 
origin. Using a pangenome-based approach, we infer structural haplotypes across 
thousands of humans identifying extensively duplicated haplotypes at higher 
frequency in modern agricultural populations. Leveraging 533 ancient human 
genomes, we find that duplication-containing haplotypes (with more gene copies 
than the ancestral haplotype) have rapidly increased in frequency over the past 
12,000 years in West Eurasians, suggestive of positive selection. Together, our 
study highlights the potential effects of the agricultural revolution on human 
genomes and the importance of structural variation in human adaptation.