Recurrent evolution and selection shape structural diversity at the amylase locus.

Autor: Bolognini D; Human Technopole, Milan, Italy., Halgren A; Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA., Lou RN; Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA., Raveane A; Human Technopole, Milan, Italy., Rocha JL; Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA., Guarracino A; Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., Soranzo N; Human Technopole, Milan, Italy.; Wellcome Sanger Institute, Hinxton, UK.; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.; Department of Haematology, Cambridge Biomedical Campus, Cambridge, UK.; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK., Chin CS; Foundation for Biological Data Science, Belmont, CA, USA., Garrison E; Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA. egarris5@uthsc.edu., Sudmant PH; Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA. psudmant@berkeley.edu.; Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA. psudmant@berkeley.edu.
Jazyk: angličtina
Zdroj: Nature [Nature] 2024 Oct; Vol. 634 (8034), pp. 617-625. Date of Electronic Publication: 2024 Sep 04.
DOI: 10.1038/s41586-024-07911-1
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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