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<p>The salivary amylase gene <i>AMY1</i> exhibits remarkable copy number variation linked to dietary shifts in human evolution. While global studies highlight its structural complexity and association with starch-rich diets, localized selection patterns remain underexplored. Here, we analyze <i>AMY1</i> copy number in 3,723 individuals from 85 populations, revealing that Indigenous Peruvian Andean populations possess the highest <i>AMY1</i> copy number globally. A genome-wide analysis shows significantly higher amylase copy numbers in Peruvian Andean genomes compared to closely related populations. Further, we identify positive selection (selection coefficient of 0.0124, log likelihood ratio of 11.1543) at the nucleotide level on a haplotype harboring at least five haploid <i>AMY1</i> copies, with a Peruvian Andean-specific expansion dated to around 10,000 years ago, coinciding with potato domestication in the region. Using ultra-long-read sequencing, we demonstrate that previously&#xa0;described recombination-based mutational mechanisms drive the formation of high-copy <i>AMY1</i> haplotypes observed in Andean population. Our study provides a framework for investigating structurally complex loci and their role in human dietary adaptation.</p>

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Rapid adaptive increase of amylase gene copy number in Indigenous Andeans

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月5日

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  • Kendra Scheer,
  • Luane J. B. Landau,
  • Kelsey Jorgensen,
  • Charikleia Karageorgiou,
  • Lindsey Siao,
  • Can Alkan,
  • Angelis M. Morales Rivera,
  • Christopher Osborne,
  • Obed A. Garcia,
  • Laurel Pearson,
  • Melisa Kiyamu,
  • María Rivera-Ch,
  • Fabiola León-Velarde,
  • Frank S. Lee,
  • Tom Brutsaert,
  • Abigail W. Bigham,
  • Omer Gokcumen

摘要

The salivary amylase gene AMY1 exhibits remarkable copy number variation linked to dietary shifts in human evolution. While global studies highlight its structural complexity and association with starch-rich diets, localized selection patterns remain underexplored. Here, we analyze AMY1 copy number in 3,723 individuals from 85 populations, revealing that Indigenous Peruvian Andean populations possess the highest AMY1 copy number globally. A genome-wide analysis shows significantly higher amylase copy numbers in Peruvian Andean genomes compared to closely related populations. Further, we identify positive selection (selection coefficient of 0.0124, log likelihood ratio of 11.1543) at the nucleotide level on a haplotype harboring at least five haploid AMY1 copies, with a Peruvian Andean-specific expansion dated to around 10,000 years ago, coinciding with potato domestication in the region. Using ultra-long-read sequencing, we demonstrate that previously described recombination-based mutational mechanisms drive the formation of high-copy AMY1 haplotypes observed in Andean population. Our study provides a framework for investigating structurally complex loci and their role in human dietary adaptation.