Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation

Structured Abstract

INTRODUCTION

Human adaptation to a wide range of diets is a hallmark of our species, sometimes even reflected in our genomic diversity. The amylase gene encodes an enzyme that digests starch, a complex carbohydrate found in many modern human diets. Genomic studies have found substantial variation in the number of amylase gene copies, which is believed to be an adaptive response to dietary changes among human populations, after the advent of agriculture. However, the sequence complexity of the amylase gene region has hindered our understanding of the evolution of its variation and functional implications over time.

RATIONALE

Recent technological advances have made it possible to resolve the sequence complexity of the amylase gene region with unprecedented accuracy and detail. Our study has reconstructed this region at nucleotide-level resolution in 98 individuals, using a combination of long-read sequencing and optical genome mapping technologies. We have now elucidated the mechanisms that have given rise to the genetic and protein variation of amylase and provided insights into the evolutionary trajectory and potential functional effects of this genomic region throughout human history.

RESULTS

Our study has identified 30 distinct structural patterns of the amylase gene region across the genomes of 98 modern-day humans. We have found evidence for negative selection at the protein level to maintain the essential function of the amylase genes. Furthermore, we identified two distinct mechanisms, with different mutation rates, that produce the copy number variation and structural patterns seen for the salivary (AMY1) and the pancreatic (AMY2A and AMY2B) genes, respectively. Analysis of archaic hominin genomes showed that some Neanderthals harbored AMY1 duplications. We also found that hunter-gatherers already had highly variable AMY1 copy numbers as early as 45,000 years ago, followed by a significant increase in the AMY1 copy number in the genomes of European farmers over the past 4000 years.

CONCLUSION

The molecular archaeology of the amylase region, one of the most structurally dynamic and fastest evolving regions of the human genome, has been comprehensively dissected in this study. Our findings suggest that the initial event leading to multiple AMY1 copies occurred far before agricultural transitions, possibly even before the human-Neanderthal split. Our results are consistent with an evolutionary scenario where an initial duplication of the AMY1 gene occurred ~800,000 years ago, leading to the generation of common structural patterns containing three AMY1 genes. Moreover, our data further demonstrate that copy number variation in the AMY1 and AMY2 genes has emerged through two distinct mechanisms. Given the frequency increase in higher AMY1 copy number patterns in the past 4000 years, selection may have acted on this existing AMY1 copy number variation, consistent with an adaptive response to the increased role of starch in diets. Taken together, our study provides a robust framework that carefully contextualizes the impact of environmental factors and human lifestyles (such as specific dietary preferences) on the evolution of complex regions of the human genome.

Implications of reconstructing complex genetic variation in the amylase locus.
The comprehensive map of the human amylase locus revealed structural variations such as duplications and inversions (top). Negative selection was observed on all amylase gene–coding sequences (bottom left). Two mechanisms were identified behind these variations: nonallelic homologous recombination (NAHR) and microhomology-mediated break-induced replication (MMBIR) (bottom-middle). Amylase gene duplications predate agriculture and possibly the human-Neanderthal split (bottom right). A putative adaptive increase in variation among European farmers was noted over the past 4000 years. [Figure created with BioRender]