The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations¹. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake², 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.

农业的采用引发了人类向富含淀粉的饮食的快速转变¹。淀粉酶基因促进淀粉消化，在一些淀粉摄入量高的现代人群中观察到淀粉酶拷贝数增加²，尽管缺乏近期选择的证据^3,4。在这里，使用来自大约 5,600 名当代和古代人类的 94 个长读长单倍型解析组装和短读长数据，我们解析了淀粉酶基因座结构变异的多样性和进化历史。我们发现淀粉酶基因在农业种群中的拷贝数高于渔业、狩猎和畜牧种群。我们确定了 28 种不同的淀粉酶结构结构，并证明在近代人类历史中，几乎相同的结构在不同的单倍型背景上反复出现。AMY1 和 AMY2A 基因分别经历了多次复制/缺失事件，突变率高达单核苷酸多态性突变率的 10,000 倍以上，而 AMY2B 基因重复共享单一起点。使用基于泛基因组的方法，我们推断了数千人的结构单倍型，在现代农业人群中以更高的频率识别了广泛重复的单倍型。利用 533 个古代人类基因组，我们发现在过去 12,000 年中，西欧亚人中含有重复的单倍型（基因拷贝数比祖先单倍型多）的频率迅速增加，这表明正向选择。总之，我们的研究强调了农业革命对人类基因组的潜在影响以及结构变异在人类适应中的重要性。