The Y chromosome usually plays a critical role in determining male sex and comprises sequence classes that have experienced unique evolutionary trajectories. Here we generated 19 new primate sex chromosome assemblies, analysed them with 10 existing assemblies and report rapid evolution of the Y chromosome across primates. The pseudoautosomal boundary has shifted at least six times during primate evolution, leading to the formation of a Simiiformes-specific evolutionary stratum and to the independent start of young strata in Catarrhini and Platyrrhini. Different primate lineages experienced different rates of gene loss and structural and chromatin change on their Y chromosomes. Selection on several Y-linked genes has contributed to the evolution of male developmental traits across the primates. Additionally, lineage-specific expansions of ampliconic regions have further increased the diversification of the structure and gene composition of the Y chromosome. Overall, our comprehensive analysis has broadened our knowledge of the evolution of the primate Y chromosome.

Y 染色体通常在决定男性性别方面发挥着关键作用，并且包含经历了独特进化轨迹的序列类别。在这里，我们生成了 19 个新的灵长类性染色体组件，并与 10 个现有组件进行了分析，并报告了 Y 染色体在灵长类动物中的快速进化。在灵长类动物的进化过程中，伪常染色体边界至少发生了六次变化，导致了拟常染色体的形成——特定的进化层以及卡他尼和扁鼻的年轻层的独立开始。不同的灵长类谱系经历了不同的 Y 染色体基因丢失率以及结构和染色质变化。对几个 Y 连锁基因的选择促进了灵长类动物雄性发育特征的进化。此外，扩增区域的谱系特异性扩展进一步增加了Y染色体结构和基因组成的多样化。总的来说，我们的综合分析拓宽了我们对灵长类 Y 染色体进化的认识。