The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.

哺乳动物雄性特异性 Y 染色体在性别决定和男性生育能力中起着关键作用。然而，由于其重复性和单倍体的性质，它经常在基因组组装中不存在并且仍然是个谜。类人猿的 Y 染色体代表了一个特殊的难题：它们的基因含量在人类和大猩猩之间比在人类和黑猩猩之间更相似，尽管人类和黑猩猩有一个更近的共同祖先。为了解决这个难题，我们在这里构建了一个包含来自所有现存类人猿属的 Ys 的数据集。我们从短序列和长序列读取生成倭黑猩猩和猩猩 Y 的组装，并将它们与公开可用的人类、黑猩猩和大猩猩 Y 组装进行比对。分析这个数据集，我们发现潘属，其中包括黑猩猩和倭黑猩猩，经历了加速的替代率。潘还表现出升高的基因死亡率。这些观察结果与潘的高水平精子竞争是一致的。此外，我们推断类人猿的共同祖先已经拥有与大多数人类和黑猩猩回文同源的多拷贝序列。尽管如此，每个物种也获得了不同的扩增序列。我们还检测到回文之间和内部的染色质接触增加（来自 Hi-C 数据），可能促进基因转换和结构重排。我们的研究结果突出了 Y 染色体进化的动态模式，并为研究濒危类人猿物种的雄性特异性扩散开辟了道路。