Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

古代 DNA 为人类历史的许多方面提供了新的见解。然而，我们缺乏对丹尼索瓦人和尼安德特人 Y 染色体的全面研究，因为大多数被测序到足够覆盖范围的标本都是女性。对两名丹尼索瓦人和三名尼安德特人的 Y 染色体进行测序表明，丹尼索瓦人的 Y 染色体在大约 70 万年前从尼安德特人和现代人类 Y 染色体共有的谱系中分裂出来，而后者在大约 37 万年前彼此分道扬镳。古代和现代人类 Y 染色体的系统发育关系不同于从常染色体基因组推断的种群关系，并反映了线粒体 DNA 系统发育，表明晚期尼安德特人的线粒体和 Y 染色体基因库均被替换。