Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale¹, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago². Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

时间基因组数据在研究进化过程（如物种形成）方面具有巨大潜力。然而，在许多情况下，跨物种形成事件的采样需要能够很好地追溯到早更新世亚纪的基因组时间序列。尽管理论模型表明 DNA 应该在这个时间尺度上存活¹，但迄今为止发现的最古老的基因组数据来自于 780-56 万年前的马标本². 在这里，我们报告了从早更新世和中更新世亚纪的三个猛犸象标本中恢复的全基因组数据，其中两个超过一百万年。我们发现早更新世期间东西伯利亚存在两个不同的猛犸象血统。其中一个谱系产生了长毛猛犸象，另一个代表了一个以前未被识别的谱系，它是第一批在北美殖民的猛犸象的祖先。我们的分析表明，北美哥伦比亚猛犸象的祖先可追溯到这两个谱系之间的中更新世杂交，混合比例大致相等。最后，我们表明，与长毛象寒冷适应相关的大多数蛋白质编码变化在一百万年前就已经存在。