Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation.

基因组和古代 DNA 数据彻底改变了古人类学和我们对人类进化的看法，具有无可争议的里程碑，例如尼安德特人和丹尼索瓦人基因组的测序。然而，使用遗传数据来识别、确定和量化进化事件（例如古代瓶颈或混合物）并不简单，因为推断可能取决于模型假设。在过去的二十年里，尼安德特人和智人血统成员杂交的想法越来越受欢迎。从不可能的理论的地位来看，它已经在人类进化生物学家中达成了共识。该理论主要由统计方法支持，这些方法依赖于人口模型最小化或忽略人口结构，尽管它广泛存在，并且如果忽视人口结构，人口结构会导致虚假人口事件的推断。我们在结构化和无混合的人类进化模型下模拟了基因组数据，发现所有测试的混合方法都在我们的模拟基因组中识别了长尼安德特人片段和一个从未发生过的混合事件。我们还观察到，几个已发布的混合模型未能预测重要的实证多样性或混合统计数据，并且我们可以从我们的结构化模型中识别出几种更好地联合预测这些统计数据的情景。使用古代 DNA 的模拟时间序列，结构化情景还可以预测实证 D 统计的轨迹。我们的结果表明，解释种群结构的模型对于提高我们对人类进化的理解至关重要，并且尼安德特人和智人之间的混合需要根据结构化模型重新评估。 除了尼安德特人案例之外，我们认为在许多物种中越来越多地记录的古代杂交事件，包括与其他古人类的杂交事件，也可能从这种重新评估中受益。