2026年8月27日，美国约翰霍普金斯大学Arjun Biddanda等科学家在《科学》发表研究，开发了TRACE方法，利用祖先重组图在无需古人类参考基因组的情况下恢复古人类基因渗入信号。

现代人与已灭绝古人类之间的混血塑造了现代个体的基因组，但重建这一历史一直受到古人类样本稀缺和缺乏未混血外群群体的限制。研究人员引入了TRACE——一种无需参考基因组和外群的方法，利用祖先重组图的特征来识别古人类血统。模拟表明，TRACE实现了高精度和低假阳性率。应用于千人基因组计划数据时，TRACE恢复了已知的尼安德特人和丹尼索瓦人基因渗入，并揭示了非洲人和非非洲人中来自未知古人类的幽灵混血。幽灵血统在尼安德特人和丹尼索瓦人血统荒漠中持续存在，挑战了将它们解释为智人特有区域的看法。在大洋洲人群中，TRACE发现深层谱系在丹尼索瓦人区域相较于尼安德特人区域更为富集，支持超古人类基因渗入的存在。TRACE使得在无需古人类参考基因组的情况下绘制古人类基因渗入图谱成为可能。

附：英文原文

Title: Recovering signatures of archaic hominin introgression using ancestral recombination graphs

Author: Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, Priya Moorjani

Issue&Volume: 2026-08-27

Abstract: Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unadmixed outgroup populations. We introduce TRACE, a reference- and outgroup-free approach that uses features of ancestral recombination graphs to identify archaic ancestry. Simulations demonstrate that TRACE achieves high precision and low false discovery rates. Applied to 1000 genomes, TRACE recovers known Neanderthal and Denisovan introgression and uncovers ghost admixture from uncharacterized hominins in both Africans and non-Africans. Ghost ancestry persists in Neanderthal and Denisovan ancestry deserts, challenging their interpretation as Homo sapiens–specific regions. In Oceanians, TRACE finds that deep lineages are enriched in Denisovan compared with Neanderthal regions, supporting super-archaic introgression. TRACE enables mapping of archaic introgression without archaic reference genomes.

DOI: 10.1126/science.aef8874

Source: https://www.science.org/doi/10.1126/science.aef8874