The inhabitants of New Guinea and its outlying islands have played an important role in the human history of the Pacific region. Nevertheless, the genetic diversity, particularly of pre-colonial communities, is still understudied. Here we present the ancient genomes of 42 individuals from Papua New Guinea (PNG). The ancient genomic results of individuals from Watom Island (Bismarck Archipelago) and the south and northeastern coasts of PNG are contextualized with new (bio-) archaeological data. The individuals’ accelerator mass spectrometry (AMS) dates span 2,500 years of human habitation, and our results demonstrate the influences of different dispersal events on the genetic make-up of ancient PNG communities. The oldest individuals show an unadmixed Papuan-related genetic signature, whereas individuals dating from 2,100 years before present carry varying degrees of an East-Asian-related contribution. These results and the inferred admixture dates suggest a centuries-long delay in genetic mixture with local communities after the arrival of populations with Asian ancestry. Two geographically close communities on the South Coast, AMS dated to within the past 540 years, diverge in their genetic profiles, suggesting differences in their interaction spheres involving groups with distinct ancestries. The inferred split time of these communities around 650 years before present coincides with intensified settlement activity and the emergence of regional trade networks.

新几内亚及其离岛的居民在太平洋地区的人类历史上发挥了重要作用。然而，对遗传多样性，特别是前殖民地社区的遗传多样性，仍然研究不足。在这里，我们展示了来自巴布亚新几内亚 （PNG） 的 42 个个体的古代基因组。来自瓦托姆岛（俾斯麦群岛）以及巴布亚新几内亚南部和东北部海岸的个体的古老基因组结果与新的（生物）考古数据进行了背景化处理。个体加速器质谱 （AMS） 测年跨越了 2,500 年的人类居住历史，我们的结果证明了不同扩散事件对古代巴布亚新几内亚社区基因构成的影响。最古老的个体显示出未混合的巴布亚相关遗传特征，而距今 2,100 年的个体则具有不同程度的东亚相关贡献。这些结果和推断的混合日期表明，在具有亚洲血统的人群到来后，与当地社区的遗传混合延迟了几个世纪。南海岸两个地理位置接近的社区，AMS 的历史可以追溯到过去 540 年内，它们的遗传图谱不同，这表明它们的互动范围存在差异，涉及具有不同祖先的群体。据推断，这些社区在距今前 650 年左右的分裂时间与定居活动的加剧和区域贸易网络的出现相吻合。