Data from: Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey

New Zealand's geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans (c. 1280 AD), its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand's extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct the first large-scale genetic survey of sub-fossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying over 5000 non-diagnostic bone fragments from archaeological and palaeontological sites, we reconstruct a rich faunal record of 111 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens, and characterise new extinct lineages of leiopelmatid frog (Leiopelma sp.) and kākāpō (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand's sub-fossil record not only contributes to our understanding of past biodiversity and pre-contact Māori subsistence practices, but also provides a more nuanced snapshot of anthropogenic impacts on native fauna following first human arrival.新西兰因其地理隔绝、缺乏本土陆生哺乳动物，以及冈瓦纳（Gondwanan）起源的特性，成为研究演化过程的理想场所。然而，自该群岛于公元1280年左右首次有人类定居以来，其独特的生物多样性便持续面临威胁；如今，据估计有49%的陆生鸟类区系已经灭绝。当前保护现存动物群的工作，有赖于对远古生态系统组成、过往灭绝事件的成因与时间节点的更深入认知。然而，要厘清新西兰已灭绝动物群的确切时空动态颇具挑战，因为仅有极小比例的动物得以保存为可通过形态识别的化石。本研究首次针对亚化石（sub-fossil）骨骼组合开展大规模遗传学调查，以阐明人类活动对新西兰环境造成的影响。研究团队通过遗传学手段，对来自考古与古生物遗址的5000余件无法通过形态学鉴定的骨骼碎片进行物种识别，由此重构了包含111个物种（鸟类、鱼类、爬行类、两栖类以及海洋哺乳动物）的丰富动物群记录。本研究报道了5种此前在新西兰考古贝冢中鲜有记录的鲸类物种，并对两类已从基因库中消失的灭绝新支系进行了特征描述：滑跖蟾科蛙类（Leiopelma sp.）与鸮鹦鹉（kākāpō，Strigops habroptilus）的单倍型。综合来看，本次对新西兰亚化石记录的分子普查，不仅增进了我们对远古生物多样性以及前殖民时期毛利人（Māori）生计方式的认知，还为人类首次定居新西兰后，人为活动对本土动物群造成的影响提供了更为细致入微的图景。