Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar

Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM) approach to faunal identification, where DNA from non-diagnostic bone fragments is extracted and sequenced in parallel. However, a large proportion of fishing communities (both past and present) live in tropical regions that have sub-optimal conditions for long-term aDNA preservation. To date, the BBM method has never been applied to fish bones before, or to fossils excavated from an exposed context within a tropical climate. Here, we demonstrate that morphologically indistinct bulk fish bone from the tropics can be identified by sequencing aDNA extracted from 100 to 300 ya archaeological midden material in southwest Madagascar. Despite the biases of the approach, we rapidly obtained family, genus, and species-level assemblage information, and used this to describe a subset of the ichthyofauna exploited by an 18th century fishing community. We identified 23 families of fish, including benthic, pelagic, and coral-dwelling fishes, suggesting a reliance on a variety of marine and brackish habitats. When possible, BBM should be used alongside osteological approaches to address the limitations of both; however, this study highlights how genetic methods can nevertheless be a valuable tool for helping resolve faunal assemblages when morphological identification is hindered by taphonomic processes, lack of adequate comparative collections, and time constraints, and can provide a temporal perspective on fish biodiversity in the context of accelerated exploitation of the marine environment.

考古鱼骨的分类鉴定，可为古代沿海族群的生存策略提供关键认知。然而，针对物种丰富的化石组合——尤其是缺乏鉴别特征的颅后骨骼材料——开展可靠的形态学鉴定颇具挑战；破碎化、风化与灼烧等作用进一步阻碍了分类进程，导致考古遗址中大量骨骼无法被识别。通过古DNA（ancient DNA, aDNA）骨骼批量宏条形码（bulk-bone metabarcoding, BBM）技术开展动物群鉴定，可在一定程度上缓解这一局限：该方法可并行提取并测序无鉴别特征的骨碎片中的遗传物质。但古往今来，多数渔业群落均栖息于热带区域，而热带环境并不利于古DNA的长期保存。迄今为止，骨骼批量宏条形码技术尚未应用于鱼骨样本，亦未用于热带气候下暴露地层出土的化石。本研究证实，针对热带区域形态难以区分的批量鱼骨，可通过对马达加斯加西南部100至300年前的考古贝冢遗存中提取的古DNA进行测序实现鉴定。尽管该方法存在一定偏倚，但我们仍快速获取了科、属、种水平的类群组合信息，并借此描述了18世纪某渔业族群所利用的鱼类区系。本次研究共鉴定出23个鱼类科，涵盖底栖、中上层与珊瑚礁栖息鱼类，表明该族群依赖多种海洋及咸淡水生境。尽管在条件允许时，骨骼批量宏条形码技术应与骨骼学方法协同使用，以弥补二者各自的局限性，但本研究仍凸显出：当形态鉴定受到埋藏学过程、对比馆藏标本不足以及时间限制的阻碍时，遗传方法仍是解析动物群组成的宝贵工具；同时，其可在海洋环境加速开发的背景下，为鱼类生物多样性研究提供时间维度的观测视角。