Exploring past biodiversity in Scotland and Ireland using environmental ancient DNA

该项目旨在使用从古代土壤和沉积物中提取的环境DNA(环境古代DNA)来完善我们对苏格兰和爱尔兰过去的生物多样性和生态系统的理解。它将从之前分析过的动物遗骸、花粉或植物大型化石的多达五个研究地点产生新的数据，这些研究地点的时间序列已经通过放射性碳或其他测年方法建立。最终的数量和具体的遗址将由学生与指导小组协商决定，但我们设想该项目将专注于我们各自系目前正在进行研究的考古和古生态遗址，例如苏格兰中北部的比彻斯特堡垒(公元1千年)，以及与爱尔兰中部的中石器遗址相关的泥炭巨石。作为这一博士项目的一部分，进行的DNA分析将提供选定研究地点当地动植物的时间戳和高分辨率‘快照’。将使用针对叶绿体基因组中trnL基因的p6环(10-146个碱基对)的叶绿体DNA代谢编码技术来评估花的多样性(参考文献1)。哺乳动物的存在将通过靶向线粒体16S基因的一小段(60-84个碱基对)来评估(参考文献1)，但目的也是包括对富含哺乳动物DNA的DNA文库进行下一代鸟枪式测序(参考文献2)。结果将与以前从选定地点产生的古环境数据进行联合分析，并置于爱尔兰和苏格兰更广泛的环境和气候序列中。该项目提供最先进的古代DNA方法(湿实验室和生物信息学)以及野外工作和采样(例如取芯)以及花粉和巨型化石分析的综合培训，作为对aDNA分析的补充。在适当的情况下，学生还将接受分析年代学和放射性碳测年的培训。

This project aims to refine our understanding of past biodiversity and ecosystems in Scotland and Ireland using environmental DNA extracted from ancient soil and sediments (environmental ancient DNA). It will generate new data from up to five study sites previously analysed for faunal remains, pollen or plant macrofossils, and for which temporal sequences are already established via radiocarbon or other dating methods. The final number and specific sites will be decided by the student in consultation with the supervisory team, but we envision that the project will focus on archaeological and palaeoecological sites currently undergoing research in our respective departments, such as the Pictish fort of Burghead in northcentral Scotland (1st millennium AD) and peat monoliths associated with a Mesolithic site in the Irish Midlands. The DNA analyses carried out as part of this PhD project will provide time-stamped and high-resolution 'snapshots' of local flora and fauna from the selected study sites. Floral diversity will be assessed using chloroplast DNA-metabarcoding techniques targeting the p6 loop (10-146 base pairs) of trnL gene in the chloroplast genome (Ref 1). The presence of mammals will be assessed by targeting a short stretch (60-84 base pairs) of the mitochondrial 16S gene (Ref 1) but with the aim to also include next-generation shotgun sequencing of DNA libraries enriched for mammalian DNA (Ref 2). The results will be co-analysed with previously generated palaeoenvironmental data from the selected sites and placed in the wider environmental and climatic sequences of Ireland and Scotland.The project offers comprehensive training in state-of-the-art ancient DNA methods (wet-lab and bioinformatics), as well as fieldwork and sampling (e.g. coring), and pollen and macrofossil analyses as a complement to the aDNA analyses. Where applicable, the student will also be trained in analysing tephrochronology and radiocarbon dates.