Exploring past biodiversity in Scotland and Ireland using environmental ancient DNA

该项目旨在利用从古代土壤和沉积物中提取的环境DNA（环境古DNA）来完善我们对苏格兰和爱尔兰过去生物多样性和生态系统的理解。它将从多达五个研究地点产生新的数据，这些研究地点以前分析过动物遗骸、花粉或植物大化石，并且已经通过放射性碳或其他测年方法建立了时间序列。最终的数量和具体地点将由学生与监督团队协商决定，但我们设想该项目将侧重于目前在我们各自部门正在研究的考古和古生态遗址，例如苏格兰中北部的伯克黑德皮克特堡垒（公元1千年）和泥炭巨石与爱尔兰中部的中石器时代遗址有关。作为博士项目的一部分，DNA分析将为选定的研究地点提供带有时间戳和高分辨率的当地动植物“快照”。利用叶绿体dna元条形码技术对叶绿体基因组中trnL基因的p6环（10-146个碱基对）进行花多样性评估（参考文献1）。哺乳动物的存在将通过针对线粒体16S基因的一小段（60-84个碱基对）进行评估（参考文献1），但目的还包括对富含哺乳动物DNA的DNA文库进行下一代霰弹枪测序（参考文献2）。结果将与先前从选定地点产生的古环境数据共同分析，并将其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）的综合培训，以及实地调查和取样（如取芯），以及花粉和大化石分析，作为aDNA分析的补充。在适用的情况下，该学生还将接受分析温度年代学和放射性碳年代的培训。

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.