湖泊沉积物古DNA揭示气候环境变化和生态演化

广泛分布的湖泊为连续沉积和保存历史时期多样化生物核酸分子提供了绝佳的自然档案。随着近年来古DNA提取和测序技术的进步以及组学技术的发展，利用湖泊沉积物古DNA重建古生态演化及其对气候变化和人类活动的差异性响应得到广泛而深入的研究。本文回顾了古DNA研究的历史背景、理论基础，以及湖泊沉积物古DNA保存的影响因素和生物信息学分析流程；重点评述了湖泊沉积物古DNA在揭示气候环境变化、生物多样性及流域生态系统演化、物种定殖与外来物种入侵、人类活动影响、环境生态功能基因演化及其在细胞器基因组和古生态时间序列分析研究中的诸多应用和进展。同时还介绍了当前研究面临的局限和挑战以及组学技术在古DNA研究中的发展概况，分析了当前研究尚存的不足，并展望了未来可能的努力方向。

Lake sedimentary ancient DNA (sedaDNA) reveals paleoclimatic change and ecological evolution

Background, aim, and scope Lake sediment records provide an archive of past climate and ecological evolution. Recent advances in paleogenomic sequencing have enabled the analysis of sedimentary ancient DNA (sedaDNA) from lakes globally, and thus allow the molecular reconstruction of long-term ecological changes and their responses to climatic change and anthropogenic impacts. Here, we summarize the historical background to the study of ancient DNA and the factors affecting DNA in lake sediments. The major bioinformatic pipelines and other recent advances, up to the present, are also reviewed. We then examine the recent applications of sedaDNA, particularly in terms of paleoclimate and evolutionary events. Finally, we recommend future research based on current knowledge and technical feasibility. Materials and methods We compiled a series of publications about sedaDNA retrieved from different environmental settings, covering multiple taxonomic groups and abundant case studies across diverse spatiotemporal scales. Results SedaDNA-based evolutionary inferences provide insights into paleoenvironmental compositions and dynamics, floral and faunal dispersal, and ecologies under selection pressures in different areas. Studies have shown that the preservation characteristics of sedaDNA are mainly controlled by environmental features, geochemical conditions, and biotic factors. The data analysis workflows for high-throughput sedaDNA sequencing assays include: (1) the segregation of environmental specimens; (2) DNA extraction and library preparation; (3) PCR amplification and next-generation sequencing; (4) phylogenetic analysis; (5) identification of endogenous sedaDNA from the environmental context; and (6) quantification of exogenous contamination and the establishment of a molecular damage model. Numerous studies have demonstrated the potential utility of the sedaDNA in lakes as a powerful tool to better understand the biological past and trace evolutionary history in real time. Discussion The characterization of past climate change, ecosystems, and anthropocentric practices through sedaDNA analyses has extended the biomolecular window to allow the establishment of a high-resolution paleogenetic framework. The origin and taphonomy of sedaDNA in lakes and the influence of biological and environmental factors affect not only the presence and relative abundance of nucleic acids, but the subsequent analytical strategies used. Although formerly restricted by the fragmentation of ancient DNA molecules, lake sedaDNA studies can now investigate ecology and evolution dating back tens of thousands of years. Conclusions The genetic signals obtained from lake sediments can provide deep insights into past landscape development, human activities, and ecological dynamics. All aspects of the methodologies and technologies used are highly significant in reconstructing the lentic ecosystem and the terrestrial environment around a lake. To date, a variety of advances and breakthroughs have been achieved with lake sedaDNA. However, key issues and challenges remain for such studies, in terms of both modern contamination and bioinformatics. Recommendations and perspectives The field of sedaDNA research is likely to take many new directions in the coming years, which will refine our understanding of important molecular histories and long-standing paleoecological questions across various fields. Here, we outline a few selected examples that may provide new insights into both recent and deep biodiversity and population dynamics. (1) The exact taphonomy of sedaDNA, which is species-specific in different aquatic deposit archives, is poorly understood and should be investigated in detail. (2) A new stage in the sedaDNA field of reconstructing the environmental drivers of evolution may be the direct comparison of sedaDNA and organic molecular compositions in ancient lacustrine sediments, aided by Fourier-transform ion cyclotron resonance-mass spectrometry (FT-ICR-MS). (3) It is predicted that future studies will use multi-proxy approaches, including paleogenomics, paleoproteomics, and ancient lipidomics, integrating the analyses of environmental proxies to clarify more-complex evolutionary questions.