Metabarcoding of ancient eukaryotic DNA from Chew Bahir, Ethiopia: Reconstruction of past biodiversity responses to drastic environmental change

Chew Bahir钻探项目（CBDP）提供了热带沉积物样品，可能跨越了过去约650 kyrs。这些核心的DNA元条形码提供了热带湖泊环境的记录，在分辨率和时间跨度上都是独一无二的。在一项初步研究中，我们可以通过基于杂交捕获的元巴编码分析来自280米长的Chew Bahir岩心沉积层中的古真核生物DNA，沉积层长达70米，相当于150 kyrs BP。沉积物样品用特异性探针（“诱饵”）进行分类群和基因特异性DNA富集，并通过下一代测序进行分析。我们的目标是进一步评估在长CBDP核心中进行DNA元条形码编码的可能性。主要的研究问题是：（1）生态系统如何对短期但显著的干扰作出反应，例如，湖内和湖周围的严重干旱或湿度增加？我们将检验这样一个假设，即单一干扰事件将使受影响的生态系统受到超出恢复能力的干扰，即，改变生态系统的关键组成部分。由于我们的真核生物范围的方法，我们将能够量化对生物多样性的影响和对生态系统功能的推断影响。(2)全球和区域气候变化的后果是什么，例如在临界点？我们将推断生态系统从一个稳定模式到另一个扰动后的转变。具体来说，我们将阐明生态位是否总是重新占据相同的物种/进化谱系，或者它们是否会被其他类群/谱系取代，潜在地改变生态系统的属性。(3)在Chew Bahir和其他非洲核心记录中，生物群落的长期趋势和变化是什么？我们将联合收割机的结果，所有采样的沉积层，以阐明在目标真核生物的发生，无论是关于物种身份，神秘的遗传变异，（半定量）相对丰度的时间趋势。这将包括以前用作环境代用品的水生生物（介形虫、枝角类、轮虫、硅藻），但也进一步包括陆地环境的关键分类群（昆虫、啮齿动物、有蹄类动物、高等植物）。(4)在Chew Bahir和其他HSPDP核心中的DNA残留物可以提取和分析多久？我们的目标是探索基于DNA的检测的生物体在更深层的核心的可能性。此外，我们的目标是进一步优化实验条件，以最大限度地检索我们的目标类群的DNA，并尽量减少潜在的方法学偏差。我们将评估半定量丰度估计的可能性和限制（通过NGS读取计数或qPCR）跨层的核心（对应于时间点）和taxa.We使用国家的最先进的DNA宏基因组学，特别针对沉积层之前，在，和之后剧烈的环境扰动（主要是湿-干和干-湿转换），推断出的岩性分析的项目合作伙伴。

The Chew Bahir Drilling Project (CBDP) provides tropical sediment samples presumably spanning the last ~650 kyrs. DNA metabarcoding across these cores provides a record of a tropical lake environment, unique in resolution and time span. In a pilot study, we could analyze ancient eukaryotic DNA from the 280 m long Chew Bahir cores in sediment layers down to 70 m, corresponding to 150 kyrs BP by hybridization-capture-based metabarcoding. Sediment samples are subjected to taxon- and gene-specific DNA-enrichment with specific probes (“baits”) and analyzed by Next-Generation-Sequencing. We aim at further evaluating the possibility for DNA metabarcoding in the long CBDP cores. The principal research questions are: (1) How does the ecosystem react to short-term but significant disturbances, e.g., dramatic droughts or increased humidity in and around the lake? We will test the hypothesis that single disturbance events will perturbate affected ecosystems beyond resilience, i.e., alterate key components of the ecosystem. Thanks to our eukaryote-wide approach, we will be able to quantify effects on biodiversity and inferred impact on ecosystem function. (2) What are the consequences of global and regional climate shifts, for example at a tipping point? We will infer ecosystem shifts from one stable mode to another after a perturbation. Specifically, we will elucidate whether ecological niches are always reoccupied by the same species/evolutionary lineage or whether they will be replaced by other taxa/lineages, potentially changing ecosystem properties. (3) What are the long-term trends and shifts in the organismal communities in the Chew Bahir and other African core records? We will combine the results of all sampled sediment layers to elucidate the temporal trend in the occurrence of target eukaryotes, both regarding species identity, cryptic genetic variation, and (semiquantitative) relative abundance. This will include planktonic organisms previously used as environmental proxies (ostracods, cladocerans, rotifers, diatoms), but further encompass key taxa of the terrestrial environment as well (insects, rodents, ungulates, higher plants). (4) How far back in time can DNA remnants in the Chew Bahir and other HSPDP cores be extracted and analyzed? We aim at exploring the possibility for DNA-based detection of organisms in the deeper layers of the cores. Furthermore, we aim at further optimizing experimental conditions as to maximizing retrieval of DNA of our target taxa and to minimizing potential methodological biases. We will evaluate possibilities and limits of semiquantitative abundance estimation (via NGS read counts or qPCR) across strata of the core (corresponding to timepoints) and taxa.We use state-of-the-art DNA metagenomics, specifically targeting sediment layers before, at, and after drastic environmental perturbations (mostly wet-dry and dry-wet transitions), inferred by lithological analyses of project partners.