Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans

在DFG SPP“TaxonOmics”第一阶段资助的项目中，我们建立了一套用于后生动物核条形码的标记，该标记依赖于动物基因组中几乎只存在于单拷贝的基因（通用单拷贝基因- USCOs）。利用目标DNA富集，我们以节肢动物为例，评估了USCOs在物种划分中的适用性和优势。在SPP的第二阶段，我们计划评估USCO条形码方法的鲁棒性，并将其性能与COI条形码进行比较。我们特别感兴趣的是USCOs容易高估物种的真实多样性，这是COI条形码所面临的一个问题。为此，我们将在之前项目的基础上增加亚种地理采样，重点关注我们在SPP第一阶段已经调查过的群体：蝴蝶、地窖蜘蛛、蜈蚣、金甲和食蚜蝇。我们还计划研究基因流——这是传统条形码方法无法实现的。进行上述研究所需的所有生物信息学步骤将整合到生物信息学管道中。在这种情况下，我们将计划评估各种序列组装和物种划分方法的性能。为了确定USCOs覆盖核基因组全长的程度，以及它们是否有聚集的倾向（后者将对依赖这些基因的统计分析产生影响），我们将应用长读DNA测序技术来确定USCOs在研究群体中选定物种核基因组中的位置。

In our project funded during phase I of the DFG SPP "TaxonOmics", we established a set of markers for nuclear barcoding of Metazoa that rests on genes that almost exclusively occur in single-copy in the genomes of animals (universal single copy genes — USCOs). Using target DNA enrichment, we assess applicability and strengths of USCOs for delimiting species on the example of selected groups of arthropods. In the second phase of the SPP, we plan to assess the robustness of the USCO barcoding approach and to compare its performance with that of COI barcoding. We are particularly interested in the susceptibly of USCOs for overestimating the true species diversity, a problem that COI barcoding is known to suffer from. For this purpose, we will increase the infraspecific geographic sampling relative to that in our preceding project, focusing on groups which were already investigated by us during phase I of the SPP: butterflies, cellar spiders, centipedes, chafer beetles, and hoverflies. We additionally plan to study gene flow— something that would not be feasible with the classical barcoding approach. All bioinformatic steps required to conduct the above research will be integrated in a bioinformatics pipeline. In this context, we will plan to assess the performance of various sequence assembly and species delimitation approaches. To determine how well USCOs cover the full length of nuclear genomes and whether or not they perhaps show a tendency to cluster (the latter would have consequences for statistical analyses relying on these genes), we will apply long-read DNA sequencing techniques to determine the position of USCOs in the nuclear genomes of selected species from the investigated groups.