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I阶段期间资助的我们的项目中，我们建立了一组用于后生动物核条形码化的标记物，其依赖于几乎仅以单拷贝存在于动物基因组中的基因（通用单拷贝基因-USC 0）。使用目标DNA富集，我们评估的适用性和优势的USCOS界定物种的例子，选定的节肢动物群体。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高估了真正的物种多样性，这是COI条形码所面临的一个问题。为此，我们将增加种下地理采样相对于我们的前一个项目，集中在我们已经调查的组在SPP的第一阶段：蝴蝶，地窖蜘蛛，蜈蚣，金龟子甲虫，和hoverflies。此外，我们计划研究基因流-这是不可行的与经典的条形码方法。进行上述研究所需的所有生物信息学步骤将被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界方法的性能。为了确定USCOs覆盖核基因组全长的程度以及它们是否可能表现出聚类的趋势（后者将对依赖于这些基因的统计分析产生影响），我们将应用长读段DNA测序技术来确定USCOs在所研究群体中选定物种的核基因组中的位置。

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.