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

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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.