Data from: Ultraconserved yet informative for species delimitation: UCEs resolve long-standing systematic enigma in Central European bees

Accurate and testable species delimitation hypotheses are essential for
measuring, surveying and managing biodiversity. Today, taxonomists often
rely on mitochondrial DNA barcoding to complement morphological species
delimitations. Although COI barcoding has largely proven successful in
assisting identifications for most animal taxa, there are nevertheless
numerous cases where mitochondrial barcodes do not necessarily reflect the
species history. For instance, what is regarded as one single species can
be associated with two distinct DNA barcodes, which can point either to
cryptic diversity or to deep within-species mitochondrial divergences with
no reproductive isolation. In contrast, two or more species can share
barcodes, for instance due to mitochondrial introgression. These intrinsic
limitations of mitochondrial DNA barcoding can only be addressed with
nuclear genomic markers, which are expensive, labour intensive, poorly
repeatable, and often require high-quality DNA. To overcome these
limitations, we examined the use of ultraconserved nuclear genetic
elements (UCEs) as a quick and robust genomic approach to address such
problematic cases of species delimitation. This genomic method was
assessed using six different bee species complexes suspected to harbour
cryptic diversity, mitochondrial introgression, or mitochondrial
paraphyly. The sequencing of UCEs recovered between 686 and 1860
homologous nuclear loci and provided explicit species delimitation
hypotheses in all investigated species complexes. These results provide
strong evidence for the suitability of UCEs as a fast method for species
delimitation even in recently diverged lineages. Furthermore, this study
provided the first conclusive evidence for both mitochondrial
introgression among distinct species, and mitochondrial paraphyly within a
single bee species.