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 without 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 are commonly only be addressed with nuclear genomic markers, which are expensive, have low repeatability, and 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 in bees. 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, we this study provided the first conclusive evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species. Less...