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