Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. 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 reflect species hypotheses. 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 within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability, and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved 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 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 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 provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.

During the Last Glacial Maximum (LGM), global sea levels were 120-130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy seadragon (Phycodurus eques, Syngnathidae), a brooder with low dispersal ability inhabiting kelp beds in temperate Australia. Reconstructions of the paleoshoreline revealed that the increase of shallow areas since the LGM was not uniform across the species’ range and we investigated the effects of these asymmetries on genetic diversity and structuring. Using targeted capture of 857 variable Ultraconserved Elements (UCEs, 2845 SNPs) in 68 individuals, we found that the regionally different shelf topographies were paralleled by contrasting population genetic patterns. In the west, populations may not have persisted through sea-level lows because shallow seabed was very limited. Shallow genetic structure, weak expansion signals and a westward cline in genetic diversity indicates a postglacial recolonization of the western part of the range from a more eastern location following sea-level rise. In the east, shallow seabed persisted during the LGM and increased considerably after the flooding of large bays, which resulted in strong demographic expansions, deeper genetic structure and higher genetic diversity. This study suggests that postglacial flooding with rising sea levels produced locally variable signatures in colonizing populations.

Premise Apocynaceae is the 10th largest flowering plant family and a focus for study of plant–insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non-model taxa, such as Apocynaceae. Methods Transcriptomes were used to design probes for targeted sequencing of putatively single-copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny. Results From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent-based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genus Apocynum. Intraspecific comparison of Elytropus chilensis individuals revealed numerous single-nucleotide polymorphisms with potential for use in population-level studies. Discussion Community use of this Hyb-Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.

Multigene families evolve from single‐copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high‐…