Resolving phylogenetic relationships of a recently and rapidly evolving lineage from western North America (Mentzelia section Bartonia, Loasaceae)

The landscape of western North America has dramatically transformed since
the Miocene to become increasingly heterogeneous, in turn promoting the
evolution of many rapidly radiating angiosperm lineages. Phylogenetic
relationships of these recently and rapidly radiating groups are difficult
to resolve as there is little genetic variation among species and a high
degree of noise from incomplete lineage sorting and hybridization.
Mentzelia section Bartonia (51 species; Loasaceae) exemplifies this
problem well. The clade has been investigated with Sanger sequencing,
RADSeq, and genome skimming methods, however, most species relationships
remain elusive due to low genetic variability. To better infer species
relationships, we applied a hybrid enrichment approach with the
Angiosperms353 probe set and implemented a novel bioinformatics workflow
that aimed to maximize phylogenetic signal and minimize noise from
low-quality sequences, paralogy, and incomplete lineage sorting. With our
phylogenomic approach, we found an increased resolution of species
relationships compared to previous studies based on nrDNA loci. Although a
few species relationships still do not have strong support, our results
indicate that our methods were effective in phylogenetic inference of this
recently and rapidly evolving lineage from western North America. To
better characterize major groups in the Section, we propose the formal
designation of three subsections: Decapetala, Multicaulis, and Multiflora.