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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. Our phylogenomic approach increased phylogenetic resolution of species relationships compared to previous studies based on nrDNA loci. Although a few species relationships still lack 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. 

Abstract Cetyltrimethylammonium bromide (CTAB)–based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a “modified” CTAB protocol without explicitly stating how the protocol had been altered, creating non‐reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies. 

Abstract Premise The use of cetyltrimethylammonium bromide (CTAB) is an effective and inexpensive method of extracting DNA from plants. The CTAB protocol is frequently modified to optimize DNA extractions, but experimental approaches rarely perturb a single variable at a time to systematically infer their effect on DNA quantity and quality. Methods and Results We investigated how chemical additives, incubation temperature, and lysis duration affected DNA quantity and quality. Altering those parameters influenced DNA concentrations and fragment lengths, but only extractant purity was significantly affected. CTAB and CTAB plus polyvinylpyrrolidone buffers produced the highest DNA quality and quantity. Extractions from silica gel–preserved tissues had significantly higher DNA yield, longer DNA fragments, and purer extractants compared to herbarium‐preserved tissues. Conclusions We recommend DNA extractions of silica gel–preserved tissues that include a shorter and cooler lysis step, which results in purer extractions compared to a longer and hotter lysis step, while preventing fragmentation and reducing time.