Iris L. s.l. is one of the most diverse and well-known genera in the Asparagales, with approximately 250–300 circumscribed species and significant economic impact. The taxonomy of the genus has suffered dramatic changes in the last century, particularly in the last decades after the application of molecular techniques. As a result several contrasting systematic arrangements are currently available to taxonomists. Many genera that were split from Iris s.str. in the past, on the basis of morphology (e.g., Hermodactylus, Iridodictyum, Juno, Pardanthopsis, and Xiphion, among others), are now a priori re-included in a very widely circumscribed Iris s.l. (incl. Belamcanda). This resulted in a more heterogeneous genus that is more difficult to define on morphological grounds. Testing congruence between taxonomic treatments and the results of recent molecular studies of Iris has never been performed, mostly due to the lack of proper taxonomic context. We generated several conventional phylogenies for Iris & outgroups using extensive sampling of taxa (187) and characters (10 plastid loci). We demonstrate that the natural history of Iris, written either as conventional molecular phylogenies or, if viewing in the context of the comparative approach, as a nested most parsimonious hierarchy of patterns, appear to be fully congruent with the narrow taxonomical treatment of the genus, restricted to the rhizomatous “bearded” taxa. The resulting topologies place Belamcanda, Pardanthopsis, and Gattenhofia as sisters to Iris s.str. and genus Siphonostylis as sister to Iris s.l. The present study clearly justifies the splitting of Iris s.l. into at least 23 genera, 18 of which have already been accepted in the past by numerous authorities. These genera are characterized by unique combinations of partly overlapping morphological characters and biogeography. Moreover, nearly the same entities, which we here recognize at a generic rank, were for centuries frequently referred to by horticulturists as “working-name” groups.

An open-access program for generating three-item statement (3TS) matrices from data such as molecular sequences does not currently exist. The recently developed LisBeth package allows for representation of hypotheses of homology among taxa or areas directly as rooted trees or as hierarchies; however, LisBeth is not a standard matrix-based platform. Here we present “TAXODIUM version 1.0” (TAXODIUM), a program designed for building 3TS-matrices from binary, additive (ordered) and non-additive (unordered) multistate characters, with both uniform and fractional weighting of the statements. TAXODIUM also facilitates, for the first time, use of Maximum Likelihood analyses with 3TS matrices, but future implementation of the 3TS analysis in a statistical framework will require more exploration.

Summary: Tragopogon includes two classic examples of recently formed allopolyploid species in North America: T. mirus and T. miscellus. Older Tragopogon allotetraploids from Eurasia offer ideal taxa for comparing the longer term outcomes of allopolyploidy. To help resolve the ancestry of one of these older polyploids, phylogenetic analyses of multiple populations of the allotetraploid T. castellanus (2n = 24) and its putative diploid parents, T. crocifolius and T. lamottei, were conducted using sequences from nuclear (internal transcribed spacer, ITS; and alcohol dehydrogenase 1A, Adh) and plastid (trnT‐trnL spacer, trnL intron, trnL‐trnF spacer and rpl16 intron) loci. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used to investigate the chromosomal constitution of T. castellanus. Our data confirm that the widely distributed T. crocifolius and the Iberian endemic, T. lamottei, are the diploid parents of T. castellanus, and that this polyploid formed at least three times. One group of populations of T. castellanus is distinct in exhibiting two pairs of rearranged chromosomes. These data suggest that some of the chromosomal variants that originate in young polyploids (here, an intergenomic translocation) may become fixed in populations, contributing to novelty in older polyploid lineages. The geographical distributions of the allopolyploids and parents are also complex, with allotetraploid populations being disjunct from one or both of the most closely related diploid parental populations.

Premise: Commonly used molecular techniques such as next‐generation sequencing require reliable methods to extract DNA quickly and efficiently. Secondary compounds within plant tissues make this requirement all the more challenging, often forcing researchers to test different extraction methods tailored to their particular species of interest in order to obtain large amounts of high‐quality genomic DNA. The opportunities provided by high‐throughput, next‐generation sequencing only exacerbate these problems, especially when trying to extract DNA from multiple species at the same time. Several methods have attempted to resolve the challenges of obtaining suitable DNA from plants; however, a rapid, high‐yield, high‐quality, and highly scalable DNA extraction method is still needed.Methods and Results: We present a rapid DNA extraction protocol that utilizes a buffer with relatively large amounts of cetyltrimethylammonium bromide (CTAB) and sodium chloride, combined with a silica maxi‐column cleanup of the extracted DNA. The new method is easy to implement using standard equipment and inexpensive reagents. The entire procedure (from grinding to the final elution) can be completed in less than two hours for a single sample and can be easily scaled to meet desired research goals. It works on diverse green plants with highly varied secondary chemistries (e.g., ferns, gymnosperms, and phylogenetically divergent angiosperms).Conclusions: Application of the protocol to various plant species yielded DNA of high quality in less than two hours and can be adjusted to extract DNA at large (maxi‐preps) or small (96‐well minipreps) scales. We anticipate that our method will be of wide utility for rapidly isolating large quantities of quality genomic DNA from diverse plant species and will have broad applications in phylogenetic studies utilizing PCR and short‐read DNA sequencing.