Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA and in the trnL-tmF region of cpDNA from 28 specimens of Jubula (Jubulaceae), and two outgroup species, was analyzed using maximum parsimony and maximum likelihood. The molecular topologies supported five to six allopatric taxa in Jubula. Relationships of most of these taxa remain unresolved due to lack of support of many deeper nodes. A principal component analysis indicated a broad overlap of morphological characters of these taxa. Based on the morphological similarities of the Jubula taxa and the observed low sequence variation, a subspecies concept is supported. This comprises the taxa J. hutchinsiae subsp. bogotensis, subsp. hutchinsiae, subsp. japonica, subsp. javanica, and subsp. pennsylvanica. With the exception of J. hutchinsiae subsp. javanica, all taxa are monophyletic. Multiple accessions of the temperate taxa J. hutchinsiae subsp. hutchinsiae and J. hutchinsiae subsp. pennsylvanica exhibit a lower sequence variation than the tropical taxa J. hutchinsiae subsp. bogotensis and J. hutchinsiae subsp. javanica.

A new fern species, Polystichum speluncicola (sect. Haplopolystichum, Dryopteridaceae), is described from a karst cave in southern Guizhou, China. The new species has deltoid-ovate pinnae and subulate microscales with dilated bases on the abaxial lamina surface (broad-type microscales), characters unknown for any other members of sect. Haplopolystichum s. s. It also has oblanceolate laminae and its pinnae are close-set, subcoriaceous, adaxially lustrous, deltoid-ovate, repand, their acroscopic bases round, and basiscopic bases cuneate, often forming 20–60-degree angle with the rachis; the basal pinnae are shorter and strongly reflexed. Palynologically, P. speluncicola has cristate sculpturing with numerous spinules on its perispore. A preliminary phylogenetic analysis based on DNA sequences from the trnL-F intergenic spacer showed that P. speluncicola, together with P. subacutidens, “P. yuanum,” and species of Cyrtomium subser. Balansana, formed an unresolved polytomy. Polystichum speluncicola can easily be distinguished morphologically from these species by broad-type microscales, deltoid-ovate pinnae, and fewer pairs of pinnae per lamina. Our phylogenetic analysis resolved Cyrtogonellum as paraphyletic in relation to Polystichum sect. Haplopolystichum s. 1.

Several cytotypes (polyploids and aneuploids) have been reported in Lepisorus thunbergianus. The relationships between these cytotypes within the species remain poorly understood. We studied populations in an area where various cytotypes of L. thunbergianus as well as two diploid species, L. angustus and L. onoei, candidate parental species that may be involved in allopolyploid origins of L. thunbergianus polyploids, occur. We determined the ploidy levels of sampled materials by direct chromosome counting and flow cytometry. We elucidated the origins of L. thunbergianus polyploids by analyzing allozyme polymorphisms, and in addition, we examined the occurrence of segmental allopolyploidy by comparing allelic variation between polyploids and their parental diploids. Six cytotypes, i.e. one diploid (2n = 50), two triploid (2n = 75 and 76) and three tetraploid (2n = 100, 101, and 102) cytotypes, were observed in L. thunbergianus, and the two diploid species, L. angustus (2n =52) and L. onoei (2n =50) were confirmed to include a single cytotype each. Allozyme analyses indicated that the tetraploid (2n =100) and hypertetraploid (2n = 102) of L. thunbergianus originated by allopolyploidy between diploid L. thunbergianus (2n = 50) and diploid L. angustus (2n = 52), since the polyploids shared alleles with these two diploids that were unique to each diploid. The allozyme patterns excluded the possibility that L. thunbergianus polyploids originated from L. onoei. The unbalanced heterozygosity and homozygosity found in the tetraploid and the hypertetraploid of L. thunbergianus indicated their segmental allopolyploidy.

Three new species of Pseuduvaria (Annonaceae) from Peninsular Thailand and Peninsular Malaysia are described and named as P. fragrans, P. gardneri, and P. glossopetala. A recent molecular phylogenetic study, based on 51 species (including P. fragrans), elucidated the evolutionary relationships within the genus. The present study includes P. gardneri and P. glossopetala in the phylogenetic analyses using maximum likelihood and Bayesian inference methods, based on five chloroplast regions (psbA—trnH spacer, trnL—F, matK, rbcL, and atpB—rbcL spacer). The new nomenclatural combination Pseuduvaria phuyensis is also validated in accordance with the phylogenetic analyses which show that Craibella phuyensis and Pseuduvaria form a well-supported monophyletic clade. The new species and new nomenclature combination bring the total number of species in Pseuduvaria to 56. The taxonomic status of the enigmatic monotypic genus Oreomitra from New Guinea is furthermore evaluated, and the name shown to be synonymous with Pseuduvaria.

A systematic revision of the Epipetrum group of Dioscorea (Dioscoreaceae), which traditionally included three taxa endemic to Chile, is presented. We evaluated the taxonomic value of macro- and micromorphological traits to delimit generic boundaries with respect to other yams and to identify and separate its taxa. The comprehensive survey included 10 qualitative and 43 quantitative traits related to all plant organs and new microanatomical features of leaf, fruits, seeds, and pollen. Discriminant analyses were conducted with three accumulative morphological data sets to test seven taxonomic hypotheses of differentiation among taxa. Our results indicate that these taxa are characterized by the combination of prominent pistillodes in male flowers and a base chromosome number of x = 7, which separate it from all other Dioscoreaceae, plus different sets of morpho-anatomical traits that differentiate it from other putatively closely related yams with unwinged seeds in Dioscorea (the Borderea group, the Nanarepenta group, the Tamus group, etc.). Dioscorea biloba is the most distinctive species. Our analyses revealed significant morphological differences between northern and southern populations of this species resulting in the recognition of two subspecies, the northern D. biloba subsp. biloba, and the new southern D. biloba subsp. coquimbana. Dioscorea humilis and D. polyanthes are morphologically similar and only differ in qualitative leaf traits. This minor variation is better treated by reducing D. polyanthes to subspecific rank in D. humilis, and the combination D. humilis subsp. polyanthes is made herein.

Phylogenetic analyses were conducted on six plastid markers and ITS from 43 accessions representing all eight currently recognized Hexalectris species with the goals of testing species circumscriptions and determining interspecific relationships. The monophyly of H. warnockii, H. grandiflora, H. brevicaulis, and H. nitida, plus the H. spicata species complex, are strongly supported. The remaining species are not monophyletic, prompting the recircumscription of H. spicata s. 1. as H. spicata s. s. and H. arizonica, H. revoluta s. 1. as H. revoluta s. s. and H. colemanii, and H. fallax as a synonym of H. parviflora. Four major morphologically distinct lineages exist within the genus: H. warnockii, H. grandiflora, H. brevicaulis, and the H. spicata species complex. Within the latter, only H. spicata s. s. and H. nitida are strongly supported as sister species among all trees. The positions of H. revoluta s. s. and H. parviflora remain unresolved due to incongruence in the plastid trees when psbA is included or excluded, while the positions of H. colemanii and H. arizonica are unclear due to incongruence between plastid and ITS topologies. The latter incongruence suggests that either or both species are of hybrid origin or that the ITS topology has been influenced by incomplete lineage sorting.

Camassia is a genus of six bulb-forming species endemic to North America that have figured prominently in the culture and sustenance of native peoples. In western North America they form a conspicuous element of wet meadows and forest openings. Species and, especially, subspecies delimitations have been problematic. Further, several hypothesized phylogenetic and biogeographic scenarios for the origin and diversification of the genus remain untested. We estimated the phylogeny of Camassia using two noncoding plastid DNA regions: rpl16 intron and trnD—trnY—trnE—trnT spacers, with the goals of evaluating 1) the delimitation of species and 2) Gould's hypotheses for the origin of species and infraspecific taxa. Maximum parsimony and Bayesian analyses provided concordant estimates of the phylogeny consistent with the monophyly of eastern American C. scilloides and western American C. howellii and C. leichtlinii. Two western American species were found to be paraphyletic—C. cusickii weakly so, but C. quamash was strongly supported as paraphyletic to C. cnsickii, C. scilloides and C. angusta. Our results are largely consistent with Gould's views that the genus originated in southwestern Oregon and diversified through eastern migration, and that C. scilloides and C. cusickii are derived from within C. quamash. Despite evidence that Camassia species hybridize, by sampling sympatric populations we detected only a single case of introgression of plastid haplotypes. This study provides the first molecular phylogenetic and phylogeographic context for evaluating evolutionary process and trait variation in this iconic genus of western North America.

Tillandsia subgenus Tillandsia as defined by Gardner includes 269 species in five groups. Within Group I, species in the Tillandsia bulbosa complex share a remarkable synapomorphy: a pseudobulb. We sampled the 13 species of pseudobulbous Tillandsia (including T. intermedia) in addition to 18 species from the five groups of subgenus Tillandsia and four species as outgroups to perform phylogenetic analyses of sequences from two nuclear ribosomal DNA markers (ITS 2 5.8S and ETS). Three combined parsimony analyses explored the effects of indels treated as missing data, fifth character states, and with the simple indel coding method. Results show that all 13 species of pseudobulbous Tillandsia are placed within a group that also includes five non-pseudobulbous species. The pseudobulb habit is optimized as a synapomorphy for this group although with three reversals. Our analyses also show that sequence variation at ITS 2 5.8S and ETS provided resolution and indels are an important source of phylogenetic information. All previously used chloroplast markers have been shown to be almost invariant even among distantly related species in Tillandsia. Therefore, both nuclear markers assayed here are promising sources of sequence variation for reconstruction of phylogenetic relationships among species of Tillandsia and other Bromeliaceae.

A new species of Tarigidia from Puerto Rico is described and illustrated. Additional micromorphological characters of the inflorescence and spikelets are included. This species constitutes the first report of the genus Tarigidia in the New World. Tarigidia axelrodii grows together with Anthephora hermaphrodita and Digitaria bicornis, showing intermediate characters. This species gives additional evidence to support Loxton's hypothesis that Tarigidia is derived from hybridization between Anthephora and Digitaria and also supports the phylogenetic hypothesis showing close relationships between Anthephora and Digitaria.

The temperate bamboos are a morphologically diverse grass lineage with a complex and problematic taxonomy. We present the first robust multilocus chloroplast phylogeny of the temperate bamboos, assess relationships among key genera with an emphasis on Arundinaria and its allies, and highlight the potential role of hybridization and reticulate evolution in this group. Utilizing a total of twelve plastid DNA regions (1 gene, 10 intergenic spacers, and 1 intron), the temperate clade was resolved to include six major lineages: Bergbamboes, the African alpine bamboos, Chimonocalamus, the Shibataea clade, the Phyllostachys clade, and the Arundinaria clade. Internal resolution varied among these six, in part reflecting sampling density and in part due to apparent evolutionary rate heterogeneity. The recovered phylogeny is largely incongruent with morphological classifications, rendering subtribes and many genera paraphyletic or polyphyletic. Some associations are consistent with existing hypotheses of intergeneric hybridization, while others may indicate convergent evolution, lineage sorting, or previously unsuspected cases of hybridization. Several robust lineages were identified within the Arundinaria clade, including the Medake subclade (Pleioblastus s. s. and allies), Sasa s. s., and the Sinicae subclade (comprising a subset of Chinese taxa currently classified in Acidosasa, Indosasa, Pleioblastus sect. Amari, and Pseudosasa subg. Sinicae). Our analyses also recovered a monophyletic Arundinaria s. s. in North America, and revealed substantial divergence between A. gigantea and A. tecta.

The angiosperm genus Myriophyllum (Haloragaceae) is among the most species-rich genera of aquatic core-eudicots. Myriophyllum has a cosmopolitan distribution with its center of diversity in Australia (> 37 endemics). The widespread invasive species of the genus (M. aquaticum, M. heterophyllum, and M. spicatum) have drawn attention from international natural resource managers. Myriophyllum species are notoriously difficult to identify using vegetative morphology alone, which commonly is all that is available for these highly clonal plants. The relationships among taxa have been difficult to determine with suspected parallelisms in sex expression, sepal and petal loss, and reduced stamen number. A molecular phylogenetic approach was taken to examine relationships among taxa and to employ molecular markers for the reliable identification of Myriophyllum species. This study included ≈ 80% of the known Myriophyllum species. Both nrDNA ITS and cpDNA matK and trnK data were used to examine phylogenetic relationships among species. The nrDNA ITS data proved highly variable and could differentiate between all but one species pair examined. These analyses also uncovered multiple cryptic species among Australian complexes. Phylogenetic results support major realignments in the subgeneric classification including a recombination for the rare monotypic genus Meziella, which was nested within Myriophyllum. Here we present the new combinations and taxa Myriophyllum subgenus Meziella, sections Pectinatum and Pelonastes, subsections lsophylleae and Nudiflorum with the new combination Myriophyllum trifidum to accommodate the former monospecific genus Meziella.

The Medicago sativa species complex includes tetraploid cultivated alfalfa and several other diploid and tetraploid taxa that are recognized either as subspecies of M. sativa or as separate species. The two principal diploid taxa are “caerulea,” with purple flowers and coiled pods, and “falcata” with yellow flowers and falcate pods. To understand the evolutionary relationships among taxa in the complex, sequence variation in two noncoding regions of cpDNA (rpl20—rps12 and tmS—tmG spacers) and three regions of mitochondrial DNA (mtDNA: nad4 intron, nad7 intron, and rpS14—cob spacer) were surveyed from 48 (37 for mtDNA) individuals representing these and other diploid taxa in the complex. These sequences afforded independent perspectives on the evolutionary history of the group, because mtDNA is maternally inherited in Medicago whereas cpDNA is biparentally inherited with strong paternal bias. Twenty and 21 haplotypes were identified for cpDNA and mtDNA, respectively. Haplotype networks were constructed and tests of differentiation were conducted. Results from cpDNA sequences supported the recognition of “caerulea” and “falcata” as differentiated taxa, despite the presence of some shared haplotypes, in agreement with morphological characters. In contrast, no significant evidence of mtDNA haplotype differentiation was observed. Incongruence between cpDNA and mtDNA is more likely explained by introgression of the mitochondrial genome than by incomplete lineage sorting of mtDNA haplotypes, given the expected smaller effective population size for uniparentally inherited mtDNA than for biparentally inherited cpDNA. Moreover, the two taxa are readily crossable, making natural hybridization possible. The long-time disagreement on whether to recognize “falcata” as a separate species or a subspecies of M. sativa s. 1. is due to the common problem of unequal rates of differentiation for different characters during speciation.

A taxonomic key, synonymy, and a molecular phylogeny of the nine species and three varieties of Croton section Heptallon (Euphorbiaceae) are presented. Section Angelandra is synonymized with section Heptallon, and the species from outside of North America that had been placed into these two sections are shown to belong in other clades within the genus. As circumscribed here, section Heptallon is a well-supported clade of annual herbs and subshrubs that ranges from central Mexico to the eastern United States. A new combination, Croton heptalon, is made. Lectotypes are designated for C. corymbulosus, C. elliottii, C. ellipticus, C. engelmannii var. albinoides, C. eutrigynus, C. heptalon, C. leucophyllus var. trisepalis, and Heptallon graveolens.

Una clave taxonómica, sinonimia, y una filogenia molecular son presentados para las nueve especies y tres variedades de Croton sección Heptallon (Euphorbiaceae). Sección Angelandra se sinonimiza con sección Heptallon, y se demuestra que las especies de fuera de Norte América que habían sido incluidas en estas dos secciones pertenecen a otros clados dentro del género. Como está circunscrita aquí, sección Heptallon es un clado con buen apoyo de hierbas anuales y subarbustos que se distribuye desde el centro de México hasta el oriente de los Estados Unidos. Se hace una nueva combinación, Croton heptalon. Se designan lectotipos para C. corymbulosus, C. elliottii, C. ellipticus, C. engelmannii var. albinoides, C. eutrigynus, C. heptalon, C. leucophyllus var. trisepalis, y Heptallon graveolens.

A new species of sect. Diffusa, Geranium pseudodiffitsum (Geraniaceae) found in Ecuador and Peru is described. The new species is morphologically most similar to G. diffusum. Leaves of G. diffusum are ±densely covered by small and appressed hairs on both surfaces, while in G. pseudodiffusum hairs are restricted to margin and nerves of the abaxial side and more rarely on nerves of the adaxial side. Additionally, G. pseudodiffusum has glandular hairs on the stems, pedicels, sepals, petioles, and sometimes on the leaf lamina, while in G. diffusum only eglandular hairs are present. A morphological comparison to related species, and a new key for the whole section is provided. In addition, a detailed description, distribution map, habitat and line drawing are provided for this new species.

A recent worldwide phylogeny of Sapindaceae inferred from nuclear and plastid DNA regions segregated the Malagasy Haplocoelum perrieri Capuron from the African Haplocoelum foliosum (Hiern) Bullock. Additional phylogenetic analyses conducted here (including material of Haplocoelum inopleum Radlk., the generic type) supported the result from the previous analysis and showed that maintaining a broad circumscription of Haplocoelum to include the Malagasy species would render the genus polyphyletic. To maintain monophyly, it is necessary to exclude H. perrkri, which we transfer to a new, monotypic genus, described here as Gereaua. This taxon is easily distinguished from the species retained in Haplocoelum by the following morphological characters: (1) sexually dimorphic inflorescences in racemules (vs. monomorphic inflorescences in fascicule of cymes); (2) 2-locular ovary (vs. 3-locular ovary); (3) rudimentary pistillode in staminate flowers (vs. no pistillode in staminate flowers); (4) corolla with 4 or 5 petals (vs. apetalous); (5) pubescent fruit (vs. glabrous fruit). Relationships between the new genus and its most closely related genera, included in the Macphersonia group, are discussed in light of molecular, morphological and biogeographic evidence. A preliminary threat assessment of Gereaua perrieri using the IUCN Red List criteria indicates a status of Least Concern.

The genus Ipomopsis (Polemoniaceae) encompasses about 29 species and 24 subspecies generally divided into three sections: sect. Ipomopsis, sect. Microgilia, and sect. Phloganthea. We employed maximum likelihood and Bayesian inference of DNA sequences from the nuclear ribosomal ITS region (ITS1, 5.8S ribosomal subunit, ITS2) and the chloroplast trnL—F region (trnL intron trnL—trnF intergenic spacer) to estimate phylogenetic relationships within this genus and its placement among other genera of Polemoniaceae. The chloroplast and combined sequences provide support for the monophyly of Ipomopsis, but only if four species previously included in the genus are removed: Ipomopsis havardii, I. sonorae, Microgilia minutiflora (= I. minutiflora), and Loeseliastrum depressum (= I. depressa). Of the three sections, two are conditionally supported as being monophyletic. Section Microgilia (with 11 species and 11 infra-specific taxa) is supported as monophyletic if I. polycladon, I. sonorae, I. depressa, and I. minutiflora (the type of the section) are removed. This clade is treated here as section Elaphocera. Section Ipomopsis is inferred to be monophyletic with the inclusion of several members of sect. Phloganthea (I. multiflora, I. pinnata, and I. polyantha). There is no support for monophyly or paraphyly of sect. Phloganthea. The Giliopsis group (I. effusa, I. guttata, and I. tenuifolia) is supported as monophyletic by both data sets, and the cpDNA sequences place it as sister to the remainder of Ipomopsis. This clade is treated as a new section, Giliopsis. Nuclear data place Giliopsis in a clade with Ipomopsis havardii, I. sonorae, Microgilia minutiflora, Loeseliastrum depressum, Eriastrum spp., Langloisia, and Dayia grantii. Using the Eocene fossil Gilisenium hueberii to calibrate the most recent common ancestor of tribe Gilieae, we estimate that Ipomopsis has its origin 28.2 ± 0.40–39.0 ± 1.14 MYA (trnL—F and ITS, respectively). Using this same relaxed clock, the node (or coalescent event) that defines the I. aggregata complex is dated at 16.2 ± 0.38 and 27.1 ± 0.83 MYA (trnL—F and ITS, respectively). The deep divergence of the I. aggregata complex suggests that reticulation, rather than lineage sorting, is the source of conflict among phylogenetic markers used to infer the placement of I. macrosiphon.

Leucothoë s. l. has been split into as many as three genera in current taxonomic work involving morphological data. In this paper, phylogenetic relationships within Leucothoë s. l. were examined using DNA sequence data from matK, ndhF, nrITS, and morphological characters. The total combined data indicate that Leucothoë s. l. species are distributed between two clades. Leucothoë racemosa and L. recurva are strongly supported as being sister taxa and are in turn sister to Chamaedaphne calyculata. These two Leucothoë species are deciduous and they exhibit “L. racemosa”-type autumn inflorescences (as does Chamaedaphne). The other six Leucothoë s. l. species (L. axillaris, L. davisiae, L. fontanesiana, L. grayana, L. griffithiana, and L. keiskei) form a strongly supported clade. Leucothoë grayana, a morphologically distinctive taxon, is sister to the other five species in this latter clade. Based on these data, it is proposed that Leucothoë s. l. should be divided into three genera: Eubotryoides (E. grayana), Eubotrys (E. racemosa and E. recurva), and Leucothoë s. s. (L. axillaris, L. davisiae, L. fontanesiana, L. griffithiana, and L. keiskei).

Phylogenetic analyses of Isodon and related genera using the nuclear ribosomal internal transcribed spacer (nrITS), cpDNA regions (trnL—trnF region and rps16 intron), and morphological data are presented. The results clarify the relationships among Isodon and its putative related genera and the question of the monophyly of Isodon and its relationship with Siphocranion. Siphocranion is a monophyletic genus and the sister clade to the remaining species; the new subtribe Siphocranioninae of tribe Ocimeae is described to accommodate it. Isodon, as currently circumscribed, is only monophyletic if Skapanthus oreophilus is included in it. Isodon forms a distinct subtribe Isodoninae within tribe Ocimeae and three strongly supported subclades are identified within the genus. In addition, a close relationship between Hanceola and Hyptis is indicated in the combined nrITS cpDNA data set with Bayesian inference and this is also supported in morphological analyses, but more studies are needed to confirm this relationship. It is evident that subtribe Hanceolinae is polyphyletic as currently defined, so subtribe Hanceolinae is restricted to accommodate Hanceola alone. The relationships between Isodon and other genera within tribe Ocimeae are still unresolved; the newly erected subtribe Isodoninae is a monophyletic group representing a distinct lineage in subtribe Ociminae. The relationships among the species of the largest subclade C of Isodon are still poorly known. Additional studies of this group with additional data and more intensive taxon sampling might help to resolve these issues.