Guerramontesia microdonta (Pottiaceae, Bryophyta) is a new genus and species from Argentina and Bolivia. It is distinct from other genera of the Pottiaceae by a combination of characters: absence of central strand in the stem, Ungulate unbordered leaves with yellow KOH colour reaction, costa at midleaf with one band of dorsal stereids, (1)2–3 guide cell layers, absence of hydroids, and sporophyte with peristome of 16 variously cleft, occasionally perforate, coarsely papillose, short and straight teeth. The species is described, illustrated and mapped. Maximum parsimony and Bayesian analyses of cpDNA sequences (trnL-trnF and trnG regions) were undertaken. The resultant trees suggest that the new genus could be one of the earlier diverging lineages within the Pottioideae and Barbuloideae subfamilies of Pottiaceae.

In this treatment we revise the circumaustral fern species of Megalastrum found primarily between 33–45° latitude South. These species are found in the Valdivian temperate rain forests of Chile and Argentina, the Juan Fernández Islands in the South Pacific, the Tristan da Cunha archipelago in the southern Atlantic, and Île Amsterdam and Île Saint-Paul in the southern Indian Ocean. Megalastrum is absent from Australia and New Zealand. Seven species are treated in total. Two species and two varieties of Megalastrum have generally been recognized in Chile and the Juan Fernández Islands. In this treatment, we recognize four species for the region, one of which is elevated to the species rank (M. glabrius stat. nov.), and one which is new (M. masafuerae sp. nov.). Within the Tristan da Cunha archipelago, two species occur: M. aquilinum comb, nov., and another here described as new, M. peregrinum sp. nov. Île Amsterdam and Île Saint-Paul harbor one species that is described here as new: M. taafense sp. nov. For each species we provide a key, descriptions, complete synonymy, discussions, specimens examined, and illustrations.

Galeandra is a neotropical genus with its center of diversity in the Amazon region. It comprises approximately 18 species of epiphytic and terrestrial herbs that are easily recognizable by their funnel-shaped labellum. We examined the phylogenetic relationships among species of Galeandra inferred from nucleotide sequences from three plastid (psbA-trnH, rpoB-trnC, and trnS-trnG) and two nuclear (ITS and ETS) DNA regions. The five data matrices were analyzed individually and in combined analyses using parsimony and maximum likelihood. We found that the epiphytic species G. devoniana is sister to the remainder of the genus, and that the other species form two groups, one consisting of epiphytic species and the other composed of terrestrial species. Adaptation to the terrestrial environment from a probable epiphytic ancestor was of great importance in the evolution of Galeandra. The relationships found in this study do not support previous infrageneric classifications.

Three morphologically and ecologically closely related new Pitcairnia species (Bromeliaceae: Pitcairnioideae), P. barbatostigma Leme & A. P. Fontana, P. glauca Leme & A. P. Fontana, and P. diversifolia Leme & A. P. Fontana, from the inselberge of Espírito Santo State, southeastern Brazil, are described and illustrated. These taxa form a putative natural complex of species, together with their close relative, P. azouryi Martinelli & Forzza, based on propagation by means of slender rhizomes; leaves forming a conspicuous bulbous-like base; basal leaf blades deciduous along a straight, strongly spirally enrolled transverse line; simple racemose inflorescence of varying shades of green and different concentrations of purple-wine irregular spots, and white lanate except for the petals; comparatively long flowers with nocturnal anthesis; naked petals, forming a tubular, zygomorphic corolla; and by the sulcate and oblate, large-sized, reticulate, more or less heterobrochate pollen grains.

In this paper we describe a new genus of Bromeliaceae, Lapanthus, restricted to the southern portion of the Espinhaço Range, Minas Gerais State, in southeastern Brazil. Two new combinations to accommodate species previously described in the genera Orthophytum and Cryptanthus and one new synonym are proposed. Lapanthus has morphological affinities with both Cryptanthus and Orthophytum, but nevertheless differs by the combination of margins of the petals ciliate, presence of lanceolate petal appendages and free stamens, and also by molecular data. Cryptanthus and Orthophytum have petals entire along the margins, and the filaments of the most internal whorl are adnate to the petals. Lapanthus stands out by having a pair of lanceolate petal appendages, which are almost completely adnate to the petals. In Orthophytum, however, appendages are cupuliform or sacciform and they are totally absent in the genus Cryptanthus. Lapanthus and Orthophytum present meiotic and mitotic chromosome numbers equal to n=25 and 2n=50, 100 and 150 respectively, while Cryptanthus presents meiotic and mitotic chromosome numbers n=17 and 2n=34, 36, 54 respectively, and this difference is considered to be an autapomorphic feature of Cryptanthus. Descriptions of the genus and species, identification keys, illustrations, photographs of living specimens, and taxonomic comments are provided.

Five new species of Eleocharis are described based on specimens from South America: Eleocharis angustispicula, E. densicaespitosa, E. hatschbachii, E. ramboana and E. urceolatoides. Diagnostic characters, description, detailed illustration and taxonomic comments are provided. In addition, we propose the lectotypification of Eleocharis glauco-virens and a new synonym to E. loefgreniana. All those species belong to Eleocharis ser. Tenuissimae, which has a pantropical distribution with some species reaching temperate areas. A preliminary key to separate the species of the series that occur in Brazil is also presented.

Analyses of genome scale data sets are beginning to clarify the phylogenetic relationships of species with complex evolutionary histories. Broad sampling across many genes allows for both large concatenated data sets to improve genome-scale phylogenetic resolution and also for independent analysis of gene trees and detection of phylogenetic incongruence. Recent sequencing projects in Oryza sativa and its wild relatives have positioned rice as a model system for such “phylogenomic” studies. We describe the assembly of a phylogenomic data set from 800,000 bacterial artificial chromosome (BAC) end sequences, producing an alignment of 2.4 million nucleotides for 10 diploid species of Oryza. A supermatrix approach confirms the broad outline of previous phylogenetic studies, although the nonphylogenetic signal and high levels of missing data must be handled carefully. Phylogenetic analysis of 12 chromosomes and nearly 2,000 genes finds strikingly high levels of incongruence across different genomic scales, a result that is likely to apply to other low-level phylogenies in plants. We conclude that there is great potential for phylogenetic inference using data from next-generation sequencing protocols but that attention to methodological issues arising inevitably in these data sets is critical.

The legume subfamily Caesalpinioideae is a paraphyletic grade, within which are nested the monophyletic subfamilies Mimosoideae and Papilionoideae. Although higher level relationships within Caesalpinioideae are now better understood, few studies have examined generic and species level relationships. A morphological and molecular phylogenetic analysis of selected members of the Brownea clade (Detarieae: Caesalpinioideae) is presented here, focusing on relationships within and among the genera Elizabetha, Heterostemon, Paloveopsis, and Paloue. Morphological characters (125) and DNA sequence data from the plastid trnL intron and nuclear ITS were used to reconstruct phlogenetic relationships. These results indicate that (1) Heterostemon is monophyletic; (2) the majority of Elizabetha species form a poorly supported, monophyletic group sister to Paloue; and (3) Paloveopsis is nested within Paloue. Intergeneric hybridization between species of Paloue and Elizabetha has been identified and traditional generic, species, and intraspecies boundaries are assessed and reevaluated using the results of the combined phylogenetic analysis.

The biogeographical history of several important vegetables is still unclear. In the gourd family, Cucurbitaceae, this applies to melon and cucumber, but also to many species of more regional importance. Cucumeropsis mannii is cultivated in West Tropical Africa for its nutritious seeds. Family-wide phylogenetic analyses suggested that it is closest to Posadaea sphaerocarpa from Central and South America, the seeds of which are also eaten and the fruit of which is made into bowls. To reconstruct these species' historical biogeography, we sequenced six plastid markers and the nuclear ribosomal ITS region for several accessions of both species, plus all relevant outgroups. Morphological traits were studied in 102 herbarium specimens representing both species. A 5,155 nucleotide-long matrix of chloroplast and nuclear DNA contained a single informative mutation in a poly-C region of nuclear ITS among six accessions that covered the species' native ranges. Next-closest species differed in all plastid markers and by ≥34 mutations in ITS1 and ITS2. Study of the morphology revealed a possible small difference in fruit shape (cylindrical-ovate versus spherical), presumably resulting from human selection on the African populations. The closest outgroups Melancium and Melothria are endemic to the neotropics, and maximum likelihood area reconstruction indicates that Cucumeropsis mannii also originated there. The near-absence of genetic and morphological differentiation implies that gene flow between Cucumeropsis manni and Posadaea sphaerocarpa stopped relatively recently, and taxonomically they should (or could) be treated as one species. Transport of seeds during the transatlantic slave trade is a possible scenario, although we cannot reject natural dispersal.

Flueggea (including Richeriella) is revised for the Flora Malesiana area. Three species are recognized. Two of them are generally small trees and they are allopatric, F. gracilis (ex-Richeriella) being present in West Malesia and F. flexuosa in East Malesia and the west Pacific. The two subspecies of the generally shrub-like F. virosa are also allopatric, with subsp. virosa having a palaeotropical distribution ending just west of New Guinea, and subsp. melanthesoides being present in New Guinea and Australia.

In an effort to further resolve relationships within the genus Limnanthes and the family Limnanthaceae a phylogenetic study was conducted using one nuclear (nrITS) and two chloroplast (trnL intron and trnS-trnG intergenic spacer) genes. In addition to surveying all currently accepted taxa within Limnanthaceae, an anomalous population of 4-petalous plants from Half Moon Bay, San Mateo County, California, was also included. Further, a series of crossing experiments were performed between Half Moon Bay plants and two closely related species (Limnanthes bakeri and L. macounii). The results of this study confirm the monophyly of two sections within Limnanthes and also suggest that Limnanthaceae may contain as few as four species of Limnanthes and the monotypic genus Floerkea proserpinacoides. Additionally, the molecular phylogenetic results and crossing experiments do not support taxonomic recognition of the Half Moon Bay population, rather it is part of a highly polymorphic Limnanthes douglasii sensu lato.

The relationships and taxonomy of the genus Thysanocarpus (Brassicaceae) are reassessed based on molecular phylogenetic analyses of nuclear ribosomal (ITS) and chloroplast (trnh-F) sequences and a critical re-examination of morphology and nomenclatural types. Based on these results, Thysanocarpus is well-supported as a member of tribe Thelypodieae, but no illuminating phylogenetic structure is found within the tribe. The independent origin of similar fruit morphology in Thysanocarpus and Athysanus is confirmed. Within Thysanocarpus,seven species are recognized: T. conchuliferus, T. curvipes, T. desertorum, T. erectus, T. laciniatus, T. radians, and T. rigidus comb. nov. Thysanocarpus laciniatus is found to have originated through hybridization. However, T. desertorum and T. rigidus, which have previously been included within T. laciniatus (as T. laciniatus var. hitchcockii and T. laciniatus var. rigidus,respectively), do not share that species' hybrid origin and are distinct both phylogenetically and morphologically. Within T. curvipes,five subspecies are recognized: T. curvipes subsp. amplectens comb. nov., T. curvipes subsp. curvipes, T. curvipes subsp. elegans comb. nov., T. curvipes subsp. longistylus comb. nov., and T. curvipes subsp. eradiatus comb. nov. Thysanocarpus curvipes subsp. elegans and T. curvipes subsp. longistylus form clades in ITS and/or trnL-F cladograms as well as showing morphological distinction. The remaining three subspecies are recognized based on a combination of morphology and geography.

Phylogenetic divergence time estimates inferred from trees optimized using maximum likelihood apply branch lengths. These branch lengths are influenced by the substitution model applied in the analysis, which can, in turn, affect divergence time estimates. To examine the effects of substitution models on divergence time estimates, we applied an empirical data set for Cornales that had 16 calibration point constraints in maximum likelihood analyses using 19 different substitution models to obtain topologies with branch lengths. Penalized likelihood was then used to obtain divergence time estimates for corresponding nodes of these topologies. Discrepancy in divergence time estimates among corresponding nodes of trees constructed with different models was small in most cases (falling within 95% confidence intervals based on the most supported model); however, we recovered instances of nodes differing by as much as 23.7% from times on corresponding nodes of the phylogeny reconstructed from our best-fit substitution model. We estimated that, on average for all nodes within a tree, divergence times differ 1.0–3.6% among the trees based on different models; however, the range of variation differs greatly among trees based on different substitution models. Discrepancy in divergence time estimates was associated with long branches, although using models similar to the best-fit model reduced this. Branches of a length within one standard deviation of mean branch lengths were an unexpected source of discrepancy regardless of the substitution model applied, although the cause of this discrepancy was unclear. We found no differences in disparity among nodes that were reconstructed in deep-, mid, or shallow-level regions of the topologies. Simulations demonstrated that use of underparameterized models affected age estimates more than use of overparameterized models. Increasing the number of calibration points can limit but not completely remove discrepancies introduced by underparameterized models.

Several representatives of Hydrangeaceae tribe Hydrangeeae are popular in the horticultural trade for their inflorescences with attractive marginal flowers, resulting in many hybrids and cultivars. However, despite previous morphological and molecular studies, the phylogenetic relationships between the nine currently recognized genera in this clade are still largely unclear, and the widely used infrageneric classification of the genus Hydrangea by McClintock (which was mainly based on the study of herbarium specimens) requires critical reevaluation. We present a partially well resolved and well supported phylogeny of the tribe Hydrangeeae based on maximum parsimony and Bayesian analyses of multiple coding and noncoding chloroplast regions (rps 16-trnK spacer, trnK intron, trnK exon, matK gene and trnK-psbA spacer). All genera, sections and subsections were included making it a representative sampling for the tribe Hydrangeeae. Hydrangea is paraphyletic with respect to the eight other genera of Hydrangeeae, requiring a classification update. The subsections Heteromallae and Petalanthe of section Hydrangea are monophyletic, the subsections Americanae, Asperae and Macrophyllae are paraphyletic. Of the two subsections of section Cornidia, one, Polysegia, is monophyletic whereas the other, Monosegia, is paraphyletic. The necessary nomenclatural changes based on these results might have a certain effect in the trade but also might encourage breeders to produce “intergeneric” hybrids between traditionally recognized genera in Hydrangeeae.

Mentzelia section Trachyphytum (Loasaceae) has 25–30 species found primarily in the western United States. Species delimitation and reconstruction of evolutionary relationships within Trachyphytum have been difficult due to restricted and continuous morphological variation. We employed phylogeny reconstructions based on morphology and DNA sequences from the plastid trnH-psbA, trnS-trnG, trnS-trnfM, ndhF-rp132, and rp132-trnL regions and the low-copy nuclear gene idh to investigate evolutionary relationships and patterns of hybridization and homoplasy among diploid species in Trachyphytum. Reconstructions indicated surprisingly high levels of genetic introgression among closely and distantly related diploids. Additionally, reconstructions based on molecular data showed that some morphological characters traditionally used to delineate groups exhibit homoplasy. However, both molecular- and morphologically-based reconstructions supported two major clades in section Trachyphytum. In agreement with prior hypotheses, the larger clade contains the taxa, M. congesta, M. desertorum, M. eremophila, M. nitens, M. pectinata, and M. thompsonii, whereas the sister clade composed of M. affinis, M. dispersa, and M. micrantha has not been previously suggested. Further, this study strengthens assertions that selected characters shared between the two annual sections, Trachyphytum and Bicuspidaria, are homoplasies.

The unified species concept and a criterion of limited homogenizing gene flow as evidenced by genetic and morphological markers were applied to species delimitation within Navarretia sinistra. Concordant patterns of variation diagnose two morphologically cryptic species. As a consequence, the basionym Gilia linearifolia is here lectotypified and re-established for this long neglected epithet. Navarretia linearifolia shows strong differentiation from N. sinistra in allozyme data and DNA sequences from chloroplast regions, nrDNA, and introns of the low copy nuclear genes idhA, idhB, and g3pdh. In macroscopic features, N. linearifolia differs from N. sinistra primarily in tendencies, rather than absolute differences. Two finer-scale features are diagnostic: pollen sexine sculpturing and mature seed color. The combination Navarretia linearifolia subsp. pinnatisecta is made for the large flowered populations of this species geographically restricted to the NW region of the California floristic province. The smaller flowered N. linearifolia subsp. linearifolia extends from California to Washington, with a more westwardly distribution compared to N. sinistra, which ranges east into Idaho, Utah, and Colorado.

Ruellia section Chiropterophila as here recognized contains 11 species endemic to areas in and around the transnational Volcanic Belt of México: the Sierra Madre del Sur, the Balsas Depression, and the Altiplano. Most of these species are rare, and nearly half are known only from one or two collections. Of the remaining six, two are restricted to single states. One species described as new to science, Ruellia laslobasensis, is distinguished from a close relative by its smaller corollas, calyces, and fruits. Ruellia chilpancingana is placed into synonymy with R. sororia. Ruellia section Urceolata is synonymized with sect. Chiropterophila. Two species previously treated in sect. Chiropterophila, Ruellia petiolaris (as R. palmeri) and R. carmenaemiliae, are excluded from the section. Phylogenetic analyses using three chloroplast markers (trnC-trnR, trnG-trnS, psbA-trnH) and one nuclear marker (ITS 5.8S) were conducted to test the monophyly of sect. Chiropterophila and to reconstruct relationships among species. Sequences were successfully generated for all species in sect. Chiropterophila; some are known only from old herbarium material. One of these, collected in 1894, is among the oldest known plant herbarium specimens to be successfully sequenced. Analyses reveal that section Chiropterophila is monophyletic but not well supported; an alternative hypothesis of nonmonophyly of the section could not be rejected. Species descriptions, botanical illustrations, and a dichotomous key to distinguish the 11 taxa in Ruellia sect. Chiropterophila are provided.

A new neotropical genus, Shuaria, with a single species, S. ecuadorica, is described from the Cordillera del Cóndor and Amazonian regions of southeastern Ecuador and is placed in the family Gesneriaceae, tribe Beslerieae. The placement of Shuaria in the tribe Beslerieae is strongly supported by molecular sequence data generated from analyses of nuclear ribosomal DNA internal transcribed spacer region (ITS), and the chloroplast DNA trnL intron, trnL-trnF intergenic spacer region. Sequence data were generated for 33 species representing most of the generic diversity from the tribes Beslerieae and Napeantheae. Shuaria is characterized by the following unique combination of relatively uncommon characters in the Gesneriaceae: arborescent habit; opposite leaf arrangement sometimes interrupted by alternate leaves; lepidote trichomes on vegetative and floral structures; small white flowers with a dorsal gibbosity at the base of the corolla tube; and a bivalved septicidally dehiscent capsule. The suite of uncommon characters initially made Shuaria difficult to place in the Gesneriaceae and within a known tribe. Shuaria is restricted to the Ecuadorian provinces of Pastaza, Morona-Santiago, and Zamora-Chinchipe in lowland Amazonian tropical wet forest and in lower montane cloud forest on the western slopes of the Cordillera del Cóndor. A key and a table are presented for differentiating Shuaria from other related genera.

Fruit anatomical characters studied herein confirm the inclusion of Delarbrea and Myodocarpus in Apiales, but as a distinct group, corroborating previous studies (based on molecular data) in the recognition of Myodocarpaceae as a new family. The fruits of these genera share some features with those of Apiaceae (especially subfamilies Mackinlayoideae and Azorelloideae) and Araliaceae, including branching and anastomosing vascular bundles and secretory canals, woody endocarps, the presence of single ventral bundles or carpophores, and dispersed crystals. However, the presence of median wings in Myodocarpus and secretory vesicles in the mesocarps (adjacent to the woody endocarp) in both genera are unknown in any other genus of the order. Fruit characters are also useful in distinguishing Delarbrea, which produces drupes with a single ventral vascular bundle and sclereids in the mesocarp, from Myodocarpus, which has schizocarps with a single carpophore and lacks sclereids. Delarbrea balansae, once treated as the sole member of Pseudosciadium, shares all the distinctive fruit features with the other species of Delarbrea, further supporting its transfer there.