A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

Pucara leucantha is transferred to Stenomesson as Stenomesson leucanthum based on the phylogenetic position of Pucara resolved by nuclear and plastid DNA sequences. An allied species, Stenomesson chloranthum, is described from the Departments of Amazonas and Cajamarca in Peru, but at lower elevations. Both of these species release their pollen in tetrads, unique within Amaryllidaceae, and have tri-lobed stigmas, unique within Stenomesson.

Seed morphology has been an important taxonomic character for the Bromeliaceae, with three distinct seed types, naked, winged, and plumose, corresponding to the traditionally recognized subfamilies, Bromelioideae, Pitcairnioideae, and Tillandsioideae, respectively. In Tillandsioideae, the type of plumose seed appendage is used, in conjunction with other characters, to help circumscribe genera. For example, Catopsis, a genus of approximately 20 species, is characterized by having an apical coma of hairs, in contrast to Guzmania, Vriesea, and Tillandsia where seeds have a basal coma of hairs. The individual hairs, apical or basal, that comprise the plumose coma of the Tillandsioideae seeds have been assumed to be homologous structures. Scanning electron and light microscopy were used to examine the details of seed hair development in representative species of Catopsis and Tillandsia. Observations made in this study confirm published details of the basal seed hair development for Tillandsia. The apical seed hairs characteristic for Catopsis are shown to have a distinctly different ontogeny, and are judged to be synapomorphic for the genus. The apical and basal plumose seed appendages diagnostic for subfamily Tillandsioideae are analogous, but are not homologous in the ontogenetic or positional sense.

Despite the controversy surrounding Cariceae generic and Carex subgeneric limits, most debates centre on a relatively small number of highly reduced unispicate taxa. This study examines Cariceae phylogeny by using all five genera (Schoenoxiphium, Kobresia, Uncinia, Carex, Cymophyllus) and four Carex subgenera (Psyllophora, Vignea, Vigneastra, Carex), with the emphasis of sampling on the tribe's taxonomically difficult unispicate groups (Uncinia, Cymophyllus, Kobresia pro parte, Carex subgenera Psyllophora, and Carex pro parte). Phylogenies based on rDNA internal and external transcribed spacer (ITS, ETS1 f) sequences indicate that the tribe consists of four primary clades (((A, B) C) D) that support a fundamental split between dioecious and androgynous unispicate taxa. Dioecious species are related to multispicate species of either Carex subgenera Carex (Clade D) or Vignea (Clade C), whereas the androgynous species of Uncinia, Kobresia, Cymophyllus, and Carex are related to multispicate species of Schoenoxiphium and Kobresia (Clades A and B). Analyses strongly indicate that the genus Carex is artificial. Moreover, trees support proposals to merge Carex subgenera Carex and Vigneastra (Clade D), and they support the monophyly of Carex subgenus Vignea and the polyphyly of Carex subgenus Psyllophora. Analyses also reject the common evolutionary link made between Schoenoxiphium and Carex subgenus Vigneastra, and the belief that Schoenoxiphium and Kobresia should be merged. The monotypic genera Cymophyllus and Vesicarex do not warrant generic status. The implications of the phylogeny for tribal inflorescence evolution are discussed.

Eragrostis is a large genus of grasses in subfamily Chloridoideae of the Poaceae. Recent phylogenetic analyses have suggested that the group may not be monophyletic, and there are a number of segregate genera that may be better placed within Eragrostis. We have used molecular sequence data from the plastid locus rps16 and the nuclear gene waxy from a broad sample of Eragrostis species and representatives of six of the seven segregate genera to address these issues. We find that Eragrostis is a monophyletic group with the inclusion of four segregate genera: Acamptoclados, Diandrochloa, Neeragrostis, and Pogonarthria. The placement of Cladoraphis and Stiburus is uncertain. Thellungia does not belong in Eragrostis and is actually more closely related to Sporobolus.

We assessed the infraspecific taxa of Coryphantha robustispina (syn. Coryphantha scheeri) by analysis of 16 morphological vegetative characters measured from 67 herbarium specimens collected throughout the range of this species within the United States, two live specimens from southeastern Arizona, five live specimens from New Mexico, six live specimens from Texas, and 279 live specimens from Pima and Santa Cruz Counties (south-central Arizona). Four spine characters exhibit strong clinal variation: central spine width, central spine form (curvature), central spine size, and lower radial spine width. Other spine characters show considerable variation but no significant clinal patterns. Central, radial, and guard spine lengths and central spine form are significantly correlated with total number of mature tubercles on the primary stem (∼ age of plant). In south-central Arizona, central spine curvature varies ontogenetically; older adults produce straighter central spines. Central, radial, and guard spine lengths, and central and radial spine widths are more correlated with length of tubercle than with age of plant. Principal component analyses indicate that morphological intergradation occurs across the east-west range of this species, indicating that neither varietal nor subspecific divisions are warranted at this time. These results raise fundamental questions regarding the legal status of Coryphantha scheeri variety robustispina, a taxon listed as endangered under the Federal Endangered Species Act.

A cladistic study based on morphological characters is presented for all 28 genera of Olacaceae as well as 26 representative genera from five other families of Santalales: Loranthaceae, Misodendraceae, Opiliaceae, Santalaceae, and Viscaceae. The data matrix consists of 80 macro-morphological, palynological, and anatomical characters. The phylogenetic trees obtained show a paraphyletic Olacaceae with four main clades. Some of these clades are congruent with previously recognized tribes, but all of subfamilies are para- or polyphyletic. Examination of character transformations confirms several assumptions of evolutionary trends within Olacaceae and Santalales, but others appear to be more complex than expected. Optimization of trophic mode on the consensus tree shows that root hemiparasitism had a single origin in Santalales. Whatever the optimization procedure used, the basal-most clade of Olacaceae consists of 12 genera, among which five are known to be autotrophs, whereas the remaining three clades (15 genera) contain four genera known to be root parasites.

The phylogenetic position of 74 taxa of Asian Sedoideae (Crassulaceae) was estimated based on analyses of the trnL-trnF intergenic spacer sequence of cpDNA and the ITS region, including the 5.8S rDNA sequence, of nDNA. Our analyses suggest that the subfamily Sedoideae is not monophyletic and the genus Sedum especially is highly paraphyletic. Recent studies based on cpDNA restriction-site variation and the matK region recognized seven clades of “major importance.” In our analyses, four major clades were recovered: Kalanchoe, Sempervivum, Aeonium, and Acre. All Asian Sedum (s.s.) tested are included in the Acre clade, and all other eastern Asian genera are in groups corresponding to the Telephium clade. The Telephium clade is split into four strongly supported subclades, Rhodiola, Hylotelephium, Phedimus, and Umbilicus, and is determined to be polyphyletic. All eastern Asian genera that were segregated from Sedum are separated in a lineage distinct from Sedum (s.s.). Hylotelephium, Orostachys, Meterostachys, and Sinocrassula are closely related, and Hylotelephium and Orostachys are polyphyletic. The infrageneric taxa within Hylotelephium and Rhodiola are indicated to be polyphyletic.

Echinopepon disjunctus, a new species of the Echinopepon torquatus species-group from the Yungas rainforest of Jujuy (Argentina), is described and illustrated. Echinopepon coulteri is here excluded from the E. torquatus group on inflorescence and floral characters; a key to the remaining species of the group is included. In addition, the floral structure of the monotypic genus Pseudocyclanthera and four species of Rytidostylis is reviewed. The aestivation of the corolla, invagination at the base of the hypanthium, nectar-secreting trichomes, synanther, and pollen morphology support a closer relationship between Pseudocyclanthera and Rytidostylis than between Pseudocyclanthera and Cyclanthera. The receptacular nature of the trichomatous base of the androecial column and style seems to be distinctive for Rytidostylis. A key to the genera Cyclanthera, Pseudocyclanthera, and Rytidostylis is also included.

Nuclear sequence data are needed for plant systematics studies in order to supplement data from the chloroplast genome and from morphology. We cloned and sequenced a partial sequence of LEAFY, from the 3′ end of the second intron to the 3′ end of the third exon, for 44 species from the three Leguminosae subfamilies, but with greater taxon sampling in the basal subfamily Caesalpinioideae. Only one copy of LEAFY was amplified in most of the Leguminosae studied, but in members of tribe Detarieae, our phylogenetic analyses suggest that two copies are present, one of which may be a pseudogene. Sampled species of Brownea Jacq. and Browneopsis Huber (Detarieae) possess a large, unique insertion, which seems to be a useful taxonomic marker for this bigeneric group. The rate of substitution in the coding sequences of LEAFY gives a phylogenetic signal at a broad spectrum of phylogenetic levels, from the intergeneric level to the family level. The second intron is highly variable, and for the copy that seems to be under relaxed selective constraint, the sequences cannot be compared between species of different tribes or subfamilies. The phylogenetic analysis of LEAFY sequences results in topologies that, overall, are consistent with past taxonomy and chloroplast sequence analyses. However, incongruence between the chloroplast trnL intron and one of the copies of LEAFY is found in the tribe Detarieae. This incongruence remains poorly explained, but may result from hidden paralogy or lineage sorting of divergent alleles. This study provides an example of the unexpected complexity that can arise when evaluating the phylogenetic utility of a low-copy nuclear gene.

A combined parsimony analysis of cpDNA trnK, nrDNA ITS/5.8S, and morphology reveals that the genus Strophostyles is monophyletic. In contrast to the conventional view of the geographic relationships of eastern North America, Strophostyles is most closely related to neotropical genera. Its sister is the South American genus Dolichopsis, which is endemic to the Chaco, a region characterized by having an annual frost interval. Strophostyles is apomorphically diagnosed by divergent stipules, persistent secondary floral bracts, calyces with four acute to sometimes attenuate lobes, and seed testa often with a cellular coat. The relationship with Dolichopsis is supported in part by a shared keel petal morphology involving a gibbous ventral margin proximal to the rostrum. Phylogenetic analysis of ITS/5.8S sequences and morphometric analysis of quantitative traits suggest that the three traditionally recognized species of Strophostyles can be recognized under the phylogenetic species concept. Strophostyles umbellata is the most genetically variable at the ITS locus and geographically centered in southern Appalachia. Strophostyles helvola shows the least amount of intraspecific genetic variation at this locus, suggesting a recent and rapid range expansion throughout eastern North America. Nucleotide sequence variation is intermediate in Strophostyles leiosperma, a species distributed primarily in central North America.

Many genera previously placed in the traditionally circumscribed Capparaceae are either unrelated or, more commonly, isolated lineages in the order Brassicales. This study examines the relationships of three of these orphan genera, Emblingia, Forchhammeria, and Tirania, in the context of a focused analysis of the core Brassicales. In order to assess relationships of these genera, analyses were conducted across Brassicales using chloroplast rbcL, ndhF, and matK sequence information. Both maximum parsimony and maximum likelihood analyses place all three genera in the well-supported core Brassicales (Brassicaceae, Capparaceae, Cleomaceae, Gyrostemonaceae, Pentadiplandraceae, Resedaceae, and Tovariaceae). The Asiatic Tirania and New World tropical Forchhammeria are closely related to two small families, the pan-temperate Resedaceae and the Australian Gyrostemonaceae. These analyses also indicate a novel placement of Emblingia as sister to all remaining members of core Brassicales. Although there is strong support for the relationships among most of these taxa, relationships of Pentadiplandraceae and Tovariaceae are weakly resolved. Thus, the core Brassicales is a biogeographically dispersed lineage that is comprised of many small and morphologically distinct clades plus the large crown group Brassicaceae s. lat. Patterns of morphological evolution appear complex, especially in floral merosity and carpel and locule number. Likewise, the evolution of breeding systems within this lineage involves recurrent shifts towards monoecy or dioecy, and possible reversals to bisexuality. Further sampling of Capparaceae tribe Stixeae is critical for any taxonomic recommendation of familial status for these orphan genera.

The first revision of the neotropical genus Potalia (Gentianaceae: Potalieae, formerly Loganiaceae) is presented. This genus was formerly considered monotypic, with Potalia amara being the only recognized species. New morphological and anatomical studies show that Potalia resinifera should be resurrected and that nine newly discovered species should be recognized; one endemic to Central America (P. turbinata), two endemic to Chocó, Colombia (P. chocoensis and P. crassa), two endemic to white-sand areas along Rio Negro and its tributaries (P. elegans and P. maguireorum; Brazil, Colombia, and Venezuela), and the last two endemic to white-sand areas in the western Amazon basin (P. coronata and P. yanamonoensis; Peru, Brazil and Colombia). Potalia amara sensu stricto is restricted to the Guianas and northeast Brazil, whereas P. resinifera is widespread in lowland Amazonia and the Andean foothills. Morphological differences between the species are primarily in fruit and inflorescence morphology, but there are also differences in plant size, leaf shape, and corolla color. Potalia resinifera shows the greatest infraspecific variation. Phylogenetic relationships between Potalia and its close relatives Anthocleista from Africa and Fagraea from tropical Asia-Australia-Pacifics are discussed. The widespread pharmacological uses of Potalia species by indigenous peoples of the Neotropics are reviewed and vernacular names are listed.

Bystropogon (Lamiaceae) is endemic to the Macaronesian Islands and represents the best-known example of a putative phytogeographic connection between these islands and the New World. Previous morphological taxonomic studies suggested that this genus is closely related to the western South American Minthostachys. Phylogenetic analyses of nucleotide sequences of the internal transcribed spacers and 5.8S subunit of nuclear ribosomal DNA and the trnL gene and trnL-trnF spacer of the chloroplast genome for 33 of the 72 genera in the Mentheae tribe were performed. Maximum parsimony analysis of the combined data set resulted in 63 most parsimonious trees. The strict consensus tree of this analysis shows with moderate bootstrap support (74%) that Bystropogon is sister to the Old World taxa Acinos, Ziziphora, and Clinopodium vulgare. When analyzed separately, the ITS and trnL/F data sets do not agree as to the sister group to Bystropogon, although none supports a sister relationship with Minthostachys. The cpDNA phylogeny strongly supports a relationship of Bystropogon with a clade of New World mint taxa (90% bootstrap value). Due to the apparent conflict between the chloroplast and nuclear characters observed in the phylogenies, we are not certain of the true biogeographic relationship of Bystropogon. Finally, in all analyses, all of the Mentheae genera sampled in this study form a monophyletic group (100% bootstrap value) and a derived clade of ten New World genera is found. These results contribute to our understanding of generic relationships within the tribe.

Phylogenetic analyses are used to examine the morphological diversity and systematics of Synthyris and Besseya. The placement of Synthyris and Besseya in Veronicaceae is strongly supported in parsimony analyses of nuclear ribosomal ITS DNA sequences. Parsimony and maximum likelihood (ML) criteria provide consistent hypotheses of clades of Synthyris and Besseya based on the ITS data. The combination of morphological characters and ITS data resolve additional clades of Synthyris and Besseya. The results show that Synthyris is paraphyletic to Besseya. In the monophyletic Synthyris clade, Besseya forms part of a Northwest clade that also includes the alpine S. canbyi, S. dissecta, and S. lanuginosa and mesic forest S. cordata, S. reniformis, S. platycarpa, and S. schizantha. The Northwest clade is the sister of S. borealis. An Intermountain clade, comprising S. ranunculina, S. laciniata, S. pinnatifida, and S. missurica, is the sister to the rest of the Synthyris clade. Constraint topologies are used to test prior hypotheses of relationships and morphological similarities. Parametric bootstrapping is used to compare the likelihood values of the best trees obtained in searches under constraints to that of the best tree found without constraints. These results indicate that topologies in which a monophyletic Synthyris is the sister of Besseya are significantly worse than the best ML tree in which Synthyris is paraphyletic to Besseya. Similarly, forcing either the monophyly of all taxa that have deeply incised leaf margins or those that have reniform laminas and broadly rounded apices results in trees that are significantly worse than the best ML tree, in which leaf margin incision and reniform laminas are homoplastic. We propose a new classification for Synthyris that emphasizes monophyletic groups. The new combination Synthyris oblongifolia is proposed.

A phylogenetic study of the genus Perideridia (Apiaceae; tribe Oenantheae) was conducted to elucidate its circumscription, infrageneric relationships, and patterns in the evolution of available morphological, anatomical, and cytological characters. Nuclear rDNA ITS sequences were procured from 84 accessions of Perideridia, representing all 14 of its species and four of its six subspecies, and five outgroup taxa, and analyzed using maximum parsimony, maximum likelihood, and Bayesian inference methods. The trees recovered by each of these optimality criteria were congruent and generally quite robust. Upon the removal of the eastern Asian Perideridia neurophylla, previously referable to Pterygopleurum neurophyllum, the genus Perideridia is monophyletic and exclusively North American in distribution. Three major clades within Perideridia are inferred; the midwestern U.S. Perideridia americana is likely sister to all other species. With the exceptions of Perideridia lemmonii and P. bolanderi (where each species comprises two separate lineages), and P. oregana (whose limits are expanded to include tetraploid populations previously referred to as P. leptocarpa), all taxa were recovered as monophyletic. Optimization of 16 non-molecular characters on a phylogeny inferred by maximum parsimony analysis of combined ITS and non-molecular data revealed high instances of homoplasy, with the clade of P. howellii and P. kelloggii, taxa characterized by monostelic roots, supported by four of six synapomorphies. The occurrence of multistelic tuberous roots in all other species of Perideridia and in the unrelated Pterygopleurum neurophyllum suggests that this uncommon character among dicots has evolved twice in the family Apiaceae.

Chaetanthera is a South American genus of 43 species in seven subgenera. Pollen grain morphology of 39 species of Chaetanthera and allied genera of Mutisiinae was surveyed using light and electron microscopy. Two palynologic groups are distinguished in Chaetanthera, defined as types I and II, the latter with the subtypes II 1 and II 2. The groups are supported by additional morphological and habit characteristics. Type I has pollen with a thinner exine (usually 5–7 μm thick), subrectangular shape, nexine outline elliptic to subrectangular, and medium-sized; type II has pollen with a thicker exine (11–18 μm thick), elliptic shape, nexine outline dumbbell-shaped, and large-sized. Subtype II 1 has columellae in the ectosexine, whereas subtype II 2 has a compact ectosexine. A palynologic alliance is established among the mutisiean genera Aphyllocladus, Gypothamnium, and Plazia (Plazia group), species of Onoseris and Urmenetea (Onoseris group), Brachyclados, Chaetanthera, Lulia, Mutisia, and Pachylaena (Mutisia group), Gerbera, Trichocline, and Uechtritzia (part of the Gerbera group), and Hyaloseris and Dinoseris on the basis of pollen similarities. These generic groups are defined by the habit and floral and fruit features, and the pollen structure is mainly useful to establish relationships among the groups. In this scheme the Mutisia group, which includes Chaetanthera, approaches the Onoseris and Gerbera groups.

In high elevation habitats of the Peruvian Andes a new population of Microseris (Asteraceae, Lactuceae) related to the single South American species, M. pygmaea, recently was discovered. Microseris pygmaea occurs at lower elevations in Chile and has originated after long-distance dispersal from a Californian progenitor. Differences in flowering traits and habitat preferences of the new population raised the question of its precise phylogenetic affiliation. The analysis of the nuclear rDNA internal transcribed spacer (ITS) region of all Microseris species revealed the Peruvian plants as part of the Chilean M. pygmaea clade. Molecular, ecological, and physiological data resulted in an interpretation of the Peruvian population as derived from Chilean progenitors instead of being remnants of stepping-stone dispersal from North America through the Andes to Chile. Differences in ITS sequences found in this study compared to earlier ones were explained by the occurrence of two different rDNA clusters in the genome of Microseris, which were preferentially amplified by differences in the PCR protocols.

Phylogenetic relationships were reconstructed using molecular (nrDNA ITS and rpl16) and morphological data for eight species in three sections (Leptosyne, Pugiopappus, and Tuckermannia) of Coreopsis that are almost exclusively restricted to California. Parsimony analyses were conducted on each of three data partitions (cpDNA, ITS, and morphology) and congruence between these topologies and data sets was assessed by inspecting the topology for “hard” incongruence and via the partition homogeneity test (PHT). The individual topologies were largely congruent (i.e., lacking “hard” incongruence), with the exception of the placement of C. calliopsidea by analyses of morphological data. Because the two molecular data sets are generally in agreement regarding the placement of this taxon, the morphological data for C. calliopsidea were excluded and a PHT test indicated no significant heterogeneity among the molecular partitions. A combined analysis supports the monophyly of the eight California species and of sections Tuckermannia and Leptosyne; however, section Pugiopappus is not monophyletic. This latter section as traditionally defined includes species that display an annual habit and dimorphic cypselae. Examining the evolution of these two features in light of the phylogeny indicates that the annual habit has either arisen twice or arose once with reversal to perenniality, and that dimorphic cypselae originated twice. The evolution of pubescent fruits and pappus scales is more complex. The three alternative reconstructions indicate that these features could either be ancestral, represent three independent gains, or result from a single gain followed by two losses.

The systematic value of morphological characters in Senecio sect. Jacobaea (Asteraceae) is studied using separate and combined parsimony analyses of morphological and DNA sequence data. These analyses are the first studies of morphological characters in a phylogenetic context in Senecio. Although the morphological data set forms a valuable addition to DNA sequences in providing greater resolution and support for several molecular-based clades, most characters are not suitable for identifying clades containing more than just a few closely related species. One of these characters, the stigmatic configuration, commonly used to study generic and subtribal limits of Senecioneae, is too variable for classification purposes in sect. Jacobaea. Among the four morphological characters that can be used to identify relatively large clades in the section are two indumentum characters. Because indumentum characters also have been found to be phylogenetically informative in other sections and genera in Senecioneae, we argue that they might be suitable for classification purposes throughout this tribe. We show that on the basis of these and other morphological characters and DNA sequences, S. gallerandianus and S. maroccanus should be included in sect. Jacobaea. This brings the total number of species in this section to 26.