The impact of unknowingly including a hybrid or an allopolyploid in which rDNA homogenization (via gene loss, concerted evolution, or some other mechanism) has not occurred to completion in a phylogenetic analysis of internal transcribed spacer (ITS) or external transcribed spacer (ETS) sequences is unclear. To investigate the impact of polymorphic sites on phylogeny reconstruction, we used ITS and ETS sequence data for diploids and allotetraploids in Tragopogon, as well as ITS data for diploid and allopolyploid species of Paeonia and Glycine, and for diploids and their hybrids in Rubus. Only very general predictions can be made regarding the placement of these polymorphic sequences. The polymorphic sequences of hybrids and allopolyploids appear (1) with a diploid parent (but not necessarily the one with which it shares more apomorphies), (2) at or near the base of the clade containing one or both parents, or (3) in a basal position relative to all other ingroup taxa in the data set. The inclusion of a polymorphic sequence may be accompanied by an increase in the number of shortest trees, less resolution in the strict consensus, and a decrease in bootstrap support for some nodes; CI and RI values are little, if at all, affected. In no case did the addition of a sequence from a hybrid or allopolyploid alter the overall topology in a major way. Our results generally parallel those of phylogenetic studies that include F₁ hybrids and their parents and use morphology.

Phylogenetic relationships among the seven genera of the Hypopterygiaceae, represented by 14 of the 21 species recognized in the family, were reconstructed based on variation in nucleotide sequences of six nuclear, mitochondrial, and plastid loci. Monophyly of the Hypopterygiaceae is strongly supported, whereas the genera Cyathophorum and Dendrohypopterygium are unambiguously polyphyletic. Cyathophorum bulbosum and C. adiantum make up a lineage sister to the remainder of the family. A lineage comprising four monotypic genera (Arbusculohypopterygium, Canalohypopterygium, Catharomnion, and Dendrocyathophorum) is sister to Lopidium plus a heterogenous clade that includes Dendrohypopterygium, Hypopterygium, Cyathophorum hookerianum, and C. parvifolium. The later two species are transferred to Hypopterygium as H. hookerianum and H. parvifolium. The Hypopterygiaceae are distinguished from their sister family, the Hookeriaceae, by their anisophylly, and by a border of two or more differentiated cells on lateral leaves, although this character also occurs in some Hookeriaceae and has been lost at least twice in the Hypopterygiaceae. Intermediate cells in the axillary hairs arose early in the evolution of the family but are lacking in the two species of Cyathophorum that form a sister group to the remainder of the Hypopterygiaceae.

To resolve phylogenetic relationships among all genera and subgenera in Osmundaceae, we analyzed over 8,500 characters of DNA sequence data from seven plastid loci (atpA, rbcL, rbcL–accD, rbcL–atpB, rps4–trnS, trnG–trnR, and trnL–trnF). Our results confirm those from earlier anatomical and single-gene (rbcL) studies that suggested Osmunda s.l. is paraphyletic. Osmunda cinnamomea is sister to the remainder of Osmundaceae (Leptopteris, Todea, and Osmunda s.s.). We support the recognition of a monotypic fourth genus, Osmundastrum, to reflect these results. We also resolve subgeneric relationships within Osmunda s.s. and find that subg. Claytosmunda is strongly supported as sister to the rest of Osmunda. A stable, well-supported classification for extant Osmundaceae is proposed, along with a key to all genera and subgenera.

Recent molecular investigations have elucidated the generic and subgeneric relationships of most vittarioid genera (Pteridaceae sensu lato pro parte). However, the phylogenetic placement of Monogramma and Rheopteris remains to be examined. The inclusion of the monotypic Rheopteris in the vittarioids has been questioned since its description half a century ago, and although the placement of Monogramma within the vittarioids is well supported with nonmolecular characters, its relationship to other members of the vittarioid clade is unknown. We present new phylogenetic evidence from plastid rbcL sequence data indicating that Rheopteris cheesmaniae is well supported as a member of the vittarioid clade, and that Monogramma is polyphyletic. Data from molecular and nonmolecular characters suggest that a clade containing Rheopteris and part of Monogramma (i.e. those species sometimes recognized in the genus Vaginularia) represents the earliest diverging lineage within the vittarioids, and that remaining members of Monogramma are derived from within Haplopteris. Our study supports the separation of Vaginularia from Monogramma sensu stricto.

A molecular phylogenetic analysis using the sequences of atpB, rbcL, accD, atpB–rbcL spacer, and rbcL–accD spacer was made for Davalliaceae with a focus on four systematically uncertain and nomenclaturally influential species. The result shows that Davalliaceae comprises six clades. Davallia plumosa is sister to Scyphularia pentaphylla and S. pycnocarpa. Scyphularia triphylla is sister to a clade comprising other Scyphularia, Davallia plumosa, D. solida, and related species, indicating that imparipinnate leaves are derived twice within the clade. Humata heterophylla is sister to the H. polypodioides group, one of two groups of Humata, in which Davallia corniculata is nested. Paradavallodes multidentatum is nested in Araiostegia Davallodes, which is a polymorphic basal clade. African Davallia chaerophylloides is allied to an Asian and Pacific group comprising D. denticulata and related species.

Morphology, species delimitation, and interspecific relationships were evaluated in a phylogenetic context in the aquatic monocotyledon genus Vallisneria using a combination of morphological and molecular (nrITS, rbcL, trnK 5′ intron) data. Contrary to previous studies that recognized few species worldwide, we distinguished 12 species by molecular data, and an additional 2–3 species by morphological differences within groups that were invariant at the molecular level. Two new Vallisneria species ( V. australis , V. erecta ) are formally described. Other potentially novel species were detected from the cultivated material examined but require further study to elucidate their taxonomic status. Phylogenetic analyses indicated that vittate (caulescent) species (including Maidenia rubra) are not basal, but nested between two groups of rosulate (rosette) species. To preserve Vallisneria as monophyletic, a new combination is made ( V. rubra ) that accommodates the transfer of M. rubra to Vallisneria. Several taxonomic characters associated with the stigma morphology of pistillate flowers were found to represent suites of features related to pollination. In most cases, these character suites corresponded to a particular arrangement of filaments in the staminate flowers. The precise geographical origin of Vallisneria remains difficult to determine. However, we conclusively documented the presence of the Old World V. spiralis in Texas (United States), which constitutes the first authentic record of this nonindigenous species in North America.

Taxonomic features of species of Panicum, previously classified in section Cordovensia, subgenus Dichanthelium, of Panicum, are reviewed and compared with those of other taxa in the Paniceae. The new genus Parodiophyllochloa is proposed on the basis of ecological and morphological features (i.e. plants growing at the edge of forests, with membranous ligules, lower glume more than 1/2 the spikelet length, lower palea and lower flower absent, and upper anthecium indurate with simple papillae all over its surface) and chloroplast ndhF sequences to include six species ranging from Mexico to Argentina. The new combinations: Parodiophyllochloa cordovensis, P. missiona, P. ovulifera, P. pantricha, P. penicillata, and P. rhizogona are proposed. The new genus is compared with other genera of the Paniceae.

Relationships within the Polygonaceae have been recently examined using rbcL sequences, with an emphasis on Polygonum and its segregates. Here we test these results with respect to Polygonum (sensu lato) with an expanded dataset, including additional species and gene regions. Specifically, we focus on inferring the relationships of Eupersicaria (Polygonum sect. Persicaria in many prior treatments), using the chloroplast genes rbcL, trnL–F, trnK intron–matK, and psbA–trnH IGS, and nuclear ribosomal ITS sequences. We conclude that Eupersicaria is monophyletic and most closely related to Tovara and Echinocaulon. In turn, this clade is most closely related to Cephalophilon. The sister group of this entire Persicaria clade contains Bistorta and a clade including Aconogonon and Koenigia, which supports the monophyly of the Persicarieae. Within Eupersicaria there appears to be a deep split between P. amphibia and the remaining species, and there is strong conflict regarding the placement of P. punctata. These results set the stage for a more detailed phylogenetic analysis of Eupersicaria.

Polygonaceae has long been recognized as a monophyletic family but the circumscription of groups within it has been in constant flux. Two groups currently recognized are the subfamilies Eriogonoideae and Polygonoideae. An analysis using three chloroplast regions (rbcL, matK, and ndhF) and increased taxon sampling of Eriogonoideae does not support this delimitation. The second intron and portions of the flanking exons of the nuclear gene LEAFY, were used to explore phylogenetic utility in Polygonaceae. The intron showed high levels of variability and was useful at low taxonomic levels, but not alignable outside of Eriogonum and allied genera. Phylogenetic analysis of data from the flanking exons of the second intron of LEAFY generally supports the major groupings found in the chloroplast analysis. A new definition of the subfamilies is proposed. Polygonoideae is restricted to what has been recognized as tribes Persicarieae, Rumiceae, and Polygoneae, with the addition of Muehlenbeckia. Eriogonoideae now includes Antigonon, Brunichia, Coccoloba, Ruprechtia, Triplaris, and Eriogonum and allied genera. The genera Eriogonum and Chorizanthe are nonmonophyletic.

As traditionally circumscribed, the family Olacaceae contains a morphologically diverse assemblage of genera that has historically caused much confusion regarding their classification. For example, Olacaceae contain parasites and nonparasites, climbing lianas and trees, and members with dichlamydous and monochlamydous perianths. This family is basalmost in the sandalwood order (Santalales), thus it represents the staging ground for many innovations that evolved in subsequent groups. The present molecular phylogenetic study has obtained DNA sequence data (nuclear SSU rDNA and chloroplast rbcL and matK) for all but two of the 28 genera in this group. Maximum parsimony and Bayesian analyses have resolved seven clades, well-supported by molecular and morphological characters. Root hemiparasitism appears to have first evolved in the clade containing Ximenia whereas clades between that one and the outgroup appear to be entirely autotrophic.

Santalaceae sensu stricto, the type family for the sandalwood order (Santalales), include approximately 40 genera and over 550 species distributed worldwide. Because the family possesses plesiomorphic and generalized traits that occur throughout the order, this diverse assemblage of hemiparasitic plants has been difficult to characterize and differentiate from related families. We present phylogenetic analyses of all genera of Santalaceae, as well as Viscaceae and selected Opiliaceae, using DNA sequences from nuclear small-subunit ribosomal DNA as well as the chloroplast genes matK and rbcL. The concatenated data set, analyzed with parsimony, likelihood, and Bayesian inference, gave congruent results, with the majority of clades fully resolved. Our results reveal that the family is polyphyletic and that the genera of Santalaceae, as traditionally classified, occur in nine well-supported clades. The South American herbaceous perennial genera Arjona and Quinchamalium are sister to Schoepfia (Schoepfiaceae). The Australian genus Anthobolus emerges as a member of Opiliaceae. Viscaceae remain intact and are well supported as monophyletic. The remaining genera included in Santalaceae occur in six well supported clades, but the relationships among these clades are not fully resolved. These clades are, based on a component generic name, Comandra, Thesium, Cervantesia, Nanodea, Santalum and Amphorogyne. Morphological features diagnostic of these clades are discussed with the intention that these results will serve as the foundation for a revised classification.

Two new species of Schoenocaulon from Mexico, S. framei and S. oaxacense, are delimited by analyses of ITS sequence data and characterized by distinct morphology and biogeography. Schoenocaulon framei, a segregate from the polyphyletic S. comatum s.l., is described for the first time; S. oaxacense is elevated to species rank, based on S. caricifolium var. oaxacense, one of two monophyletic varieties comprising polyphyletic S. caricifolium s.l. Schoenocaulon framei is distinguished by unusual sunken stomata on the abaxial leaf surface and ligulate, weakly auriculate tepals, each with a smooth basal nectariferous zone; the basal perigonal gland of S. oaxacense is a glandular depression, and its tepals are ligulate. Both new species also are well-supported cladospecies with ITS sequence data according to the apomorphic species concept. Our results confirm the importance of molecular phylogenetic analyses in decisions relating to species circumscription, especially when such analyses are carefully correlated with morphological markers. The study also demonstrates the ease in applying the major phylogenetic species concepts and suggests that the apomorphic and diagnostic phylogenetic species concepts may result in identical specific circumscriptions.

The Cucurbitaceae genus Austrobryonia, with four species endemic to Australia, is described, illustrated, and placed in a phylogenetic context based on molecular and morphological data. In the Flora of Australia (Telford 1982), all four species were provisionally included in Mukia, but not formally described. Austrobryonia argillicola , A. centralis , A. micrantha , and A. pilbarensis are adapted to arid central regions of Australia. All species are known from several (7–27) localities, and their distributional ranges are allopatric. A phylogenetic analysis of plastid and nuclear DNA sequences that includes all four species in a family-wide context revealed that Austrobryonia is the closest living relative to a Eurasian and Mediterranean clade consisting of Bryonia L. and Ecballium L. An rbcL molecular clock, calibrated with Cucurbitaceae fossils, dates this rare biogeographic disjunction to minimally 42 my ago (with an error of ca. ± 25%), while the crown group of Austrobryonia may be about 8 my old.

Tribe Podalyrieae is a group of papilionoid legumes that are largely endemic to the Cape Floristic Region of South Africa, possessing fire survival strategies with both nonsprouting and sprouting species. A phylogenetic study of the tribe was undertaken using gene sequences obtained from the internal transcribed spacer (ITS) of nuclear ribosomal DNA as well as the plastid rbcL gene (107 species). Several clades were identified within the tribe. Subtribe Xiphothecinae consists of the genera Amphithalea and Xiphotheca. Subtribe Podalyriinae was paraphyletic. Based on the results of this study, Liparia (except L. calycina) and Podalyria are sister genera with Stirtonanthus sister to both of these. While Podalyria and Stirtonanthus are monophyletic, the monophyly of Liparia is still uncertain. Virgilia and Calpurnia are closely related and Cyclopia retains an isolated, monophyletic position within the tribe. Cadia is monophyletic and sister to the rest of the Podalyrieae. The placement of this genus has, until now, been uncertain due to their actinomorphic flowers that are unusual among papilionoid legumes. The data from this study indicate that actinomorphic flowers may be interpreted as an apomorphy for Cadia and it shares many characters with Podalyrieae. We therefore propose that Cadia be transferred to Podalyrieae from the paraphyletic tribe Sophoreae. The age of the root node of the tribe Podalyrieae s.s. was estimated at 30.5 ± 2.6 million years (Ma) using nonparametric rate smoothing (NPRS) and 34.7 Ma (confidence intervals: 25.1–44.1 Ma), using a Bayesian relaxed clock, indicating that a major radiation has taken place during the middle to late Miocene and early Pliocene. Finally, we found that nonsprouting species have a higher rate of molecular evolution than sprouting species.

Quercus ellipsoidalis (Hill's oak), an endemic of east-central North America, is morphologically similar to Q. coccinea (scarlet oak) and is subsumed into that species in several floristic treatments. This study uses data from more than 250 amplified fragment length polymorphism (AFLP) markers to investigate whether Q. coccinea and Q. ellipsoidalis are genetically distinct from one another. Whereas Q. coccinea and Q. ellipsoidalis separate from one another in all analyses, Q. velutina (black oak) populations collected from the geographic range of both Q. coccinea and Q. ellipsoidalis do not separate out by geographic region. This, combined with the strong differentiation between Q. coccinea and Q. velutina but weak differentiation between Q. ellipsoidalis and Q. velutina, supports the view that Q. coccinea and Q. ellipsoidalis are not simply regional variants of a single taxon. Moreover, while there is no evidence from the molecular data we collected of hybridization between Q. coccinea and Q. ellipsoidalis, the data suggest that there may be gene flow between Q. ellipsoidalis and Q. velutina. A clearer understanding of the relationships among these taxa is essential to understanding the taxonomy of Quercus section Lobate in eastern North America.

Gesneriaceae tribe Gloxinieae is a diverse clade of approximately 19 genera and 215 species. As with many tropical lineages, patterns and timing of diversification are poorly understood. This is a particular difficulty in groups such as the Gesneriaceae that have no fossil record. Here we explore maximum likelihood and Bayesian inference of phylogenetic relationships in the tribe based on nuclear, chloroplast, and morphological data sets, use Fitch parsimony optimization (FPO) and dispersal vicariance (DIVA) analyses to explore biogeographic patterns in the Gesnerioideae, and use penalized likelihood calibrated by geological events in the Caribbean and South America to explore timing of movement of lineages among Caribbean, Central American, and South American land masses and islands. Likelihood and Bayesian analyses increase support of previous hypotheses of relationships using parsimony and provide additional resolution in some parts of the phylogeny. FPO and DIVA analyses suggest that the most likely scenario for movement among Central American, Caribbean, and South American areas was either an early dispersal to Central America and the Caribbean prior to diversification of the Gloxinieae clade with subsequent back dispersal to South America, or the ancestor of the Gloxinieae had a broad distribution across Central America and Andean/western South America. Estimations of the timing of movement of these lineages among these land masses suggests that the Greater Antilles/Aves Ridge landbridge likely played a role in dispersal events and that the Gloxinieae/Gesnerieae lineage likely arrived in the Central America/Caribbean zone at least 26 million years ago.

Within the past decade, Scrophulariaceae sensu lato has been shown to be polyphyletic and, as a result, is currently undergoing major systematic revision. The traditionally recognized family is now generally considered to comprise several smaller families including the newly expanded Plantaginaceae, a family of 12 tribes, 92 genera, and approximately 2000 species. Recent evidence from molecular phylogenetics supports the inclusion of the tribe Gratioleae within the Plantaginaceae. Gratioleae includes 16–40 genera, depending on generic circumscription, many of which have yet to be assessed phylogenetically. Amphianthus is a monotypic genus whose systematic affinities have long been poorly known. We included Amphianthus, 10 additional Gratioleae genera, and several outgroup genera from Plantaginaceae in a phylogenetic investigation to examine the relationships of Amphianthus. We present the most complete phylogeny of the Gratioleae to date and provide evidence from chloroplast DNA sequences of the ndhF gene and the trnS–trnG–trnG intergenic spacer and intron that unequivocally place Amphianthus within Gratiola, and discuss the morphological evidence supporting our findings. Based on this evidence, we transfer the sole species of Amphianthus (Amphianthus pusillus) to Gratiola, establishing the new name Gratiola amphiantha and placing Amphianthus in synonymy with Gratiola.

Solanum series Conicibaccata contains about 40 wild potato (section Petota) species distributed from southern Mexico to central Bolivia. It contains diploids (2n = 2x = 24), tetraploids (2n = 4x = 48) and hexaploids (2n = 6x = 72) and some polyploids are likely allopolyploids. Our morphological phenetic study in an Andean site in central Peru (12°S, 3200 m altitude) is a replicated study from one done in the north central United States (45°N, 180 m elevation) but uses more species (28 vs. 25), accessions (173 vs. 100), and morphological characters (72 vs. 45) and also includes members of related series Piurana. Both US and Peruvian studies provide phenetic support with Canonical Discriminant Analyses (but poorly if at all with Principal Components Analyses) to distinguish the following species or species groups in series Conicibaccata: 1) S. agrimonifolium and S. oxycarpum as a possible single species, and 2) S. longiconicum (tetraploids from Mexico and Central America), 3) the South American Conicibaccata diploids as a possible single species, except for 4) S. trinitense that is distinctive, 5) the South American tetraploids as a group except for 6) S. flahaultii that is distinctive. However, character states among these species or species groups are often present only by using a range of widely overlapping character states (polythetic support). We suspect that our continuing molecular studies will support the synonymy of many of these species.

Abstract—The systematic position of Feddea (Asteraceae) has been enigmatic ever since its publication in 1925. The latest taxonomic accounts of the family left it either unplaced within subfamily Asteroideae or unplaced within tribe Inuleae. Macro-morphological and electron microscopy data (scanning electron microscopy and transmission electron microscopy) indicated that Feddea is not part of an early branching lineage of the Asteraceae, contrary to what had been suggested in initial taxonomic accounts. Feddea has style branches with a 2-banded (vs. continuous) stigmatic surface, thus differing from early diverging lineages of the family. Among Asteroideae, Feddea is diagnosed by discoid capitula with all florets bisexual, long-caudate anthers, noncarbonized cypselae, and pollen with a narrow cavus region, columellae without internal foramina, but with a complex basal columellate layer. A phylogenetic reconstruction based on nucleotide sequences of the chloroplast gene ndhF showed that Feddea is sister to the Heliantheae s.l. There were, however, no clear morphological synapomorphies shared with that tribe and we therefore propose Feddeeae as a new unispecific tribe to accommodate this critically endangered genus restricted to Eastern Cuba.

The circumscription and infrageneric classification of Campanula is highly controversial. Independent and combined data from nuclear and chloroplast sequences (trnL-trnF, ITS) were analyzed with Bayesian and parsimony methods to elucidate the phylogenetic relationships of Campanula and allied genera, and explore the biological processes that occurred during the evolution of this genus. The main sections and subgenera of Campanula and related genera were sampled extensively. Chromosome numbers, corolla types, habit and capsule dehiscence were mapped on the trees to search for evolutionary patterns. The phylogenetic analyses revealed that Campanula, as currently circumscribed, is not monophyletic. This genus is divided into two main clades: a large core of Campanula species that includes related genera (Adenophora, Asyneuma, Azorina, Campanulastrum, Diosphaera, Edraianthus, Githopsis, Hanatnisaya, Heterocodon, Legousia, Michauxia, Petromarula, Physoplexis, Phyteuma, Trachelium, and Triodanis), and a clade constituted by Musschia plus two Campanula species. The large core of Campanula is divided into two main groups, a rapunculoid and a campanuloid group. Both Bayesian and Parsimony analyses indicate that the main morphological characters used in classifications, such as flower shape and capsule dehiscence, have arisen in parallel. Strong selective pressures from pollinators are suggested to explain floral convergence. We put forward two different proposals in order to accomplish a classification of Campanula that more accurately reflects the evolution of this genus.