Comparison of molecular and morphological data on St Helena: Elaphoglossum

The endemic elaphoglossoid ferns, Elaphoglossum dimorphum, E. nervosum and Microstaphyla furcata of St Helena, form a closely related group within section Lepidoglossa when analysed phylogenetically using sequences from the chloroplast trnL intron (partial) and trnL-F intergenic spacer. Microstaphyla furcata, traditionally placed in its own genus, is clearly shown to belong to Elaphoglossum confirming the previous transfer of this species to Elaphoglossum as E. bifurcatum. There is hardly any trnL-F sequence divergence between the species, in fact sequences of E. nervosum and E. dimorphum are identical. These results are consistent with the possible origin of E. dimorphum as a hybrid between E. bifurcatum and E. nervosum or with the view that the three species are the result of a recent radiation. The potential conflict between phylogenetic and morphological distinctness in determining species conservation priorities is discussed.     

Primary hemiepiphytism and gametophyte morphology in <Emphasis Type="Italic">Elaphoglossum amygdalifolium</Emphasis> (Dryopteridaceae)

Elaphoglossum amygdalifolium holds a critical phylogenetic position as sister to the remaining ca. 600 extant species of Elaphoglossum and may provide important insight into the evolution of epiphytism in this clade of ferns. Here, we present the first examination of growth habit and gametophyte morphology for this species. We show that the cordate to elongate-cordate gametophytes occur up to 0.5 m above the ground on the base of tree trunks. Unlike the gametophytes of all other studied species of Elaphoglossum, rhizoids are absent along the thallus margin and the hairs present on the margin lack whitish waxy caps; both differences are pleisiomorphic for the genus. Sporelings of E. amygdalifolium produce a single long root that grows straight into the soil where it branches profusely. Mature sporophytes have long-creeping rhizomes that climb to heights of at least 3 m and produce two types of roots: “feeding roots” that reach the ground and “clasping roots” that anchor the sporophyte to its host plant. Our observations reveal that E. amygdalifolium is a primary hemiepiphyte, the first example of this growth habit to be documented in Elaphoglossum. Results of an ancestral state reconstruction of growth habit in bolbitidoid ferns show that both primary hemiepiphytism and holoepiphytism are equally likely to be the ancestral character state for Elaphoglossum.     

Elaphoglossum clathratum sp. nov. (Dryopteridaceae) from the eastern side of the Andes in Ecuador

Elaphoglossum clathratum F. B. Matos & R. C. Moran sp. nov. (Dryopteridaceae), which grows at middle elevations on the eastern side of the Andes in Ecuador, is described, illustrated, and compared to its most similar species. It is unusual in Elaphoglossum by having lamina margin scales that are strongly clathrate. Research on the phylogeny of the genus has shown that the new species belongs to Elaphoglossum sect. Polytrichia. However, it is unique in the subulate‐scaled clade of Elaphoglossum by having planar, not subulate, scales.     

Six new species of Elaphoglossum (Elaphoglossaceae)

The fern genusElaphoglossum is well represented in wet, mountainous regions of Latin America, from which many species have recently been described. Six more new species ofElaphoglossum are reported:E. bryogenes from Ecuador andE. caudulatum, E. diminutum, E. delasotae, E. lellingeri, E. subcordatum, andE. xiphiophorum from Colombia.     

Exon primed intron-crossing (EPIC) markers reveal natural hybridization and introgression in Actinidia (Actinidiaceae) with sympatric distribution

Interspecific hybridization is widespread among plants. Understanding the phylogenetic relationships among species is necessary for revealing the potential hybridization events. Actinidia, best known as kiwifruit genus found throughout a wide range in eastern Asian from Indonesia to Siberia. In this study, phylogenetic relationships of Actinidia species with sympatric distributions were investigated using three chloroplast introns (trnL-F, atpB-rbcL and rpl32-trnL) and three Exon primed intron-crossing (EPIC) markers. Chloroplast phylogeny supports non-monophyly of the five species studied excluding Actinidia fulvicoma var. lanata. The non-monophyly was also revealed by EPIC markers. Our results showed EPIC markers are more variable and informative for phylogenetic inference than that of chloroplast markers. The incongruences between loci from the plastid and nuclear DNA phylogenic trees may stem from incomplete lineage sorting or historical introgression hybridization. Incomplete lineage sorting may explain the non-monophyly between Actinidia chrysantha (section Maculatae) and other four species (section Stellatae), and introgression hybridization and high level of interspecific gene flow may explain the non-monophyly among the species of sect. Stellatae. Thus, natural hybridization and introgression may be common in Actinidia with sympatric distribution.     

Molecular identification of species in Prunus sect. Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants

Abstract Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB‐rbcL, trnH‐psbA, trnL‐F, trnS‐G, atpF‐H, rbcL, matK, rpoB, rpoC1, nad1, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nad1) have very low variation rates, whereas atpB‐rbcL, atpF‐H, trnH‐psbA, trnL‐F and trnS‐G show more variability. The most variable loci, atpB‐rbcL and trnH‐psbA, can distinguish three of the five species. Two two‐locus combinations, atpB‐rbcL+trnL‐F and atpB‐rbcL+atpF‐H, can resolve all five species. We also find that identification powers of the loci are method‐dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods.     

DNA variation within Juncaceae: comparison of impact of organelle regions on phylogeny

A phylogenetic analysis of the Juncaceae was conducted to assess relationships among the genera Juncus, Luzula and five other small South American genera (Distichia, Marsippospermum, Oxychloë, Patosia and Rostkovia). We examined parallel datasets from organelles (mtDNA: atp1 gene, cpDNA: trnL intron, trnL-F intergenic spacer, rbcL gene) with respect to qualities relevant to the phylogenetic analysis of the Juncaceae. The main aim of our work was to produce a robust phylogeny of the Juncaceae validated by data from both organelles. Our data confirm the monophyly of the genus Luzula, but do not provide support for monophyly of the genus Juncus. The majority of taxa clustered within two subgenera, Agathryon and Juncus, morphologically supported by the presence or absence of bracteoles and cymose or racemose inflorescences, respectively. The subgenus Juncus is divided into two separate clades, the first closely related to the subgenus Agathryon and the second in the most basal part of the tree. Moreover, small South American genera clustered together with Juncus sect. Graminifolii and also with Juncus sect. Juncus. In fact, comparison of results from separate analyses of mitochondrial and plastome genes demonstrates that the general resolution of main topology of the atp1 tree is similar to the separate rbcL tree; the genus Juncus is better resolved, but the genus Luzula remains mainly polytomic.     

Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia

Cyrtomidictyum Ching and Cyrtogonellum Ching are two eastern Asian endemic genera whose taxonomic affinities and phylogenetic relationships have long been controversial. The main uncertainty surrounds the separation of the two genera from the species-rich genus Polystichum. Here we present a phylogenetic study focusing on the phylogenetic relationships of these polystichoid ferns. We reconstructed the relationships based on DNA sequence variation in four chloroplast genome regions, rbcL, atpB, and the intergenic spacers (IGS) rps4-trnS and trnL-trnF. Maximum likelihood and Bayesian inference analyses confirm earlier results that were based on less comprehensive taxon sampling and either only a single gene (rbcL) or two IGS (rps4-trnS and trnL-trnF). Cyrtomidictyum is the sister of the clade of polystichoid ferns that includes Cyrtogonellum, Cyrtomium subser. Balansana and three sections of Polystichum. Cyrtogonellum groups with several species of Polystichum, and constitutes the sister taxon to Polystichum sect. Sphaenopolystichum. We support the recognition of Cyrtomidictyum as circumscribed initially, rather than expansion of the genus to include either several Polystichum species or Cyrtogonellum, some Polystichum and Cyrtomium species. The monophyly of Cyrtomidictyum is supported by morphological characters such as once-pinnate leaves, free venation, prolongated leaf apices, and exindusiate sori. Two synapomorphic indels in the chloroplast genome, one 15-bp deletion in rps4-trnS, and one 3-bp insertion in trnL-trnF further differentiate Cyrtomidictyum from other polystichoid ferns. The close affinity of Cyrtogonellum to section Sphaenopolystichum of Polystichum s.s. is highly supported by molecular data. However, no shared morphological characters or molecular indels have been detected, although the distinctness of Cyrtogonellum is shown by a 13-bp insertion in the rps4-trnS alignment.     

The proliferous species of Elaphoglossum (Elaphoglossaceae) and their relatives

Thirteen taxa of the fern genusElaphoglossum reproduce vegetatively by a bud borne at the retuse apex of the sterile frond. These and six of their nonproliferous close relatives, all of tropical America, are discussed and described. All but one belong to various species groups in the closely allied sectionsSetosa andUndulata, the remaining one belonging to sectionLepidoglossa. Fourteen of the taxa are new:E. boryanum var.eutecnum, E. cardioglossum, E. entecnum, E. exsertipes, E. herpestes, E. inciens, E. nanoglossum, E. omissum, E. phoras, E. phyllitidis, E. plumosum f. maternum, E. pseudoboryanum, E. rufum, andE. wardiae.     

A revision of Dryopteris sect. Diclisodon (Dryopteridaceae) based on morphological and molecular evidence with description of a new species

Dryopteris sect. Diclisodon is a small section of ferns with about 12 species mainly distributed in East Asia. Here, we carried out morphological and phylogenetic analyses of this section. A new species from southwest China, D. gaoligongensis, is described and illustrated. Dryopteris gaoligongensis resembles D. indonesiana and D. sparsa, but differs by having a creeping rhizome and large 4-pinnate fronds. We also show that D. glabrior Ching & Z.Y. Liu is a distinct species; however, because it is a later homonym of D. glabrior Copel., it should be renamed D. renchangiana. We conclude that a species previously known as D. nitidula, also an illegitimate homonym, should be recognized with a new name, D. sinonepalensis. We resolve the phylogenetic position of D. yoroii as sister to other sampled species of D. sect. Diclisodon. Our phylogenetic analyses confirm the distinctiveness of D. gaoligongensis, D. renchangiana, and D. sinonepalensis. A key to species of D. sect. Diclisodon in China is provided.     

A new species and molecular phylogeny of Brazilian succulent Euphorbia sect. Brasilienses

A new species of Euphorbia sect. Brasilienses V.W. Steinm. & Dorsey is described. Euphorbia tetrangularis Hurbath & Cordeiro is endemic to the Serra de Montevidéu, a part of the Espinhaço Range located in the state of Minas Gerais, Brazil. It differs from other species within the section based on the following characters: 4-ribbed branches, green cyathia, and green cyathial glands with erect appendages. This new species would qualify as critically endangered (CR) according to IUCN criteria. An inferred phylogeny based on a combined dataset of nuclear (ITS1) and plastid regions (psbA-trnH, trnC-ycf6, matK, atpI-atpH, psbJ-petA, trnQ-rps16?×?1) confirms the monophyly of Euphorbia sect. Brasilienses and supports the recognition of E. tetrangularis. The phylogeny also suggests that this group probably underwent a recent radiation.     

Phylogenetic relationship of Clauseneae (Rutaceae) inferred from plastid and nuclear DNA data and taxonomic implication for some major taxa

Using sequences of the nuclear ribosomal ITS region as well as the chloroplast DNA trnL‐trnF and atpB‐rbcL regions, this study aims to provide further insight into the phylogenetic relationships within Clauseneae and its relationship to Citreae (Rutaceae). Using maximum likelihood (ML) and Bayesian inference (BI), we reconstructed the phylogeny of Clauseneae based on trnL‐F, atpB‐rbcL and ITS sequences. Our data matrix contained 91 accessions, representing 72 species and varieties from 31 genera and two outgroups, including new and extensive sampling of species and varieties representing four genera in the tribe Clauseneae. In the subfamily Aurantioideae, six major clades were resolved with strong support: 1) Micromelum clade: Micromelum; 2) Glycosmis clade: Glycosmis; 3) Bergera clade: Murraya sect. Bergera; 4) Clausena clade: Clausena; 5) Murraya clade: Murraya sect. Murraya + Merrillia; 6) Citreae clade: Citreae. Micromelum, Glycosmis, Clausena and Merrillia were confirmed as monophyletic. In contrast, Murraya s.l. was reconstructed as polyphyletic. Murraya sect. Bergera clustered with Clausena while Murraya sect. Murraya and Merrillia together formed a clade that is sister to the tribe Citreae. All members from Citreae were clustered into a natural group. The genus Micromelum was found to be primitive in this subfamily and more close to Glycosmis. Based on the phylogeny and morphological characters, we discuss the taxonomy of some members of Clauseneae and conclude that the current tribal and generic classification need further revision.     

Phylogeny of Androcymbium (Colchicaceae) based on morphology and DNA sequences

The inclusion of species of Colchicum within Androcymbium in a previous cpDNA phylogeny of the Colchicaceae, questioned the monophyly of Androcymbium, and it was proposed to unite the two genera in Colchicum. Here we expand the previous phylogenetic analyses of Androcymbium by increasing the taxon sampling and adding more data. The analysis include 29 of the 57 species of Androcymbium, more cpDNA (trnL intron, trnL-trnF IGS, trnY-trnD IGS, and trnH-psbA IGS), and nDNA (RNApol2 intron 23) regions, and morphological and life-history traits data. Both parsimony and Bayesian inference were used. According to our data there is no reason to expand Colchicum to include Androcymbium, but we support the inclusion of Bulbocodium and Merendera within Colchicum. Morphology and life history traits are the main arguments in favor of recognizing Androcymbium as a well-circumscribed genus. In the phylogeny two Androcymbium groups are clearly differentiated: (1) one including species from Western and Eastern South Africa, Namibia, and North Africa, and (2) one including species from the north west of South Africa and south of Namibia.     

Erysiphe paracarpinicola: A new species of Erysiphe sect. Uncinula on Carpinus cordata (Betulaceae)

A phylogeny of Erysiphe sect. Uncinula on Carpinus spp. was reconstructed using the 28S rDNA sequences and a combined alignment of the 28S, ITS, and IGS rDNA sequences. The analysis was supplemented with morphological data obtained from examination of voucher specimens. A sequence of Erysiphe sect. Uncinula on C. cordata formed a distinct lineage separated from sequences of other Erysiphe species on Carpinus spp., indicating a cryptic species, which is described as E. paracarpinicola. The new species is genetically as well as morphologically most similar to E. carpinicola s. str., but differs in having fewer asci per chasmothecium (mainly 3–5 vs 4–10) and shorter chasmothecial appendages. A key to species of Erysiphe sect. Uncinula on Carpinus spp. is provided.     

Erysiphe wadae: a new species of Erysiphe sect. Uncinula on Japanese beech

 A new species of Erysiphe sect. Uncinula is described and illustrated from Japan. Erysiphe wadae sp. nov., found on Japanese beech (Fagus crenata, Fagaceae), is characterized by having two types of appendages, i.e., a long (true) appendage arising from the equatorial zone of the ascomata, and a short appendage arising from the upper part of the ascomata. This characteristic is shared by E. simulans, E. australiana, E. flexuosa, E. liquidambaris, E. prunastri, and E. togashiana. Erysiphe wadae differs from the latter five species in its brown-colored appendage. Erysiphe simulans is most similar to E. wadae, but differs in its loosely uncinate appendage and smaller number of ascospores. Identity of the nucleotide sequences of the rDNA ITS region is 92.3% between the two species. The significance of the two types of appendage in taxonomy and phylogeny of powdery mildews is discussed based on molecular phylogenetic analysis. Received: November 8, 2002 / Accepted: January 29, 2003 Acknowledgments We are grateful to Drs. Yukio Harada and Hideki Naito for help in collecting powdery mildew specimens; Dr. Uwe Braun for providing the specimen of E. flexuosa; and Mr. Tetsuya Hirata and Miss Sanae Matsuda for nucleotide sequences of E. togashiana and E. flexuosa. This work was partially supported by a Grant-in-Aid for Scientific Research (No. 13660047) from Ministry of Education, Culture, Sports, Science and Technology, Japan.     

Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA

We present a comprehensive phylogeny derived from nuclear ribosomal DNA (nrDNA) for 214 samples representing 98 species and five varieties, including 44 species and five varieties native to China. Our collection of 25 species and five varieties (44 samples) covering all five sections of the genus (Comber) distributed in China also were included in the internal transcribed spacer (ITS) database. This study incorporates previous research with an emphasis on Chinese species, including the controversial subsection, Sinomartagon 5c Comber. In the phylogenetic tree obtained by maximum parsimony (PAUP) and maximum likelihood (RAxML) analyses, the samples were divided into four major groups. Our results suggest that the subsection (subsect.) 5c Comber should be classified into the true subsect. 5c and the section (sect.) Lophophorum. And the latter was divided into three subsections (subsect. Lophophorum I, subsect. Lophophorum II, and subsect. Lophophorum III). Based on molecular phylogenetic analysis and fluorescence in situ hybridization, we report that L. henryi and L. rosthornii are closely related, and we propose their classification into subsect. Leucolirion 6a. Our results support Comber’s subdivision of sect. Leucolirion, which was primarily based on bulb color. Chinese species were divided into five sections: sect. Martagon, sect. Archelirion, sect. Leucolirion, sect. Sinomartagon, and sect. Lophophorum. These findings contribute to our understanding of the phylogeny, origin, and classification of Lilium.     

Molecular phylogenetic reconstruction of Osmanthus Lour. (Oleaceae) and related genera based on three chloroplast intergenic spacers

Although polyphyly of Osmanthus has been suggested by different authors, the conclusions of previous studies have lacked robust support due to limited sampling or a paucity of phylogenetic characters. In this study, the phylogeny of Osmanthus was explored using sequences of three informative chloroplast regions (psbJ-petA, rpl32-trnL and rps16-trnQ), including all the five sections of the genus and eight closely related genera. The results confirm that Osmanthus, as presently circumscribed, is a polyphyletic group, containing three or four distinct lineages, i.e. sect. Leiolea (lineage I), sect. Notosmanthus (lineage III), sects. Osmanthus (excluding O. decorus), Siphosmanthus and Linocieroides (lineage IV), and an uncertain lineage including only O. decorus (lineage II). These results emphasize that the generic delimitation within subtribe Oleinae is in need of revision. In addition, this study found that the four cultivar groups of sweet osmanthus formed a paraphyletic clade, implying that cultivated sweet osmanthus might originate from several species.