Chloroplast trnL-trnF Region Research Articles

Evolutionary history of the Eurasian steppe plant Schivereckia podolica (Brassicaceae) and its close relatives

The genus Schivereckia (Brassicaceae) – presently included in the genus Draba – comprises two species, S. podolica and S. doerfleri. Schivereckia podolica is an eastern European species with disjunct distribution in Russia, Ukraine, and Podolian-Galician outposts. Schivereckia doerfleri is reported from alpine fields of the Balkan Peninsula and from mountain chains of northern Anatolia, Turkey. Schivereckia podolica shares its ecological and biogeographic characteristics with a number of other steppe plants. The ‘relic hypothesis’ interprets the present locations of Schivereckia and its associates as relics of a formerly continuous distribution belt of a cold periglacial steppe vegetation.We employed nuclear ITS and chloroplast trnL-trnF region, and DNA fingerprinting (RAPD) to elucidate the evolutionary history and historical biogeography of Schivereckia. RAPD data prove isolation by distance and mirror the present disjunct geographical distribution pattern of Schivereckia podolica. Phylogenetic analyses revealed that Schivereckia might be polyphyletic and nested within a highly supported clade of central Asian, Caucasian and North American Draba species. Time divergence estimation and ancestral area reconstruction support the interpretation of species of the Schivereckia subclade as periglacial relic. Our results argue for a continuous persistence of certain steppe species since the Pleistocene, and support the view that the modern steppes of Europe have derived partly from Pleistocene glacial steppes.

One for all: molecular study of Polygala major complex (Polygalaceae) in Southwest Asia

Ten species of Polygala closely related to P. major are recorded in Southwest Asia. Most of them were described as local endemics of the Transcaucasia. However, species of the P. major complex are often difficult to identify, having rather subtle and changeable morphological features that could not be treated as essential. The phylogenetic analysis of sequences of the nrITS/ETS and chloroplast trnL–trnF regions (intron and spacer) showed their extreme similarity. Based on the molecular evidence and main diagnostic morphological features, the ten species of the P. major complex are synonymized under P. major. Typifications of eight combinations in Polygala from Western Asia and Europe are also clarified.

Phylogenetic Relationships in the Genus <i>Spiraea</i> (Rosaceae) Inferred from the Chloroplast DNA Region, <i>trn</i>L-<i>trn</i>F

The 26 taxa of genus Spiraea (Rosaceae) in 14 Korean taxa and four taxa of them doubled in the world itself were collected and investigated phylogenetic relationships within these taxa using the chloroplast trnL-trnF region. Sequence variation within the genus Spiraea was mostly due to insertion/deletion. Total alignment sequence of trnL-trnF region in genus Spiraea was 1004 positions, of which 126 were parsimony-informative, 149 variable, 23 singleton, and 847 constant characters. The base furtherance did not show a significant difference among total taxa. Although many taxa of genus Spiraea were well separated each other, many branches were not congruent with the taxon positions with botanical names. In addition, sequences of the chloroplast trnL-trnF region for same species are different from each other according to authors. The taxonomic identification of genus Spiraea are in need of revision.

Molecular characterization of phylogeneticrelationships in Fritillaria species inferred from chloroplast trnL-trnF sequences

The genus Fritillaria embraces about 165 taxa in the family Liliaceae. In this study, the molecular phylogenetic relationships between 10 Fritillaria taxa were presented. Fritillaria spp. were collected from their natural habitats, and specimens with different morphological features were obtained via selective breeding. Specimens with the desired characters were presented as promising candidate cultivars for ornamental use. Phylogenetic analysis was based on DNA sequences of the chloroplast trnL-trnF region. The phylogeny was constructed using the neighbor joining, maximum parsimony, maximum likelihood, and Bayesian inference methods. The data showed that the examined Fritillaria spp. were evidently diverged into 2 Fritillaria subgenera. Members of the subgenus Fritillaria formed one clade while the other clade contained the subgenera Theresia and Petilium. Separation within the latter clade was strongly supported with bootstrap values, whereas resolution within the subgenus Fritillaria remained ambiguous. This analysis revealed the feasibility of the chloroplast trnL-trnF region DNA sequence for phylogeny of the Fritillaria species. Our study is the first phylogenetic analysis in Fritillaria spp. based on the trnL-trnF region. Fingerprint data of these cultivars would be a valuable source for their identification and for the generation of new cultivars in future.

TrnL-trnF 서열에 의한 한국 귤나무속과 두 근연 식물종의 계통분류학적 연구

귤나무속은 운향과(Rutaceae)에 속한다. 동남아시아, 미얀마, 중국 운남에서 기원된 것으로 알려져 있다. 이 속의 분류관계는 복잡한데 클론번식과 야생식물과 교잡이 빈번하다. 식물에서 속간 속내 계통관계 추론을 위해 널리 이용되고 있는 엽록체 trnL-trnF 부위가 있다. 이 귤나무속과 두 근연한 탱자나무속과 금감속에 속하는 7종간 계통 관계를 평가하였다. 많은 삽입이 발견되었고 속내 종간 변이는 결실/삽입에 의한 것으로 밝혀졌다. 이 속의 레몬과 당귤나무은 네 계통도(MP, ML, ME, and NJ)에서 모두 같은 분지군을 형성하여 가장 근연관계에 있었고 광귤나무(향귤나무)과 자매군을 형성하였다. 유자나무는 이들과 많은 서열 차이를 나타내었다. 외부 분지군은 낮은 지지도를 나타내었다. Citrus is a common term and genus (Citrus) of flowering plants in the rue family, Rutaceae. Citrus is believed to have originated in the part of Southeast Asia bordered by Northeastern India, Myanmar (Burma) and the Yunnan province of China. The taxonomy and systematics of the genus are complex and the precise number of natural species is unclear, as many of the named species are clonally propagated hybrids, and there is genetic evidence that even some wild, true-breeding species are of a hybrid origin. One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the chloroplast trnL-trnF region. We evaluated the seven taxa with the trnL-trnF region to estimate phenotypic relationships within the genera Citrus, Poncirus, and Fortunella in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within Citrus was mostly due to insertion/deletion. Within the genus Citrus, C. lomonia and C. sinensis were relatives and sistered with C. aurantium in the four phylogenetic analyses (MP, ML, ME, and NJ). However, some external nodes were poorly supported.

A molecular phylogenetic study of Mannia (Marchantiophyta, Aytoniaceae) using chloroplast and nuclear markers

Phylogenetic relationships of 36 samples of Mannia and other Aytoniaceae were inferred based on sequences of the chloroplast trnL-trnF region and partial nuclear ribosomal LSU (or 26S) gene and using Targionia hypophylla and Athalamia hyalina as outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted on individual and combined molecular datasets. All phylogenetic tree topologies showed polytomies but suggest that Mannia has evolved from within Asterella and that there are two supported Mannia clades. Because Mannia is paraphyletic, with A. gracilis most closely related to M. triandra and M. pilosa, A. gracilis is transferred to Mannia. The major morphological differences between those genera are reevaluated. Based on molecular and morphological evidence Mannia is divided into the subgenera Mannia and Neesiella; Asterella subg. Graciles becomes a synonym of Mannia subg. Neesiella.

Phylogeny and biogeography of Croton alabamensis (Euphorbiaceae), a rare shrub from Texas and Alabama, using DNA sequence and AFLP data

Croton alabamensis (Euphorbiaceae s.s.) is a rare plant species known from several populations in Texas and Alabama that have been assigned to var. texensis and var. alabamensis, respectively. We performed maximum parsimony, maximum likelihood, and Bayesian analyses of DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and 5.8S regions and chloroplast trnL-trnF regions from collections of the two varieties of C. alabamensis and from outgroup taxa. C. alabamensis emerges alone on a long branch that is sister to Croton section Corylocroton and the Cuban endemic genus Moacroton. Molecular clock analysis estimates the split of C. alabamensis from its closest relatives in sect. Corylocroton at 41 million years ago, whereas the split of the two varieties of C. alabamensis occurred sometime in the Quaternary. Amplified fragment length polymorphism (AFLP) analyses were performed using two selective primer pairs on a larger sampling of accessions (22 from Texas, 17 from Alabama) to further discriminate phylogenetic structure and quantify genetic diversity. Using both neighbour joining and minimum evolution, the populations from the Cahaba and Black Warrior watersheds in Alabama form two well-separated groups, and in Texas, geographically distinct populations are recovered from Fort Hood, Balcones Canyonlands, and Pace Bend Park. Most of the molecular variance is accounted for by variance within populations. Approximately equal variance is found among populations within states and between states (varieties). Genetic distance between the Texas populations is significantly less than genetic distance between the Alabama populations. Both sequence and AFLP data support the same relationships between the varieties of C. alabamensis and their outgroup, while the AFLP data provide better resolution among the different geographical regions where C. alabamensis occurs. The conservation implications of these findings are discussed.

Character divergences and convergences in canopy-dwelling Loranthaceae

The Loranthaceae is the largest plant family with aerial branch parasites termed mistletoes. Three genera of Loranthaceae are terrestrial root parasites and the remaining 72 genera are aerial parasites. Several characters, including habit, haustorial type, germination pattern, pollen morphology, chromosome number, inflorescence morphology and flower merosity, fusion, symmetry and size, are considered to reflect evolutionary relationships within the family. Convergence is a common evolutionary pattern and can confound interpretations of evolution. We investigated character evolution by mapping character states onto a phylogenetic tree based on the nuclear ITS and chloroplast trnL–trnF regions. Convergences in form were found in several characters, including habit, haustorial type, flower symmetry and merosity. These convergences typically correspond to ecological parameters such as pollination syndrome or stresses associated with the canopy habit. Other characters such as chromosome number and germination pattern illustrate divergent evolution among clades.

Genetic variation is not concordant with morphological variation in the fern Asplenium hookerianum sensu lato (Aspleniaceae)

Species status cannot be adequately determined when partitions are based on only a single morphological character. For instance, the sympatry of plants with broad and narrow pinnules in the fern Asplenium hookerianum sensu lato from New Zealand creates the impression that two entities are present. The narrow-pinnuled plants are sometimes segregated as a distinct species, A. colensoi. However, this variation in pinnule morphology could equally be infraspecific, and only additional data can resolve this uncertainty. Analyses using AFLP DNA-fingerprinting and DNA sequencing of the chloroplast trnL-trnF region indicate that genetic variation in A. hookerianum sensu lato is not concordant with pinnule morphology. Consequently, the recognition of A. colensoi is not supported.

Phylogenetic relationships inSaussurea (Compositae, Cardueae)sensu lato, inferred from morphological, ITS andtrnL-trnF sequence data, with a synopsis ofHimalaiellagen. nov.,LipschitziellaandFrolovia

Raab-Straube, E. von: Phylogenetic relationships in Saussurea (Compositae, Cardueae) sensu lato, inferred from morphological, ITS and trnL-trnF sequence data, with a synopsis of Himalaiella gen. nov., Lipschitziella and Frolovia. — Willdenowia 33: 379–402. — ISSN 0511-9618; © 2003 BGBM Berlin-Dahlem.DNA sequences from the nuclear ribosomal ITS and from the chloroplast trnL-trnF regions of 47 species of all six subgenera and 13 sections of Saussurea were analysed. The cladogram resulting from ITS sequence data indicates that Saussurea in its present circumscription is paraphyletic. S. sect. Elatae and S. subg. Jurinocera together are sister to the genus Jurinea. The affinities of S. subg. Frolovia are unclear, while representative species of the remaining four subgenera and ten sections form a strongly supported monophyletic group. Within this clade, the delimitation of S. subg. Eriocoryne and S. subg. Amphilaena against S. subg. Saussurea is not evident. The trnL-trnF intergenic spacer sequences show a remarkable synapomorphy, a 21bp insertion, for Jurinea cyanoides, S. deltoidea, S. ceratocarpa and S. frolovii, supporting the paraphyly of Saussurea. These results correspond to differences in morphological characters of achenes and pappus, which also suggest that S. sect. Elatae, S. subg. Jurinocera and S. subg. Frolovia are not closely related to the remainder of the genus. Consequently, S. sect. Elatae is separated as the new genus Himalaiella, and the small generic segregates Frolovia and Lipschitziella are resurrected. A synopsis of these three genera is presented and the new combinations Himalaiella abnormis, H. afghana, H. albescens, H. auriculata, H. chenopodiifolia, H. chitralica, H. deltoidea, H. foliosa, H. heteromalla, H. nivea, H. peguensis, Frolovia frolovii and F. gorbunovae are validated.