Phylogeny of extant genera in the family Characeae (Charales,Charophyceae) based on rbcL,sequences and morphology

Extant genera of Characeae have been assigned to two tribes: Chareae (Chara, Lamprothamnium, Nitellopsis, and Lychnothamnus) and Nitelleae (Nitella and Tolypella), based on morphology of the thallus and reproductive structures. Character analysis of fossil and extant oogonia suggest that Tolypella is polyphyletic, the genus comprising two sections, one in each of the two tribes. Eleven morphological characters and sequence data for the Rubisco large subunit (rbcL) were used to reconstruct the phylogeny of genera, including the two sections of Tolypella. Parsimony analysis of the rbcL data, with all positions and changes weighted equally, strongly supports the monophyly of the Characeae. The two Tolypella sections form a robust monophyletic group basal to the family. Transversion weighting yielded the same tree but with a paraphyletic Tolypella. The rbcL data strongly support monophyly of tribe Chareae but tribe Nitelleae is paraphyletic. Parsimony analysis of morphological data produced one unrooted tree consistent with monophyly of the two tribes; on this tree the Tolypella sections were paraphyletic. Combining morphological with rbcL data did not change the results derived from rbcL sequences alone. The rbcL data support the monophyly of the Characeae and Coleochaete, which together form a monophyletic sister group to embryophytes.     

Molecular Phylogeny of the Suborder Leucodontineae (Musci; Leucodontales) Inferred from rbcL Sequence Data

rbcL sequence data (1324 bp on average). Our analyses indicate (1) that Antitrichia is distantly related to the other members of Leucodontaceae and should be excluded from the family, (2) that Cryphaeaceae form a monophyletic clade, not with Anomodontaceae and Leptodontaceae, but with Leucodontaceae, refuting the placement of Leucodontaceae and Cryphaeaceae in different superfamilies, (3) that Forsstroemia, variously classified in Leucodontaceae, Cryphaeaceae or Leptodontaceae, forms a monophyletic clade with Neckera (Neckeraceae), and (4) that the presumed monophyly of Anomodon and that of Anomodontaceae are not supported. Received 18 September 1999/ Accepted in revised form 27 December 1999     

Physical map and gene organization of the mitochondrial genome from the unicellular green alga Platymonas (Tetraselmis) subcordiformis (Prasinophyceae)

the entire mitochondrial genome (mt genome) of the unicellular green alga Platymonas subcordiformis (synonym Tetraselmis subcordiformis; Prasinophyceae) was cloned and a physical map for the four restriction enzymes Hind III, Eco RI, Bgl II and Xba I was constructed. The mt genome of P. subcordiformis is a 42.8 kb circular molecule, coding for at least 23 genes. Hybridization and sequence analysis revealed the presence of a ca. 1.5 kb inverted repeat on the mt genome of P. subcordiformis. Phylogenetic analyses based on sequences of several coxI genes were carried out. Our data indicate that mitochondria from P. subcordiformis and from land plants form a natural, monophyletic group.     

Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci

This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using DNA sequence data. We employed DNA from a nuclear protein-coding gene (histone H3), two nuclear ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), one mitochondrial protein-coding gene (cytochrome c oxidase subunit I), and one mitochondrial ribosomal gene (16S rRNA). A series of analyses were performed on independent and combined data sets. All these analyses were executed using direct optimization with parsimony as the optimality criterion, and analyses were repeated for nine combinations of parameters affecting indel and transversion/transition cost ratios. Maximum likelihood was also explored for the combined molecular data set, also using the direct optimization method, with a model equivalent to GTR + I + Γ that accommodates gaps. The results of all nine parameter sets for the combined parsimony analysis of all molecular data (as well as ribosomal data) and the maximum-likelihood analysis of all molecular data support monophyly of Polyplacophora. The resulting topologies mostly agree with a division of Polyplacophora into two major lineages: Lepidopleuridae and Chitonida (sensu Sirenko 1993). In our analyses the genus Callochiton is positioned as the sister group to Lepidopleuridae, and not as sister group to the remaining Chitonida (sensu Buckland-Nicks & Hodgson 2000), nor as the sister group to the remaining Chitonina (sensu Buckland-Nicks 1995). Chitonida (excluding Callochiton) is monophyletic, but conventional subgroupings of Chitonida are not supported. Acanthochitonina (sensu Sirenko 1993) is paraphyletic, or alternatively monophyletic, and is split into two clades, both with abanal gills only and cupules in the egg hull, but one has simple cupules whereas the other has more strongly hexagonal cupules. Sister to the Acanthochitonina clades is Chitonina, including taxa with adanal gills and a spiny egg hull. Schizochiton, the only genus with adanal gills that has an egg hull with cupules, is the sister-taxon to one of the Acanthochitonina clades plus Chitonina, or alternatively basal to Chitonina. Support values for either position are low, leaving this relationship unsettled. Our results refute several aspects of conventional classifications of chitons that are based primarily on shell characters, reinforcing the idea that chiton classification should be revised using additional characters.     

基于叶绿体trnL-F,rbcL序列和核核糖体ITS序列探讨蓼属（蓼科）头状蓼组的系统发育

选用叶绿体基因trnL-F,rbc-L序列和核核糖体ITS序列对蓼属头状蓼组的分类和系统发育进行了分析。以药用大黄为外类群,用最大简约法对3个片段的单独和联合矩阵分别构建系统发育树。结果表明,头状蓼组是一个较自然的类群,与春蓼组、刺蓼组和金线草属的亲缘关系较近;支持头状蓼组作为一组放在春蓼属,细茎蓼和蓝药蓼从头状蓼组转移至冰岛蓼属;不支持将刺蓼组并入头状蓼组;对于小叶蓼的系统学位置有待于进一步研究。     

Prasiolales (Trebouxiophyceae,Chlorophyta) of the Svalbard Archipelago: diversity,biogeography and description of the new genera Prasionella and Prasionema

Species of Prasiolales (Trebouxiophyceae, Chlorophyta) are among the most common terrestrial and freshwater algae in polar regions. Comprehensive molecular studies of this group are available for Antarctica, but not yet for Arctic regions. We examined the diversity of the Prasiolales in the Svalbard Archipelago combining morphological observations of field-collected material, culture studies, molecular data (plastid rbcL and tufA sequences) and literature records. We confirmed the widespread occurrence of Prasiola crispa and P. fluviatilis, species recorded from Spitsbergen since the 19th century. Molecular phylogenetic analyses led to the discovery of two new genera of Prasiolales. Prasionema payeri is morphologically identical to filamentous stages of P. crispa, but represents an early-diverging lineage in the order. Prasionella wendyae is a colonial alga reproducing by aplanospores; its phylogenetic position is among the basal lineages of the order, but it could not be reliably reconstructed due to weak statistical support. The inclusion of P. wendyae in the prasiolalean phylogeny determined the paraphyly of Rosenvingiella, requiring the establishment of the new genus Rosenvingiellopsis for R. constricta. A poorly known species described from Spitsbergen, Ulothrix discifera, is transferred here to Rosenvingiella. Whereas some species of Prasiolales have bipolar distribution (P. crispa), others appear to be restricted to one or other of the poles. Our results suggest that polar regions are still a major repository of unknown algal diversity and highlight the importance of continued field surveys and the use of molecular data.     

A morphological and molecular assessment of the genus Sinotubimorpha (Halymeniaceae, Rhodophyta)

A critical reassessment of the morphological features of two closely related red algal genera,Grateloupia C.Agardh and Sinotubimorpha W.X.Li & Z.F.Ding (Halymeniaceae),pointed out that members of the t...     

Biogeography and systematics of Hildenbrandia (Rhodophyta,Hildenbrandiales) in North America: inferences from morphometrics and rbcL and 18S rRNA gene sequence analyses

Morphometric analysis and phylogenetic analysis of sequences of the rbcL chloroplast gene (which codes for the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme) and the nuclear 18S ribosomal RNA (rRNA) gene were carried out on 26 specimens of marine and freshwater Hildenbrandia from North America. Nineteen marine specimens were collected from Alaska to Costa Rica on the Pacific coast and from Newfoundland to Connecticut on the Atlantic coast. Seven freshwater samples were collected from Texas, Costa Rica, St Lucia and Puerto Rico. Three groups of samples were distinguished by morphometric analysis: one containing all freshwater samples (H. angolensis Welwitsch ex West et West), one consisting of a marine sample with parallel tetrasporangial divisions (H. occidentalis Setchell ex Gardner) and one group with non-parallel tetrasporangial divisions (H. rubra (Sommerfelt) Meneghini. These groupings were partially incongruent with those obtained by analyses of the molecular data. Parsimony and distance analyses of the rbcL gene resulted in trees in which Atlantic and Pacific clades were largely resolved. However, an Alaskan sample was included in the Atlantic group, which may indicate a trans-Arctic invasion event. The freshwater samples were paraphyletic for the rbcL gene, among the marine collections, which supports the concept of multiple invasions establishing the freshwater populations in North America. The 18S rRNA gene sequence data indicate that the freshwater samples are monophyletic with the exception of the unresolved position of the H. occidentalis sample. The freshwater samples form a monophyletic clade when multiple outgroups are used. The rbcL data appear to be mutationally saturated above approximately 17% divergence, which makes interpretation of phylogenetic signal among distant groups difficult. This may be a result of the asexual reproduction of the alga.     

Molecular phylogenetic position of the genera Stephanonympha and Caduceia (Parabasalia) inferred from nuclear small subunit rRNA gene sequences

Nuclear small subunit (SSU) rRNA gene sequences were obtained by polymerase chain reaction from trichomonad symbionts of termites that belong to the Devescovinidae (Caduceia versatilis) and polymastigont Calonymphidae (Stephanonympha nelumbium). The unidentified SSU rRNA sequence Nk3, previously obtained from the termite Neotermes koshunensis, has also been shown to derive from a Stephanonympha sp. by in situ hybridization. These sequences were analysed in a broad phylogeny including nearly all identified parabasalid sequences available in the databases, and some as yet unidentified sequences likely deriving from the new order Cristamonadida (Devescovinidae, Calonymphidae, and hypermastigids Lophomonadida). A global phylogeny of parabasalids reveals a partial agreement between the clades identified in this work and the last classification of this phylum into four orders. However, this classification is still incongruent with our data and new taxonomic considerations are proposed. The analysis confirms the monophyly of the Cristamonadida and separates this order into two groups: the first unites nearly all the Devescovinidae including Caduceia and the Calonymphidae Coronympha and Metacoronympha, whereas the second group is composed of a few Devescovinidae, Lophomonadida, and Calonymphidae such as Stephanonympha. Caduceia is closely related to Devescovina, corroborating the marked morphological similarity between these two genera whereas Stephanonympha groups together with the Calonymphidae Snyderella and Calonympha. These data also confirm the polyphyly of the families Devescovinidae and Calonymphidae and support the arrangement of the axostyle-pelta complexes as a valuable character for taxonomic considerations within the Calonymphidae.     

Phylogeny of Rhaponticum (Asteraceae, Cardueae-Centaureinae) and related genera inferred from nuclear and chloroplast DNA sequence data: taxonomic and biogeographic implications

BACKGROUND AND AIMS: The precise generic delimitation of the Rhaponticum group is not totally resolved. The lack of knowledge of the relationships between the basal genera of Centaureinae could imply that genera whose position is as yet unresolved could belong to the Rhaponticum group. On the other hand, the affinities among the genera that are considered as members of this group are not well known. The aim of the study is to contribute to the phylogenetic and generic delineation of the Rhaponticum group on the basis of molecular data. METHODS: Parsimony and Bayesian analyses of the combined sequences of one plastid (trnL-trnF) and two nuclear (ITS region and ETS) molecular markers were carried out. The results of these analyses are discussed in the light of the biogeographic history. KEY RESULTS: The Rhaponticum group appears as monophyletic, and closely related to the genus Klasea. The results confirm the preliminary generic delimitation of the Rhaponticum group, with the new incorporation of the genus Centaurothamnus. Ochrocephala is supported as a separate genus from Rhaponticum and, contrary to this, Acroptilon and Leuzea appear as merged into the genus Rhaponticum. Several nomenclatural rearrangements are made in Klasea and Rhaponticum. CONCLUSIONS: The new molecular evidence is consistent with the morphological and karyological data, and suggests particularly coherent biogeographic routes of migration and speciation processes for the genus Rhaponticum. The biogeographic inference proposes a Near East and/or Caucasian origin for the genus. Furthermore, representatives of Rhaponticum could have reached Europe in two different ways: (1) expansion across central Asia to eastern Europe, and (2) expansion through the Near East, North Africa and then to the Iberian Peninsula and the Alps.     

Recent developments in the systematics of the Gigartinaceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis and morphological evidence

The phylogenetic systematics of the Gigartinaceae is discussed for seven genera and three undescribed generic lineages and 65 taxa representing 62 species based on an analysis of rbcL sequences and morphological evidence. An examination of rbcL trees resulting from analyses of these taxa identifies seven lineages: (i) ‘Gigartina’ alveata; (ii) Rhodoglossum/Gigartina; (iii) Chondracanthus; (iv) Ostiophyllum; (v) Sarcothalia; (vi) ‘Gigartina’ skottsbergii; and (vii) a large clade containing Iridaea/‘Sarcothalia’, Mazzaella and Chondrus. These lineages and Chondrus are strongly supported; however, two groups, Iridaea/‘Sarcothalia’ and Mazzaella, receive no bootstrap support. The morphology of the female reproductive system is investigated with the aid of computer-generated, color-coded tracings of photographs of cystocarps seen in cross section at different developmental stages. Seven basic cystocarp types were found which corresponded to species groups seen in rbcL trees. These were: (i) a ‘Gigartina’ alveata group in which the carposporangia-bearing filaments develop apomictically from gametophytic cells; (ii) a Rhodoglossum/Gigartina group in which gonimoblast filaments penetrate the surrounding envelope fusing progessively with envelope cells; (iii) a Chondracanthus group in which gonimoblast filaments penetrate the envelope but fuse with envelope cells only at late developmental stages; (iv) a Sarcothalia group in which the gonimoblast filaments displace an envelope composed mainly of secondary gametophytic filaments and link to envelope cells by terminal tubular gonimoblast cells; (v) an Iridaea group similar to the Sarcothalia group, but with an envelope composed of a mixture of medullary cells and secondary gametophytic filaments; (vi) a Mazzaella group that lacks a true envelope and in which gonimoblast filaments connect to modified gametophytic cells by means of terminal tubular cells; (vii) a Chondrus group in which gonimoblast filaments penetrate the medulla and link to modified medullary cells by means of conjunctor cells forming secondary pit connections. The further separation of these groups into genera is based largely on tetrasporangial characters.     

Evidence for the Polyphyly of Haworthia (Asphodelaceae Subfamily Alooideae; Asparagales) Inferred from Nucleotide Sequences of rbcL, matK, ITS1 and Genomic Fingerprinting with ISSR-PCR

Abstract: Four molecular markers have been studied to examine the phylogenetic position of the South African plant genus Haworthia Duval within the succulent Asphodelaceae. Sequence data of the chloroplast genes mat K and rbc L were compared to the nuclear markers ITS1 and ISSR (Inter Simple Sequence Repeat) analysis. Both lines of molecular data, chloroplast and nuclear DNA, indicate that Haworthia is polyphyletic, forming two distinct clades. Most taxa previously combined as Haworthia subgenus Haworthia branch off early in the alooid chloroplast trees forming a strongly monophyletic group, whereas subgenus Hexangulares forms a polyphyletic assemblage comprising other alooid genera. The nuclear markers ITS1 and ISSR fingerprinting support the two groups as distinctly different, therefore confirming the division seen in chloroplast DNA. The practical implication is that the generic concept of Haworthia may have to be restricted to H. subgenus Haworthia or alternatively, that the groups of Haworthia be treated as infrageneric taxa within a broadened (Linnaean) concept of Aloe.     

Molecular phylogeny of the genus<Emphasis Type="Italic">Hypericum</Emphasis> (Hypericaceae) from Korea and Japan: evidence from nuclear rDNA ITS sequence data

As part of our ongoing phylogenetic study of genusHypericum, nuclear ribosomal DNA internal transcribed spacer sequences were analyzed for 36 species ofHypericum as ingroup and two species ofThornea as outgroup. This sampling included most of the previously described species from both Korea and Japan. The ITS phylogeny suggested that the surveyedHypericum species belong to a monophyletic section,Trigynobrathys, and a polyphyletic section,Hypericum. In addition, two monotypic sections,Sampsonia andRoscyna, were identified. Members of sectionHypericum occur in four different lineages worldwide, which imply at least four independent origins. The Korean and Japanese species of sectionHypericum form a monophyletic group, except forH. vulcanicum. Instead, that particular species belongs to a distinct monophyletic group withH. scoreri andH. formosa from other geographic areas, and is a sister to sectionTrigynobrathys. The Korean and Japanese species of sectionTrigynobrathys show a monophyletic origin.H. sampsonii is now recognized as a distinct section rather than being a member of sectionsHypericum orDrosocarpium, as had been indicated previously. Our results differ somewhat from those of recent morphological and cytological studies. The phylogenetic relationships among Korean and Japanese species have now been mostly resolved via ITS phylogeny.