Phylogenetic studies on the Thamnocalamus group and its allies (Gramineae: Bambusoideae) based on its sequence data.

Phylogenetic analyses, using the parsimony method and the neighbor-joining method, of 31 species of the Thamnocalamus group and its allies based on internal transcribed spacer (ITS) sequences in nuclear ribosomal DNA are presented. Two species from Arundinaria and Acidosasa were used as outgroups. The ITS phylogeny strongly supports the monophyly of the Thamnocalamus group and its allies, which have pachymorph rhizomes and semelauctant synflorescences with three stamens. Within this clade, Chimonocalamus pallens was resolved in the basal position. The Thamnocalamus group, including species placed in Thamnocalamus, Fargesia (Sinarundinaria, Borinda), and Yushania, may be polyphyletic/paraphyletic according to the ITS phylogeny, but internal support was relatively low. All three sampled species of Ampelocalamus were resolved as a monophyletic group and may be related to Drepanostachyum hookerianum. Two taxa of Thamnocalamus and the species Gaoligongshania megalothyrsa were resolved as monophyletic despite their different morphological characters, but again with a low bootstrap support. Within the Fargesia yunnanensis subclade, the sister relationship of Fargesia fungosa and Fargesia edulis was supported. Another subclade, the Fargesia communis clade, was also weakly supported as monophyletic. However, further resolution within the Thamnocalamus group has not been provided by this sequence data. The results indicate that reevaluation of relationships within this group is necessary.     

Phylogeny of Eleusine (Poaceae: Chloridoideae) based on nuclear ITS and plastid trnT-trnF sequences

Phylogenetic relationships in the genus Eleusine (Poaceae: Chloridoideae) were investigated using nuclear ITS and plastid trnT-trnF sequences. Separate and combined data sets were analyzed using parsimony, distance, and likelihood based methods, including Bayesian. Data congruence was examined using character and topological measures. Significant data heterogeneity was detected, but there was little conflict in the topological substructure measures for triplets and quartets, and resolution and clade support increased in the combined analysis. Data incongruence may be a result of noise and insufficient information in the slower evolving trnT-trnF. Monophyly of Eleusine is strongly supported in all analyses, but basal relationships in the genus remain uncertain. There is good support for a CAIK clade (E. coracana subsp. coracana and africana, E. indica, and E. kigeziensis), with E. tristachya as its sister group. Two putative ITS homeologues (A and B loci) were identified in the allotetraploid E. coracana; the 'B' locus sequence type was not found in the remaining species. Eleusine coracana and its putative 'A' genome donor, the diploid E. indica, are confirmed close allies, but sequence data contradicts the hypothesis that E. floccifolia is its second genome donor. The 'B' genome donor remains unidentified and may be extinct.     

西藏特有竹子Arundinaria macclureana的名实辨正

Arundinaria macclureana是在现代植物学中根据在西藏采集的标本描述的第一个竹子。其模式标本是1938年采集的,但只有花枝,没有地下茎、秆箨等重要特征。尽管如此,该种还成为了新属Borinda的模式种。在研究了其模式标本后,使本文第一作者联想起1991年在藏东南采集的西藏箭竹（Fargesia setosa）。西藏箭竹的模式标本采集于1977年,但只有营养体,没有花枝。在对比研究两个名称的模式后,确认二者实为同种。经与共同作者一起讨论,认为其正确学名为Fargesia macclureana,但该种所在的筱竹属群的关系还有待进一步的研究。     

The Identity of an Endemic Tibetan Bamboo,Arundinaria macclureana ( Gramineae,Bambusoideae)

Arundinaria macclureana Bor was the first bamboo described in modern taxonomy based on Tibetan material. Since the type bears only flowering branches without critical vegetative characteristics such as rhizomes and culm- sheaths, its identity has long been doubtful. Even so, it provides the type of a newly created genus, Borinda. By checking the type specimens of A1 macclureana as well as the type of Fargesia setosa T. P. Yi, which is a species only known by its vegetative state, and by collecting in the field, a conclusion is reached that these two entities are conspecific. Fargesia macclureana, a name published in less- received literature is the correct name for this endemic Tibetan bamboo, although re- evaluation of the relationships within the Thamnocalamus group is needed.     

Genetic Variation and Evolution of the Alpine Bamboos (Poaceae: Bambusoideae) using DNA Sequence Data

Thamnocalamus , Fargesia and Yushania, of the alpine bamboos and one species of Ampelocalamus as an out-group were studied. The results indicated that Thamnocalamus spathiflorus var. crassinodus and the Fargesia spathacea clade form the basal groups but bootstrap support was weak. Among the rest of the species, including species previously placed in Fargesia (plus Borinda) and Yushania, the F. yunnanensis subclade and the F. communis subclade were recognized but internal support for such groups was again low. The result indicated that, Fargesia and Yushania as delimited by morphological characters, are not monophyletic in the ITS phylogeny and require further resolution. We revealed relatively high levels of genetic variability in the alpine bamboos and showed that the ITS region could be used to improve generic delimitation of the woody bamboos in general. Received 18 September 2000/ Accepted in revised form 9 May 2001     

Molecular phylogeny of Laetiporus and other brown rot polypore genera in North America

Phylogenetic relationships were investigated among North American species of Laetiporus, Leptoporus, Phaeolus, Pycnoporellus and Wolfiporia using ITS, nuclear large subunit and mitochondrial small subunit rDNA sequences. Members of these genera have poroid hymenophores, simple septate hyphae and cause brown rots in a variety of substrates. Analyses indicate that Laetiporus and Wolfiporia are not monophyletic. All North American Laetiporus species formed a well supported monophyletic group (the "core Laetiporus clade" or Laetiporus s.s.) with the exception of L. persicinus, which showed little affinity for any genus for which sequence data are available. Based on data from GenBank, the southern hemisphere species L. portentosus also fell well outside the core Laetiporus clade. Wolfiporia dilatohypha was found to represent a sister group to the core Laetiporus clade. Isolates of Phaeolus, Pycnoporellus and members of the core Laetiporus clade all fell within the Antrodia clade of polypores, while Leptoporus mollis and Laetiporus portentosus fell within the phlebioid clade of polypores. Wolfiporia cocos isolates also fell in the Antrodia clade, in contrast to previous studies that placed W. cocos in the core polyporoid clade. ITS analyses resolved eight clades within Laetiporus s.s., three of which might represent undescribed species. A combined analysis using the three DNA regions resolved five major clades within Laetiporus s.s.: a clade containing conifer-inhabiting species ("Conifericola clade"), a clade containing L. cincinnatus ("Cincinnatus clade"), a clade containing L. sulphureus s.s. isolates with yellow pores ("Sulphureus clade I"), a clade containing L. sulphureus s.s. isolates with white pores ("Sulphureus clade II") and a clade containing L. gilbertsonii and unidentified isolates from the Caribbean ("Gilbertsonii clade"). Although there is strong support for groups within the core Laetiporus clade, relationships among these groups remain poorly resolved.     

Phylogeny of the Neotropical Alibertia group (Rubiaceae), with emphasis on the genus Alibertia, inferred from ITS and 5S ribosomal DNA sequences

Phylogenetic relationships of 38 species of the Alibertia group (Rubiaceae) and two outgroup species were investigated using the nuclear ribosomal 5S nontranscribed spacer (5S-NTS) and the internal transcribed spacers (ITS). Analysis of the data sets separately and in combination resulted in several well-supported and congruent groupings. However, the three analyses yielded different results as to the branching order of the basal clades. With the exception of Alibertia hispida, the species in the genus Alibertia appear in one weakly to moderately supported clade. This clade is in turn composed of two strongly supported subclades. One comprises several Alibertia species, including the type (A. edulis), three Borojoa species, and Randia tessmannii. The other subclade consists of Alibertia species only. This division is also generally supported morphologically by fruit size, corolla size, number of corolla lobes, and pollen aperture (porate vs. colporate). The sister group to the Alibertia clade comprises Duroia with Amaioua species internested. The close relationship of Ibetralia and Kutchubaea is corroborated. In addition, Alibertia hispida is a member of this strongly supported clade. Likewise, the two "Genipa" species are supported as a monophyletic group in 100% of the bootstrap replicates. It is concluded that the 5S spacer is superior to the commonly used ITS region in terms of resolution and robustness among closely related taxa.     

Phylogeny of the subgenus sophophora (Diptera: drosophilidae) based on combined analysis of nuclear and mitochondrial sequences

Sequences from the nuclear (nu) alcohol dehydrogenase gene, the nu 28S ribosomal RNA locus, and the mitochondrial cytochrome oxidase II gene were used both individually and in combined analyses to infer the phylogeny of the subgenus Sophophora (Diptera: Drosophilidae). We used several optimality criteria, including maximum likelihood, maximum parsimony, and minimum evolution, to analyze these partitions to test the monophyly of the subgenus Sophophora and its four largest species groups, melanogaster, obscura, saltans, and willistoni. Our results suggest that the melanogaster and obscura species groups are each monophyletic and form a closely related clade. The Neotropical clade, containing the saltans and willistoni species groups, is also recovered, as previous studies have suggested. While the saltans species group is strongly supported as monophyletic, the results of several analyses indicate that the willistoni species group may be paraphyletic with respect to the saltans species group.     

Phylogenetic relationships of the Rhizophoraceae in China based on sequences of the chloroplast gene matK and the internal transcribed spacer regions of nuclear ribosomal DNA and combined data set

The chloroplast gene matK and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from 17 samples of 13 species representing 6 genera of the angiosperm family Rhizophoraceae from China. Phylogenetic analyses were initially conducted based on sequences of the matK gene and the ITS regions, respectively, using Byrsonima crassifolia and Bunchosia armeniaca (Malpighiaceae) as outgroups. The partition–homogeneity test indicated that the two data sets are homogeneous. A combined analysis of the matK and ITS data generated a well supported phylogeny, which is topologically congruent with the two gene trees based on the Templeton test. The combined phylogeny shows that each genus formed a monophyletic group and the monophyletic relationships of the mangrove genera and of the inland genera were strongly supported.     

Phylogeny of the festucoid grasses of subtribe Loliinae and allies (Poeae, Pooideae) inferred from ITS and trnL-F sequences

Analyses of ribosomal ITS and chloroplast trnL-F sequences provide phylogenetic reconstruction for the festucoids (Poeae: Loliinae), a group of temperate grasses with morphological and molecular affinities to the large genus Festuca. Parsimony and Bayesian analyses of the combined ITS/trnL-F dataset show Loliinae to be monophyletic but unresolved for a weakly supported clade of 'broad-leaved Festuca,' a well-supported clade of 'fine-leaved Festuca,' and Castellia. The first group includes subgenera Schenodorus, Drymanthele, Leucopoa, and Subulatae, and sections Subbulbosae, Scariosa, and Pseudoscariosa of Festuca, plus Lolium and Micropyropsis. The second group includes sections Festuca, Aulaxyper, Eskia, and Amphigenes of Festuca, plus Vulpia, Ctenopsis, Psilurus, Wangenheimia, Cutandia, Narduroides, and Micropyrum. Subtribes Dactylidinae and Cynosurinae/Parapholiinae are sister clades and are the closest relatives of Loliinae. Vulpia is polyphyletic within the 'fine-leaved' fescues as revealed by the two genome analyses. Lolium is resolved as monophyletic in the ITS and combined analyses, but unresolved in the trnL-F based tree. Conflict between the ITS and the trnL-F trees in the placement of several taxa suggests the possibility of past reticulation events, although lineage sorting and possible ITS paralogy cannot be ruled out.     

Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra

A homeotic gene, LEAFY, has been suggested to be a single-copy gene in diploid angiosperms. Nucleotide sequences of the second intron of this gene, along with those of several regions of the chloroplast genome (trnL-trnF, trnD-trnY-trnE-trnT, and matK-trnK) and nuclear ribosomal ITS, were obtained from the species of Neillia and Stephanandra to examine the phylogenetic utility of the intron and to elucidate the phylogenetic relationships among species of the two genera. PCR amplification of the second intron of LEAFY using universal degenerate primers produced PCR products in sufficient quantity for successful direct sequencing. The length of the intron ranged from 591 to 622 base pairs (bp) in Neillia and Stephanandra, except in N. thibetica (ca. 1370 bp), and sequence analysis of this region from multiple accessions revealed low levels of infraspecific variation. Comparison of the LEAFY data with ITS and cpDNA data demonstrated that the LEAFY intron was the most variable and useful for phylogenetic analysis at the species level, providing many more phylogenetically informative characters per 100 bp (7.4) than either ITS (3.2) or cpDNA (0.7). Phylogenetic analyses of LEAFY data using both maximum parsimony and likelihood methods generated well supported and highly resolved gene trees with few homoplasies (CI=0.97). Stephanandra is monophyletic and is nested within Neillia in both LEAFY and cpDNA trees, while the relationship is poorly resolved by ITS data. LEAFY and cpDNA data, however, strongly conflicted with each other with respect to the position of Stephanandra: LEAFY trees placed Stephanandra as sister to the ((N. affinis, N. gracilis), N. thyrsiflora) clade whereas cpDNA data suggested Stephanandra is sister to N. uekii. Both gene trees, however, are nearly identical to each other when Stephanandra is excluded. A hybrid origin of Stephanandra is suggested as a plausible hypothesis to explain the incongruence between LEAFY and cpDNA data sets, though gene duplication/loss and lineage sorting events cannot be ruled out as possibilities.     

Molecular phylogeny and biogeography of African diploid barbs, ‘Barbus’, and allies in Africa and Asia (Teleostei: Cypriniformes)

African diploid barbs (‘Barbus’, Clypeobarbus, Barboides, etc.) are a group of small cyprinids with a body size less than 20 cm and widely distributed in drainages across Africa. These species constitute a significant component of African freshwater fish fauna. This study is the first to focus on the molecular systematics and biogeography of African diploid barbs ‘Barbus’ and its African and Asian allies using both mitochondrial and nuclear genes. We test for monophyly of groups, determine interspecific relationships and estimate the time of divergence of 52 species of ‘Barbus’ and allies using two mitochondrial and four nuclear genes. Resulting trees demonstrate that ‘Barbus’ and allies (Systomus, Barboides, Clypeobarbus and African tetraploid barbs) form a strongly supported clade; however, ‘Barbus’ is not resolved as monophyletic. Divergence time analyses identify the separation between Systomus and ‘Barbus’ plus African allies may have occurred around 26 MYA. In addition to the phylogenetic results, these findings highlight the need for more thorough taxonomic and systematic studies on ‘Barbus’ and allies using morphological and additional molecular data and greater taxon sampling, including the type species of the genus Enteromius, ‘Barbus’ potamogalis.     

西藏特有竹子Arundinaria macclureana 的名实辨正

Arundinaria macclureana 是在现代植物学中根据在西藏采集的标本描述的第一个竹子。其模式标本是
1938 年采集的, 但只有花枝, 没有地下茎、秆箨等重要特征。尽管如此, 该种还成为了新属Borinda 的模
式种。在研究了其模式标本后, 使本文第一作者联想起1991 年在藏东南采集的西藏箭竹( Fargesia setosa) 。
西藏箭竹的模式标本采集于1977 年, 但只有营养体, 没有花枝。在对比研究两个名称的模式后, 确认二
者实为同种。经与共同作者一起讨论, 认为其正确学名为Fargesia macclureana, 但该种所在的筱竹属群的
关系还有待进一步的研究。     

东南亚地区五加科植物进化关系的初步研究

东南亚五加科包含14个属约500种,本文应用ITS片段对该区五加科植物的进化关系作了初步研究.研究显示该地区五加科植物具有复杂的起源,很多属属于亚洲掌状复叶类群或Hedereae族的一支中.该区特有类群Harmsiopanax形态上非常特殊,但其系统位置尚未不明朗.在Brassaiopsis属中,有几种形态差异较大的种,但它们属同一单系,加之各种问ITS序列差异较小,故应是新近起源于马来亚半岛和苏门达腊岛的种类.Wardenia simplex聚类在Brassaiopsis一支中,故不支持将Wardenia作为独立的属.东南亚地区对于Schefflera属的发育非常重要,已有的证据显示该区的Schefflera属植物属于该属的Heptapleumm类群.马来亚与泰国南部的Dendropanax lancifolius并没有与Dendropanax属的核心类群聚在一起,其系统地位需进一步研究.Macropanax maingayi是非常特殊的一个种,曾被独立分出,成立了单种属Hederopsis.本文的分析清楚表明它属于Macropanax属.Aralia merrillii因为其不同寻常的攀缘特性而被独立出来,建立了单种属Acanthophora,但ITS序列分析支持将它置于Aralia属中.新增的取样继续支持Arthrophyllum的单系性.Osmoxylon的原初分布范围在东南亚,它是五加科系统进化树上孤立的类群.     

Freshwater ascomycetes: two new species of Lindgomyces (Lindgomycetaceae, Pleosporales, Dothideomycetes) from Japan and USA

During independent surveys of freshwater ascomycetes in Japan and USA two new species of Lindgomyces were collected from submerged wood in freshwater. These species are described and illustrated based on morphological data and phylogenetic relationships based on analyses of nuclear ribosomal sequence data (partial SSU and LSU, and ITS). Lindgomyces apiculatus, collected in Japan, is characterized by immersed to erumpent, globose to subglobose ascomata; fissitunicate, cylindrical to clavate asci; and fusiform, one-septate ascospores with acute ends and short terminal appendages. Lindgomyces lemonweirensis, collected in Wisconsin, USA, differs from L. apiculatus in having clavate to cymbiform asci and oblong to fusiform ascospores that are distinctively multiguttulate and surrounded by an oval, ephemeral gelatinous sheath. The new species formed a strongly supported clade within the family Lindgomycetaceae (Pleosporales, Dothideomycetes) based on analyses of combined SSU and LSU sequence data. In addition phylogenetic analyses with ITS sequence data support the establishment of the new taxa as separate species within Lindgomyces because they were separated from each other and other Lindgomyces species based on maximum likelihood bootstrap and Bayesian analyses.     

The phylogenetic relationships among some Randia (Rubiaceae) taxa

Phylogenetic relationships among some Randia (Rubiaceae, Gardenieae) taxa were estimated based on sequence variation in the nuclear ribosomal internal transcribed spacers (ITS) and rps 16 intron (cpDNA). During the investigation of rpsl6 intron of 9 studied Central American Randia species, two well supported subclades were separated. Analysis of ITS data of 16 Randia species shows 3 major clades. A group of mainly lowland, South American Randia species is moderate supported (75%). Species from Mexico form a strongly supported (97%) clade, but the Central American and Mexican Randia species are low supported (58%). However the last two groups are well supported together (95%). The molecular delimination is well in line with the size of leaves combined with the texture of exocarp.     

Phylogenetic analysis of the subfamily Alpinioideae (Zingiberaceae), particularly Etlingera Giseke, based on nuclear and plastid DNA

Parsimony analyses based on DNA sequence data of the plastid group II intron rps16 and the internal transcribed spacer (ITS) were performed in order to examine the relationship of the pantropical subfamily Alpinioideae in Zingiberaceae (Zingiberales). Special emphasis was given to the large genus Etlingera placed in the tribe Alpinieae. A total of 50 taxa were included in the analysis. The strict consensus tree obtained by combining all data (280 parsimony informative characters of ITS, rps16, and coded indels) is well resolved with strongly supported clades. The subfamily Alpinioideae (excluding Pommereschea and Rhynchanthus) is strongly supported as monophyletic. The basal part of the tree is unresolved but a clade containing the derived genera of Alpinieae (Geocharis, Amomum, Hornstedtia, and Etlingera) is strongly supported. The establishment of Etlingera as the inclusive name for Achasma, Geanthus, and Nicolaia is also strongly supported: Etlingera is monophyletic with Hornstedtia as sister group.     

Phylogeny and morphological evolution of tribe Menispermeae (Menispermaceae) inferred from chloroplast and nuclear sequences

The Menispermaceae family contains ca. 72 genera with 450 species that are almost entirely tropical. Its phylogeny at the tribal level has never been examined using molecular data. Here we used DNA sequences of the chloroplast matK gene and trnL-F regions, and the nuclear ITS region to study the delimitation and position of the tribe Menispermeae within the family and its subtribal monophyletic groups. Family-wide phylogenetic analyses of the chloroplast data produced two strongly supported clades. The first clade contains two subclades: Coscinieae including Arcangelisia and Anamirta, and Tinosporeae sensu lato including Fibraureae, supported by morphological characters, such as traits of the cotyledon, stylar scar and embryo. The second clade consists of the tribes Menispermeae sensu DC. and Tiliacoreae Miers. All our analyses surprisingly recognized that tribe Menispermeae is not monophyletic unless tribe Tiliacoreae is included, suggesting that characters of cotyledon and stylar scar are very important for the infrafamilial classification, and that endosperm presence vs. absence was over-emphasized in traditionally tribal division of the family. Our topologies indicate a secondary loss of endosperm. The monophyly of two subtribes of the tribe Menispermeae, Stephaniinae and Cissampelinae, is supported by the cpDNA and ITS data, as well as by morphological characters, including aperture types and shapes, and colpal membrane features of pollen grains, and sepal number of male flowers. The Cocculinae was recognized as a paraphyletic group containing the remaining genera of the tribe Menispermeae.