Phylogeny of Chinese <Emphasis Type="Italic">Polystichum</Emphasis> (Dryopteridaceae) based on chloroplast DNA sequence data (<Emphasis Type="Italic">trnL-F</Emphasis> and <Emphasis Type="Italic">rps4-trnS</Emphasis>)

Polystichum is one of the largest and most taxonomically complex fern genera in China. The evolutionary relationships of Chinese Polystichum and related genera, and the relationship between our Polystichum phylogeny and ecogeographic distribution, were tested by the use of DNA sequence data. Fifty-one species of Polystichum and 21 species in allied genera were sequenced for the plastid intergenic spacers rps4-trnS and trnL-F. Maximum parsimony and Bayesian phylogenetic analyses of both individual and combined data sets showed that Chinese Polystichum as commonly recognized was paraphyletic: one clade (the CCPC clade) included Cyrtomidictyum lepidocaulon, two Cyrtogonellum species, three Cyrtomium species, and a small number of Polystichum species usually occurring on limestone. A second clade, Polystichum sensu stricto, included the remainder of the Polystichum species; these often occur on non-limestone substrates. The remaining Cyrtomium species formed the third clade. Three subclades resolved within Polystichum sensu stricto (s.s.) clade do not correspond with recent sectional classifications, and we outline the issues relevant to a new classification for the genus. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogenetic systematics of the monotypic genus Hayataella (Rubiaceae) endemic to Taiwan

Hayataella (Rubiaceae) is a monotypic genus endemic to Taiwan that comprises H. michelloides. In recent years, Hayataella was considered to be synonymous with Ophiorrhiza; however, no specific data have been reported, and the systematic treatment of Hayataella has been unclear. To elucidate the systematic treatment of Hayataella, molecular phylogenetic analyses based on ITS of nrDNA, atpB–rbcL, and trnK/matK of cpDNA were conducted with four Ophiorrhiza species. In the Bayesian and the most parsimonious trees, H. michelloides was included in the Ophiorrhiza clade. The monotypic status of Hayataella is, therefore, not considered appropriate, and the combination Ophiorrhiza michelloides (Masam.) H. S. Lo is supported.     

Seven new calochroid and fulvoid species of Cortinarius

We describe seven new European species of Cortinarius. All species are based on analyses of morphological and DNA sequence data. They all belong to a well-supported clade comprising most species traditionally treated in Cortinarius subgenus Phlegmacium sections Fulvi and Calochroi (i.e. the/Calochroi clade). All taxa are either fulvoid (containing anthraquinoid pigments) or calochroid (without these pigments). Morphological and ecological data are presented for all species and compared with similar species. A dichotomous key is presented for C. calochrous and similar species, including all six newly described calochroid species. The calochroid species C. albertii, C. chailluzii, C. cisticola, C. sancti-felicis, C. selandicus and C. vesterholtii spp. nov., and the fulvoid species C. langeorum sp. nov. are described.     

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.     

Molecular phylogeny of the Acre clade (Crassulaceae): Dealing with the lack of definitions for Echeveria and Sedum

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the “Acre clade”, a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European–Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera – Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.     

基于cpDNA和rDNA ITS片段分析西南地区青杨派杨树的系统发育与进化关系

西南地区青杨派杨树种质资源丰富,可为杨树遗传改良提供珍贵的基因资源,但树种之间形态学差异细微,该研究以山杨作为外类群,测定了西南地区及其他地区杨属青杨派17个种(杂种)共36份样本的3个叶绿体片段(atpF-atpH、trnL-F和matK)和核糖体ITS片段,并对其进行系统发育分析,以探讨西南地区青杨派树种的系统进化关系。结果表明:(1)在所有样本中,3个叶绿体片段atpF-atpH、trnL-F、matK的长度分别为605~634bp、957~1 010bp、819bp,3个片段拼接后的联合序列包含29个变异位点和15个信息位点;ITS片段对齐后的长度为646bp,变异位点19个,信息位点17个。(2)基于叶绿体联合序列和ITS片段的杨属青杨派树种的平均遗传距离分别为0.001 3和0.003 6。叶绿体联合片段的MP和Bayes系统树树型基本一致,青杨派树种可以划分为2组,第1组由青杨、三脉青杨、大青杨和辽杨构成;第2组中的小叶杨、小青杨、川杨、德钦杨、昌都杨、乡城杨、康定杨、西南杨、滇杨和藏川杨不能有效区分,且均与缘毛杨的遗传关系较近。(3)基于ITS的系统树与叶绿体联合片段构建的系统树差异不大,仅在于第2组中的小青杨与小叶杨、川杨等差异明显,与第1组中的树种紧密聚拢。     

Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) inferred from 18S rDNA sequences with emphasis on the relationships in the genus Oedogonium based on ITS-2 sequences

The phylogeny of Oedogoniales was investigated by using nuclear 18S rDNA sequences. Results showed that the genus Oedocladium, as a separated clade, was clustered within the clade of Oedogonium; whereas the genus Bulbochaete was in a comparatively divergent position to the other two genera. The relationship among the species of Oedogonium was discussed, focusing on ITS-2 phylogeny analyzed combining with some morphological characteristics. Our results showed that all the dioecious nannandrous taxa involved in this study were resolved into one clade, while all the monocious taxa were clustered into another clade as a sister group to the former. The report also suggests that the dioecious macrandrous taxa form a paraphyly and could be more basally situated than the dioecious nannandrous and the monoecious taxa by means of molecular phylogeny and morphotype investigations.     

基于分子证据确认秦岭藤属与驼峰藤属(夹竹桃科)的系统位置

秦岭藤属(Biondia Schltr.)是中国特有属,约13种,驼峰藤属(Merrillanthus Chun&Tsiang)是仅在我国与柬埔寨分布的单种属,目前两个属均被归并到白前属(Vincetoxicum Wolf),由于取样和系统发育分析尚存一些欠缺,因此其系统位置和归属尚需进一步确认。该文使用2个核糖体基因序列片段(ITS、ETS)、5个叶绿体基因序列片段(psbA-trnH、trnG、trnL、trnL-F、trnT-L),以及二者的合并数据,重建娃儿藤亚族(Tylophorinae)(包含属的模式秦岭藤[B.chinensis Schltr.=V.shaanxiense(Schltr.) Meve&Liede]与驼峰藤[M.hainanensis Chun&Tsiang=V.hainanense(Chun&Tsiang) Meve, H. H. Kong&Liede])的系统发育树。结果表明：秦岭藤属与驼峰藤属均包含在白前属中,秦岭藤与青龙藤[B.henryi(Warb.) Tsiang&Li=V.henryi(Warb....     

The phylogenetic relationships of Cynoglottis (Boraginaceae- Boragineae) inferred from ITS, 5.8S and trnL sequences

A molecular phylogenetic analysis of Cynoglottis was performed to evaluate previous hypotheses based on non-molecular evidence concerning the position of this genus within Boraginaceae tribe Boragineae. ITS-5.8S and trnL_UAA sequences from the nuclear and chloroplast non-coding genomes were obtained for four Cynoglottis taxa and selected members of the related genera Anchusa, Anchusella, Gastrocotyle, Brunnera and Pentaglottis. Cynoglottis is monophyletic, but neither trnL nor ITS support a close relationship with Brunnera, unlike previously supposed on morphological grounds. Brunnera is, instead, related to the southwestern European monotypic genus Pentaglottis, with which it forms a basal clade. ITS-5.8S sequences show that Anchusa thessala, a southeastern European annual species of Anchusa subg. Buglossellum, is sister to Cynoglottis and that the two taxa form a clade which also includes the Balkan endemic Gastrocotyle macedonica. Species of Anchusa subg. Anchusa form a separate lineage with high bootstrap support, suggesting that this heterogeneous genus is paraphyletic with respect to Cynoglottis. ITS sequences also discriminate between the Balkan-Apenninic diploid C. barrelieri and the Anatolian tetraploid C. chetikiana, albeit with low support. The molecular results are discussed in the light of karyological, morphological and chorological aspects.This work has been supported by M.I.U.R. 40% 2003 and the University of Firenze.     

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

4种薯蓣属植物的分子鉴别和亲缘关系研究

为揭示薯蓣属植物的亲缘关系,根据叶绿体matK、rbcL、trnL-F和psbA-trnH序列片段,对小花盾叶薯蓣(Dioscorea sinopatviflora)、盾叶薯蓣(D.zingibiernsis)、黄独(D.bulbifera)和山药(D.polystachya)进行种间分子鉴别研究,并探讨这4个片段在薯蓣属植物系统发育上的意义。结果表明,4种薯蓣属植物共22份材料的matK、rbcL、trnL-F和psbA-trnH序列片段的长度分别为1026~1142 bp、1156~1178 bp、744~822 bp和355~599 bp。用PAUP 4.0b10和贝叶斯推断构建的系统发育树分析表明,云南的黄独与盾叶薯蓣的亲缘关系较近;小花盾叶薯蓣与盾叶薯蓣的亲缘关系很近;而非洲的黄独与云南的黄独的亲缘关系很远。但仅用这4个cpDNA片段还不能完全区分小花盾叶薯蓣和盾叶薯蓣,这说明基于这4个序列片段的系统发育证据与4种薯蓣属植物属内的分类划分并不十分吻合。     

Further fragmentation of the polyphyletic genus Polyalthia (Annonaceae): molecular phylogenetic support for a broader delimitation of Marsypopetalum

The species-rich genus Polyalthia has previously been shown to be highly polyphyletic, with species represented in at least five different clades. The Polyalthia species that are associated with Marsypopetalum and Trivalvaria (as revealed either by previous phylogenetic studies or inferred on the basis of comparative morphology) were included in a molecular phylogenetic study based on three chloroplast DNA regions (matK, rbcL and trnL-F). Maximum parsimony, maximum likelihood and Bayesian analyses consistently revealed that several Polyalthia species form a well-supported clade with Marsypopetalum pallidum, and that this clade is sister to Trivalvaria. Diagnostic morphological characters for the clades are re-evaluated and shown to be congruent with the molecular phylogeny. Five Polyalthia species (P. crassa, P. littoralis, P. lucida, P. modesta and P. tristis) are accordingly transferred to Marsypopetalum.     

Phylogenetic relationships among species and genera of Lycoperdaceae based on ITS and LSU sequence data from north European taxa

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses. Morphological characters of species within and among identified clades are discussed.     

Molecular evidence for the inclusion of the Korean endemic genus “<Emphasis Type="Italic">Echinosophora</Emphasis>” in<Emphasis Type="Italic"> Sophora</Emphasis> (Fabaceae), and embryological features of the genus

Although Echinosophora Nakai has been known as a monotypic and endemic genus of Papillionoideae of Fabaceae in Korea, it has been controversial whether it is distinct from or merged with Sophora. To resolve this matter, we conducted molecular phylogenetic analyses using nucleotide sequence data from the plastid rbcL gene and trnL (UAA) intron. Parsimony analysis, using a total of 53 taxa of the Papillionoideae (including E. koreensis [Nakai] Nakai and several species of Sophora and related genera) and using 20 taxa of Caesalpinioideae and Mimosoideae as outgroups, showed that, although the examined species of Sophora are split into two clades, E. koreensis formed a common clade with S. tomentosa (the type species of the genus) and S. flavescens. E. koreensis therefore should be treated as S. koreensis Nakai, and the generic name Echinosophora be eliminated. We also investigated the embryology of S. koreensis (=E. koreensis) and S. flavescens and found that no differences existed between them. Our molecular study, like other studies, strongly suggested that Sophora is polyphyletic. In this study we presented a summary of embryological features of the core Sophora for future critical comparison with related and unrelated taxa.     

Genetic diversity and phylogenetic position of the subclass Astomatia (Ciliophora) based on a sampling of six genera from West African oligochaetes (Glossoscolecidae, Megascolecidae), including description of the new genus Paraclausilocola n. gen

To more confidently assess phylogenetic relationships among astome ciliates, we obtained small subunit (SSU) rRNA sequences from nine species distributed in six genera and three families: Almophrya bivacuolata, Eudrilophrya complanata, Metaracoelophrya sp. 1, Metaracoelophrya sp. 2, Metaracoelophrya intermedia, Metaradiophrya sp., Njinella prolifera, Paraclausilocola constricta n. gen., n. sp., and Paraclausilocola elongata n. sp. The two new species in the proposed new clausilocolid genus Paraclausilocola n. gen. are astomes with no attachment apparatus, two files of contractile vacuoles, and an arc-like anterior suture that has differentiations of thigmotactic ciliature on the anterior ends of the left kineties of the upper surface. Phylogenetic analyses were undertaken using neighbor-joining, Bayesian inference, maximum likelihood, and maximum parsimony. The nine species of astomes formed a strongly supported clade, showing the subclass Astomatia to be monophyletic and a weakly supported sister clade to the scuticociliates. There were two strongly supported clades within the astomes. However, genera assigned to the same family were found in different clades, and genera assigned to the same order were found in both clades. Thus, astome taxa appear to be paraphyletic when morphology is used to assign species to genera.     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.     

A molecular phylogeny of the genus Lygodium (Schizaeaceae) with special reference to the biological control and host range testing of Lygodium microphyllum

Lygodium microphyllum, first naturalized in the 1960s, has aggressively invaded forest-dominated wetlands in southern and central Florida. The indeterminate growth of this invasive climbing fern creates thick rachis mats which climb over shrubs and trees smothering the underlying growth and carrying ground fires into the forest canopy. Foreign surveys for natural enemies identified 20 species of insects and two species of mites. Host range testing of three insect species and one mite included five Lygodium species (L. palmatum, L. volubile, L. cubense, L. venustum, and L. oligostachyum) native to the United States and the West Indies. A molecular phylogeny of the genus was conducted using the trnL intron and the trnL-F intergenic spacer of chloroplast DNA to determine the relationship of L. microphyllum to other Lygodium species. Three major clades appeared, one with L. palmatum and L. articulatum (the most basal), a second with L. reticulatum and L. microphyllum, and a third comprising the other species examined. Lygodium microphyllum appeared at the end of a long branch approximately equidistant from all species of interest preventing the correlation of genetic distance and host range behavior. However, inspection of the results of host range experiments showed a relationship between the presence of a related biotype or species of the insect on a related alternate host and the ability of that insect to develop on that alternate host. Ancestral host usage and ecological fitting are examined as possible explanations for the acceptance of L. palmatum by the tested musotimine insects.