Species delimitation in the European species of Clavulina (Cantharellales, Basidiomycota) inferred from phylogenetic analyses of ITS region and morphological data

The identification of the conventionally accepted species of Clavulina (Cantharellales, Basidiomycota) in Europe (Clavulina amethystina, Clavulina cinerea, Clavulina cristata, and Clavulina rugosa) is often difficult and many specimens are not straightforwardly assignable to any of those four species, which is why some authors have questioned their identity. In order to assess the status of those species, a morphological examination was combined with the molecular analysis of the ITS region. The same six major clades were obtained in the Bayesian and parsimony phylogenetic analyses, and all six clades were well-supported at least by one of the analyses. Morphological characters, such as the overall branching pattern, the presence and intensity of grey colour, the cristation of the apices, and basidiospore size and shape were to various extents correlated with the phylogenetic signal obtained from the ITS region. The congruence between the molecular analyses and morphology, rather than geographical origin, suggests the existence of several species that can be delimited using a combined phylogenetic and morphological species recognition. The analyses revealed that C. cristata and C. rugosa are well-delimited species. In contrast, more than one taxa could be subsumed under the names C. amethystina and C. cinerea, the taxonomical complexity of which is discussed. The ITS region is proved to be adequate to separate phylogenetic species of Clavulina.     

Phylogenetic analyses and chromosome evolution in Convallarieae (Ruscaceae sensu lato), with some taxonomic treatments

The tribe Convallarieae, comprising 10 genera and 95 species, has recently been transferred from its own family to Ruscaceae sensu lato. In this study, sequence data from trnK and rbcL were analyzed for 19 species in 8 genera, and chromosome morphology was analyzed for 17 species in 7 genera. The parsimony analysis of trnK and rbcL sequences showed that Convallarieae are monophyletic. Although early branches did not receive strong bootstrap support, Convallaria diverged at the first branch, followed by Speirantha. The rest of the tribe was split into three, well-supported clades: one with Reineckea, the second with Campylandra and Rohdea, and the third with Tupistra, Tricalistra, and Aspidistra. Two monotypic genera, Rohdea and Tricalistra, were embedded in a clade of Campylandra and of Tupistra, respectively. Three karyotypes were distinguished in the tribe on the basis of the basic number and morphology of metaphase chromosomes: Convallaria type (with x=19 and unimodal chromosome length), Tupistra type (with x=19 and trimodal chromosome length), and Aspidistra-elatior type (with x=18 and trimodal chromosome length). The character-state distribution in the molecular tree showed that the Convallaria type is plesiomorphic, from which was derived the Tupistra type and subsequently the Aspidistra-elatior type. Taxonomic treatments to transfer Campylandra to Rohdea and Tricalistra to Tupistra are also given.     

Phylogenetic relationships of JapaneseAster (Asteraceae, Astereae) sensu lato based on chloroplast-DNA restriction site mutations

RFLPs of cpDNA were examined for 18 species ofAster, six species ofKalimeris, two species ofMiyamayomena and one species and one variety ofHeteropappus from Japan, using 16 restriction endonucleases. Approximately 275 restriction sites were surveyed, and a total of 74 restriction site mutations was detected, and 31 of these were phylogenetically informative. Sixteen most parsimonious trees constructed from Wagner parsimony analysis indicated the polyphyly ofKalimeris andMiyamayomena sensu Kitamura;K. miqueliana belongs to a different clade from the remaining species ofKalimeris, and two species ofMiyamayomena did not make a single clade. This result suggests that the shortening or loss of pappus have happened parallelly in different evolutionary lineages. We must be careful to assess the pappus character in taxonomy and phylogeny, and it is desirable to examine their phylogenetic relationships using a molecular data.     

Phylogenetic position of Octosporea muscaedomesticae (Microsporidia) and its relationship to Octosporea bayeri based on small subunit rDNA analysis

Comparative phylogenetic analysis of the small subunit rDNA sequence of Octosporea muscaedomesticae (Flu, 1911) (type species) (Microsporidia) isolated from the blowfly Phormia regina (Diptera:Calliphoridae) is presented. Neighbor Joining bootstrap, Maximum Parsimony and Maximum Likelihood analyses with 38 microsporidian taxa representing five major clades of Microsporidia placed O. muscaedomesticae on a separate branch within a clade containing parasites of freshwater hosts. O. muscaedomesticae differed from Octosporea bayeri, a parasite of the microcrustacean, Daphnia magna (Cladocera:Daphniidae) by 29% demonstrating that the latter microsporidium is not closely related to the type species at the generic level, and should not be placed within the genus Octosporea, a conclusion that is further supported by morphological and developmental differences. Considering the number of disparately related hosts from which Octosporea species have been previously described based mostly on developmental and morphological characters it is likely that many will not fit the current definition of the genus, and it is possible that molecular analysis of these species will show that this genus as defined represents a polyphyletic grouping of unrelated taxa.     

中国柳莺属鸟类分类研究进展

柳莺属(Phylloscopus)是广泛分布于旧大陆地区的小型食虫鸟类,目前全世界已知66种,其中约50种见于亚洲。该属鸟类外部形态十分相近且同域分布种数较多,历来是鸟类分类学中的研究难点及热点。2003年贾陈喜等介绍了20世纪90年代以来发表的分布于我国的柳莺属鸟类新种及相关分类学变动,涉及3个新描述种和9个由亚种提升的种,共计30种26亚种。2003年以来关于柳莺属鸟类的分类学研究取得了许多新的成果,同时我国境内也发现了一些新的分布记录。综合最新的文献及分布资料,整理得知我国现有柳莺属鸟类41种31亚种,与2003年的状况相比已有较大的变化。主要表现在:新描述种方面,德国学者Martens等2008年描述了黄腹柳莺(P.affinis)种组中的一新种———华西柳莺(P.occisinensis);2010年瑞典学者Alstrm等报道在越南和老挝地区新发现的灰岩柳莺(P.calciatilis)已被证实在我国有分布;亚种提升为种方面,如日本柳莺(P.xanthodryas)自极北柳莺(P.borealis)中独立,冠纹柳莺(P.claudiae)和西南冠纹柳莺(P.reguloides)分开等;分类地位再评议方面,如灰头鹟莺(Seicercusxanthoschistos)实为灰头柳莺(P.xanthoschistos)等;新分布纪录方面,如欧柳莺(P.trochilus)在内蒙古达里诺尔湖地区发现确切记录等。现今对柳莺属鸟类分类学方面的研究已明显呈现出传统形态学、分子遗传学、声谱分析及野外鸣声回放实验等新老技术手段相整合,多方面多角度地阐述问题的局面。中国是世界柳莺属鸟种分布最多的国家(其中有9种仅在或主要于我国境内繁殖),但我国鸟类学者关于该属鸟类的研究工作并不多见。柳莺属鸟类在分类学和进化生物学等领域具有重要的研究价值,我国鸟类学工作者应当引起足够的重视和关注。     

Chemosystematic evaluation of Aloe section Pictae (Asphodelaceae)

The chemosystematic value of UV-absorbing leaf constituents was considered in previously uncharacterised representatives of Aloe section Pictae, the problematic maculate species complex. Comparative data indicate that the anthrone C-glycoside, 6′-malonylnataloin (7-hydroxychrysaloin 6′-O-malonate) is typical of maculate species in East Africa, but is unconvincing as a synapomorphy for section Pictae. A naphthalene derivative found widely in Aloe, plicataloside, was detected in Aloe greatheadii. Biogeographical trends were observed in the occurrence of the flavonoids isoorientin (luteolin-6-C-glucoside) and isovitexin (apigenin 6-C-glucoside). Isoorientin is a common constituent of tropical and sub-tropical species of Aloe, whereas isovitexin is restricted to a few southern African species. Isoorientin and isovitexin co-occur in the southern African maculate species Aloe parvibracteata, and the disjunct West African maculate species, Aloe macrocarpa. This is the first report of isoorientin and isovitexin in maculate species of Aloe; the presence of flavonoids in section Pictae is of taxonomic interest.     

Phylogenetic status of Vavilovia formosa (Fabaceae-Fabeae) based on nrDNA ITS and cpDNA sequences

The phylogenetic status of the monotypic genus Vavilovia was studied using nrDNA ITS and cpDNA trnL-F and trnS-G regions. The results from the analysis of each dataset and the combined dataset, revealed that Vavilovia is closely related to Pisum, forming a group that is sister to Lathyrus. The molecular data and some morphological and biological characteristics strongly indicate that Vavilovia should be subsumed under Pisum, as Pisum formosum.     

Phylogenetic relationships among Southeast Asian climbing bamboos (Poaceae: Bambusoideae) and the Bambusa complex

A phylogenetic analysis of Bambusa and allies based on the plastid DNA non-coding regions rps16-trnQ, trnC-rpoB, trnH-psbA and trnD-T, and a partial nuclear GBSSI gene, was carried out. This included representatives from all four Bambusa subgenera (including type species), a group of segregate Southeast Asian genera distinctive by their climbing–scrambling culms (Dinochloa, Holttumochloa, Kinabaluchloa, Maclurochloa, Soejatmia, Sphaerobambos), and two other Bambusinae genera (Dendrocalamus, Gigantochloa). The results do not support the present subgeneric classification of Bambusa. The climbing Southeast Asian genera, all of which include species previously placed in Bambusa, are distinct from the “core Bambusa group” (type species and alliance) and the Bambusa complex generally.     

Karyomorphology of Maianthemum sensu lato (Polygonatae, Ruscaceae)

We report results of karyotype analyses using nine species of Maianthemum from China. The species, except M. atropurpureum (with 2n=72), had 2n=36, and the results support the earlier suggestion that Maianthemum has x=18 with 2n=36 in most species. The species examined, however, showed marked differences in karyotype, particularly in the numbers of metacentric, submetacentric, and acrocentric chromosomes as well as in the number of satellites. In addition, we distinguished three different modes based on the number of clear gaps in chromosome length variation: unimodal, bimodal, and trimodal. The unimodal variation (with no gap) was found in M. dahuricum and M. atropurpureum, the bimodal variation (with one gap) in M. tatsienense, and the trimodal variation (with two gaps) in M. bifolium, M. forrestii, M. japonicum, M. henryi, M. purpureum, and M. lichiangense. In the trimodal variation, the positions of the two gaps may differ from species to species. In addition, the frequency of acrocentric chromosomes per complement was generally higher in the trimodal variation than in the unimodal and bimodal variations. Results of our analyses, which had not been clearly presented prior to this, may provide a better understanding of species evolution in the tribe Polygonatae.     

Morphometric analysis of six Gerbillus species (Rodentia,Gerbillinae) from Tunisia

Size and shape changes in the skull of the genus Gerbillus were investigated using geometric morphometrics. Six species from Tunisia were studied (G. gerbillus, G. campestris, G. nanus, G. tarabuli, G. simoni and G. latastei). Statistical analyses of shape variability allowed us to discriminate three morphological groups which are congruent with the three groups suggested by previous morphological and molecular studies. However, our results contrast with previous molecular investigations. In fact, according to results obtained by the use of principal component analysis, canonical variate analysis and UPGMA, we found a higher degree of divergence between the subgenus Dipodillus and the other two subgenera Gerbillus and Hendecapleura. This fact suggests that the morphometric differences observed among species within the genus Gerbillus are not mainly related to phylogeny. To reconciliate the molecular and morphological approaches, we propose a hypothesis of differential rates of phenotypic evolution in the genus Gerbillus. In this view, the species belonging to the subgenus Dipodillus evolved apomorphic features of the skull likely related to a higher degree of habitat specialization. By contrast, the more generalist Gerbillus and Hendecapleura subgenera show less differentiated plesiomorphic morphology.     

Phylogenetic analysis of the pathogenic bacteria Spiroplasma penaei based on multilocus sequence analysis

A pathogenic Spiroplasma penaei strain was isolated from the hemolymph of moribund Pacific white shrimp, Penaeus vannamei. The shrimp sample originated from a shrimp farm near Cartagena, Colombia, that was suffering from high mortalities in ponds with very low salinity and high temperatures. This new emerging disease in a marine crustacean in the Americas is described as a systemic infection. The multilocus phylogenetic analysis suggests that S. penaei strain has a terrestrial origin. Evolutionary relationship trees, based on five partial DNA sequences of 16S rDNA, 23S rDNA, 5S rDNA, gyrB, rpoB genes and two complete DNA sequences of 16S-23S rDNA and 23S-5S rDNA intergenic spacer region, were reconstructed using the distance-based Neighboring-Joining (NJ) method with Kimura-2-parameter substitution model. The NJ trees based on all DNA sequences investigated in this study positioned S. penaei in the Citri-Poulsonii clade and corroborate the observations by other investigators using the 16S rDNA gene. Pairwise genetic distance calculation between sequences of spiroplasmas showed S. penaei to be closely related to Spiroplasma insolitum and distantly related to Spiroplasma sp. SHRIMP from China.     

Systematics and evolution of the genus Torrubiella (Hypocreales, Ascomycota)

Torrubiella is a genus of arthropod-pathogenic fungi that primarily attacks spiders and scale insects. Based on the morphology of the perithecia, asci, and ascospores, it is classified in Clavicipitaceae s. lat. (Hypocreales), and is considered a close relative of Cordyceps s. 1., which was recently reclassified into three families (Clavicipitaceae s. str., Cordycipitaceae, Ophiocordycipitaceae) and four genera (Cordyceps s. str, Elaphocordyceps, Metacordyceps, and Ophiocordyceps). Torrubiella is distinguished morphologically from Cordyceps s. lat. mainly by the production of superficial perithecia and the absence of a well-developed stipitate stroma. To test and refine evolutionary hypotheses regarding the placement of Torrubiella and its relationship to Cordyceps s. lat., a multi-gene phylogeny was constructed by conducting ML and Bayesian analyses. The monophyly of Torrubiella was rejected by these analyses with species of the genus present in Clavicipitaceae, Cordycipitaceae, and Ophiocordycipitaceae, and often intermixed among species of Cordyceps s. lat. The morphological characters traditionally used to define the genus are, therefore, not phylogenetically informative, with the stipitate stromata being gained and/or lost several times among clavicipitaceous fungi. Two new genera (Conoideocrella, Orbiocrella) are proposed to accommodate two separate lineages of torrubielloid fungi in the Clavicipitaceae s. str. In addition, one species is reclassified in Cordyceps s. str. and three are reclassified in Ophiocordyceps. The phylogenetic importance of anamorphic genera, host affiliation, and stipitate stromata is discussed.     

Mycobiota associated with the ambrosia beetle Scolytodes unipunctatus (Coleoptera: Curculionidae, Scolytinae)

Ambrosia beetles (Coleoptera: Scolytinae) are associated with strictly entomochoric and mutualistic fungi. We studied the mycobiota associated with Scolytodes unipunctatus, ambrosia beetles that infest Cecropia trees in Central America. Isolates were characterized using morphology and rDNA sequences (ITS region, LSU, and SSU rDNA). Four species are described here: Raffaelea scolytodis sp. nov. (Ophiostomatales), Gondwanamyces scolytodis sp. nov., Custingophora cecropiae sp. nov., and Graphium sp. (Microascales). The genus Custingophora is emended to include Knoxdaviesia anamorphs of Gondwanamyces based on uniformity of DNA sequences and phenotype.     

Characterization of a Plasmopara species on Ambrosia artemisiifolia, and notes on P. halstedii, based on morphology and multiple gene phylogenies

Common ragweed (Ambrosia artemisiifolia) is an invasive and highly allergenic plant species, on which two species, Plasmopara halstedii and Plasmopara angustiterminalis, have been recognized to cause downy mildew disease. In this study, morphological and molecular patterns of seven Plasmopara specimens collected from A. artemisiifolia in Canada, Hungary, and USA were compared with those of P. halstedii and P. angustiterminalis from Helianthus and Xanthium, respectively. Analyses of partial sequences of three genes, namely those for the large subunit (28S) of rDNA, cytochrome c oxidase subunit II (COX2), and NADH dehydrogenase subunit I (ND1) of mtDNA, were carried out to examine the phylogenetic relationships among these specimens using both Bayesian and maximum parsimony methods. All the phylogenetic analyses revealed that the downy mildew pathogens infecting A. artemisiifolia in Hungary and North America clearly represent a lineage distinct from other Plasmopara taxa investigated. The shape of sporangia and the width of trunks and branches also allowed the separation of the specimens parasitic to A. artemisiifolia from P. halstedii on Helianthus annuus and P. angustiterminalis on Xanthium strumarium. Surprisingly, the Hungarian and the Canadian specimens were more closely related to each other than to those from the USA based on COX2 and ND1 mtDNA data, although the D1/D2/D3 sequences of 28S rDNA were identical in all these Plasmopara specimens. The regional distribution of the mtDNA haplotypes seen in this study suggests a transatlantic migration has occurred and would be interesting to follow up with a more detailed sampling. To investigate the diversity within P. halstedii sensu lato, infecting different host plant species, specimens from six asteraceous genera, Ambrosia, Flaveria, Helianthus, Siegesbeckia, Solidago, and Xanthium, were also included in molecular analyses. These represented six distinct lineages according to the host plant genera. These findings might serve as a basis for a taxonomical reassessment of the P. halstedii complex and also for the delimitation of several well-defined species within this complex.