Multiple gene genealogies and species recognition in the ectomycorrhizal fungus Paxillus involutus

Paxillus involutus (basidiomycetes, Boletales) is a common ectomycorrhizal fungus in the Northern Hemisphere. The fungus displays significant variation in phenotypic characters related to morphology, physiology, and ecology. Previous studies have shown that P. involutus contains several intersterility groups and morphological species. In this study, we have used concordance of multiple gene genealogies to identify genetically isolated species of P. involutus. Fragments from five protein coding genes in 50 isolates of P. involutus collected from different hosts and environments in Europe and one location in Canada were analysed using phylogenetic methods. Concordance of the five gene genealogies showed that P. involutus comprises at least four distinct phylogenetic lineages: phylogenetic species I (with nine isolates), II (33 isolates), III (three isolates), and IV (five isolates). The branches separating the four species were long and well supported compared with the species internodes. A low level of shared polymorphisms was observed among the four lineages indicating a long time since the genetic isolation began. Three of the phylospecies corresponded to earlier identified morphological species: I to P. obscurosporus, II to P. involutus s. str., and III to P. validus. The phylogenetic species had an overlapping geographical distribution. Species I and II differed partly in habitat and host preferences.     

Phylogenetic relationships of Ceratitis fruit flies inferred from nuclear CAD and tango/ARNT gene fragments: Testing monophyly of the subgenera Ceratitis (Ceratitis) and C. (Pterandrus)

Systematic studies of Ceratitis (Tephritidae) fruit flies using molecular (i.e., COI, ND6, and period genes) and morphological (plus host-use characters) data have recently challenged the monophyly of the subgenera Ceratitis (Ceratitis) and Ceratitis (Pterandrus). In this paper, we report on the phylogenetic utility of three single-copy nuclear gene regions (two non-overlapping fragments of the carbamoylphosphate synthetase, CPS, locus of CAD, and a fragment of tango) within these taxa and investigate evolutionary relationships based on a concatenated ca. 3.4 kb data set that includes the six protein encoding gene regions. Results indicate that the CAD and tango genes provide useful phylogenetic signal within the taxa and are compatible with the previously studied genes. The two subgenera, as currently classified, are not monophyletic. Our molecular phylogenetic analyses support a revised classification in which (1) the subgenus C. (Pterandrus) comprises two lineages called A and B, (2) the C. (Pterandrus) B species should be included in C. (Ceratitis), and (3) the newly defined subgenera C. (Pterandrus) (=Pterandrus section A) and C. (Ceratitis) [=C. (Ceratitis) + C. (Pterandrus) section B] are reciprocally monophyletic.     

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.     

Differentiation and phylogeny of the olivaceous warbler Hippolais pallida species complex

The pattern of phenotypic and molecular variation within the polytypic olivaceous warbler H. pallida was examined. This species is distributed in the southern parts of the western Palaearctic, central Asia and in the arid parts of northern Africa, and also in parts of the sub-Saharan Sahel zone. Based on morphology, five subspecies, at times assigned to three groups, have been identified. By comparing morphological, behavioural, vocal and molecular variation, we investigated the phenotypic and phylogenetic relationships within the Hippolais pallida group. The morphological and genetic data of the present study support the view of splitting the olivaceous warbler into a western (former subspecies opaca) and an eastern form (former subspecies elaeica, pallida, reiseri and laeneni). Opaca is consistently and significantly larger than the other taxa in all size measurements, even if it does share morphological properties with elaeica in characters associated with migration. The song of the polytypic pallida differs clearly from that of opaca, and is remarkably consistent within its wide range which comprises four subspecies. The molecular analysis, and the resulting phylogenetic pattern, clearly separated opaca on a single branch distant from the other subspecies. The eastern form consists of two non-overlapping haplotype groups: elaeica with relatively diverse mtDNA variation, and the three African subspecies pallida, reiseri and laeneni, which all share the same or closely related mtDNA haplotypes. It remains open whether the African taxa should be regarded as three valid subspecies of the Eastern olivaceous warbler, or if they are better treated as a single African subspecies.     

Delimiting species boundaries within Dermanyssus Dugès, 1834 (Acari:Dermanyssidae) using a total evidence approach

The genus Dermanyssus is currently composed of 24 hematophagous mite species and includes the Poultry Red Mite, Dermanyssus gallinae, a serious pest in poultry houses. Morphologically, Dermanyssus species fall into two groups corresponding to Moss’ gallinae-group and to hirsutus-group + Microdermanyssus. Species of the gallinae-group exhibit high levels of morphological variability, and are nearly impossible to distinguish. Species of the second group display consistent characters and host associations and are easily distinguishable. Species of the gallinae-group tend to be the major problems in poultry houses and it is unknown whether D. gallinae is the only pest, or if there are numerous cryptic species present in the system.Twenty species of Dermanyssus were tested phylogenetically based on 46 morphological characters. A subset of species, mainly of the gallinae-group, represented each by several populations, was sequenced for two mitochondrial and one nuclear gene regions. This allowed testing their specific status and their interrelationships based and on morphological and molecular characters. The molecular data was analysed separately and in combination with morphological characters. As expected, morphology did a poor job resolving relationships.Molecular data proved more informative. The resulting phylogenetic hypotheses brought some information about interrelationships among species of the gallinae-group showing a split into two main clades. The invasion of human managed environments seems to occur only in taxa within one of the two clades. The host spectrum seems to get enlarged in more derived taxa in the same clade. A delineation of six species within the gallinae-group is provided. Additionally, a key for morphological identification of these species is provided. D. gallinae appears to be the only pest in poultry houses, but is composed of several different and more or less strongly isolated lineages. A new species found from the black swift is described.     

Phylogeographic patterns in Leccinum sect. Scabra and the status of the arctic-alpine species L. rotundifoliae

We investigated inter- and intraspecific phylogenetic relationships in the ectomycorrhizal fungal genus Leccinum section Scabra. Species of this section are exclusively associated with Betula and occur throughout the Northern Hemisphere. We compared the phylogenetic relationships of arctic, alpine, boreal and temperate accessions of section Scabra based on DNA sequences of the single-copy nuclear gene Gapdh and the multiple-copy nuclear region 5.8S-ITS2. Exclusively arctic lineages were not detected in species that occur both in arctic-alpine or boreal regions, except in L. rotundifoliae that was restricted to cold climates. L. scabrum and L. holopus showed an intercontinental phylogeographic pattern, and L. variicolor showed a pattern unrelated to geographical distribution. Molecular clock estimates indicated that L. rotundifoliae is as old as other species in section Scabra. Individual gene trees suggest that interspecific hybridisation occurred several times in the evolution of section Scabra.     

Molecular characterization of strawberry pathogen Gnomonia fragariae and its genetic relatedness to other Gnomonia species and members of Diaporthales

Gnomonia fragariae is a poorly studied ascomycete belonging to Diaporthales. Originally G. fragariae was considered a saprophyte occurring on dead tissues of strawberry plants. Recently this fungus was found in Latvia and Sweden, and it was proven to be the cause of severe root rot and petiole blight of strawberry. Thirteen isolates of this pathogen and several other Gnomonia species occurring on rosaceous hosts were characterized by molecular analysis using nucleotide sequences of partial LSU rRNA gene and the total ITS region. The homologous regions from relevant diaporthalean taxa available in the GenBank were also included and compared with the taxa sequenced in this study. Phylogenetic analyses revealed that G. fragariae, G. rubi, and Gnomonia sp. (CBS 850.79) were genetically different from G. gnomon, the type species of the genus, and other members of Gnomoniaceae. The analyses showed that G. fragariae and Hapalocystis were genetically very closely related, forming a phylogenetic clade, which is possibly presenting a new family in the Diaporthales. Morphological comparisons of the Gnomonia species on the basis of commonly used criteria for the taxonomy of Diaporthales, so far did not reveal any evident features for the polyphyletic status of Gnomonia.     

西南地区6种魔芋属植物基于cpDNA序列的遗传多样性研究

研究野生作物资源的遗传变异及分化机制对种质资源的收集与改良具有重要意义。魔芋是我国西南地区的特色经济作物,但由于受到人为活动干扰,野生种群不断衰退。为评估西南地区魔芋属(Amorphophallus)野生群体的遗传多样性,探究代表性物种的系统发育地位,该研究利用3个叶绿体DNA(cpDNA)片段,分析了魔芋6个物种的遗传多样性,重建了种间系统发育关系。结果表明:(1)西南地区野生魔芋群体的遗传多样性普遍较低,虽然单倍型多样性(H_d)均值为0.428,但近一半群体只有1个单倍型,6个物种整体水平上的单倍型多样性在0.704到0.983之间。(2)在6个物种间检测到高水平的遗传分化,遗传分化系数(F_ST)值在0.481到0.967之间。(3)系统发育分析表明,选取的27个魔芋种主要聚成3个分支:非洲分支、东南亚分支和东亚大陆分支。疣柄魔芋(A. paeoniifolius)隶属于东南亚分支,而东亚大陆分支A包含花魔芋(A. konjac)和西盟魔芋(A. krausei),东亚大陆分支B由东亚魔芋(A. kiusianus)、滇魔芋(A. yunnanensis)和东京魔芋(A. tonkinensis)构成。生境隔离与人为干扰造成了西南地区野生魔芋群体较低的遗传多样性,魔芋属东亚大陆分支的分化可能与早期的快速扩张和生态适应有关。该研究为西南地区魔芋资源的合理保护、可持续利用和杂交育种提供了参考资料。     

The phylogenetic placement of the Leucogastrales, including Mycolevis siccigleba (Cribbeaceae), in the Albatrellaceae using morphological and molecular data

The morphology of many hypogeous fungi converges on a homogeneous reduced form, suggesting that disparate lineages are subject to a uniform selection pressure. The primary goal of this study was to evaluate the morphology and infer the phylogeny of the Leucogastrales with Mycolevis siccigleba using a Bayesian methodology. A comprehensive morphological assessment was used for an a priori phylogenetic inference to guide the sequencing effort. All structures except spore ornamentation pointed to the Albatrellaceae as the most likely sister taxon. Polyporoletus sublividus, a close relative of Albatrellus, produces ornamented basidiospores with a similar structure to M. siccigleba basidiospores. The ITS from 30 taxa was used for the molecular phylogenetic analysis. P. sublividus was found sister to Mycolevis. Leucophleps spinispora and L. magnata formed a group sister to the Polyporoletus/Mycolevis group, whereas Leucogaster was polyphyletic with respect to the core of the Leucogastrales and sister to A. caeruleoporus. This relationship was expected as previously undescribed chlamydospores produced by members of Albatrellus had a similar morphology to the basidiospores of L. rubescens.     

The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited

Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding RPB1 for each species to examine the cause of incongruencies in previously published phylogenies. MP, minimum evolution, and Bayesian analyses were performed using the combined three-region data set and the single-gene data sets. The position of Ostropales nested in Lecanoromycetes is confirmed in all single-gene and concatenated analyses, and a placement as sister to the rest of Lecanoromycetes is significantly rejected using two independent methods of alternative topology testing. Acarosporales and related taxa (Acarosporaceae group) are basal in Lecanoromycetes. However, if the these basal taxa are excluded from the analyses, Ostropales appear to be sister to the rest of Lecanoromycetes, suggesting different ingroup rooting as the cause for deviating topologies in previously published phylogenies.     

Urogonimus macrostomus (Digenea: Leucochloridiidae) from the rustic bunting, Emberiza rustica, in Japan

Some trematodes were found in the cloaca of a rustic bunting (Emberiza rustica) captured in Tsushima Islands, Japan. From their morphological characters and distribution, the flukes were identified as Urogonimus macrostomus. The phylogenetic relationship between this fluke and related species was inferred from the 28S rRNA gene sequences, and the gene sequence of the fluke was found to differ at only 4 nucleotide positions from that of U. macrostomus reported from Ukraine. This is the first report of this species in Japan.     

Molecular taxonomy and ecology of Pseudallescheria, Petriella and Scedosporium prolificans (Microascaceae) containing opportunistic agents on humans

The main purpose of the present paper is to establish the connection between phylogenetic and morphological data and ecological features of strains of Pseudallescheria, Petriella, and Scedosporium. For the phylogenetic analysis sequences of the ITS region and the large subunit (partial sequences) of the rDNA were used. Cultural characteristics were observed on MEA 2 % and Weitzman-Silva Hutner Agar. Results showed, that three major groups could be differentiated, corresponding to Pseudallescheria, Petriella and S. prolificans. Among Petriella species only Pe. setifera is reasonably delimited. Pe. musispora was found to be synonymous with Pe. setifera. S. prolificans proved to be a homogenous species on the basis of ITS-sequences. Morphologically, Pseudallescheria and Petriella are distinguished by ostiolate vs non-ostiolate ascomata, a bipartition reflected also in ITS sequence data. We hypothesise a secondary loss of the ostiole of Pseudallescheria due to its ecological preferences. Infraspecific grouping within the highly variable species P. boydii is consistent for at least one clade in the ITS tree. The evolution of lineages with increased virulence within P. boydii is discussed.     

Taxonomic re-evaluation of the Taiwanese montane earthworm Amynthas wulinensis Tsai,Shen & Tsai, 2001 (Oligochaeta: Megascolecidae): Polytypic species or species complex?

Body size and colouration are two characters commonly used in the taxonomy of many animal taxa. However, they are seldom used by earthworm taxonomists because they are subject to environmental influences and tend to vary intraspecifically. In the present study, DNA sequences of the mitochondrial COI gene are used to evaluate whether specimens of the megascolecid earthworm Amynthas wulinensis Tsai, Shen & Tsai, 2001 that differ in body size and/or colouration belong to different genetic lineages. Phylogenetic analyses and morphological comparisons indicate that A. wulinensis in the previous broad sense is a species complex composed of three species differing in body size, colouration, and genital markings. Consequently, two new species, Amynthas lini and Amynthas meishanensis, are described. Taxonomic affinities of the A. wulinensis species complex are discussed, as is the feasibility of using body size and colouration in earthworm taxonomy.     

A combined molecular and morphological approach to species delimitation in black-fruited, endolithic Caloplaca: high genetic and low morphological diversity

A revision based on the morphological and genetic analyses of 133 specimens of black-fruited, endolithic Caloplaca belonging to subgenus Pyrenodesmia is presented. The material was collected in 16 sites distributed along a transept from Gargano (Central Italy) to the southeastern Alps, from sea level to ca 1500 m. The nuclear ITS was sequenced for all the mycobionts and selected representatives of photobionts. Except for the sorediate C. erodens, all species share the same algal lineage of Trebouxia as photobiont. The haplotype analysis of the mycobionts revealed an unexpected, high genetic heterogeneity. Three main morphotypic clusters were recognized among five species: C. albopruinosa (syn. C. agardhiana auct.), C. alociza, C. badioreagens, C. erodens, and C. variabilis. A phylogenetic analysis, including already available Caloplaca sequence data, revealed that these lichens form a monophyletic group within the genus. For each species, notes on ecology, distribution in Italy, and nomenclature are given.     

Revision of some Thecaphora species (Ustilaginomycotina) on Caryophyllaceae

Specimens of Thecaphora saponariae s. lat. from several caryophyllacean host plants belonging to the genera Cerastium, Dianthus, Petrorhagia, Saponaria, Silene, and Stellaria were studied by means of both LM, SEM, and molecular phylogenetic analyses using ITS and LSU rDNA sequences. The data show that T. saponariae s. lat. is not uniform but represents several taxa. Molecular phylogenetic analyses, correlated with morphology of the sori, spore balls, and spores, permitted the recognition of five species. Two new species, Thecaphora italica and T. cerastii are described, and two new combinations, T. alsinearum and T. melandrii are proposed. The anamorph of Thecaphora saponariae is reported for the first time. A lectotype is designated for Sorosporium silenes-inflatae. Evolutionary aspects are discussed.     

The halotolerant fungus Glomerobolus gelineus is a member of the Ostropales

Glomerobolus gelineus is a halotolerant species with a unique method of ballistic propagation. The absence of both sexual and asexual spores made reliable placement of this species, based on morphology alone, within the current fungal classification problematical. A phylogenetic analysis of the large and small nuclear ribosomal subunit and the second largest subunit of RNA polymerase II placed this fungus within the Ostropales, an order comprising lichenized and saprobic species, with good statistical support. Subsequently, a more detailed analysis that combined the nuc LSU rDNA and the mt SSU rDNA confirmed a close relationship to the Stictidaceae. The phylogenetic placement of G. gelineus is also supported by morphological characters. We postulate that the hyphoma lobes of Glomerobolus correspond to the periphysoidal layer in the apothecium of Stictis, and the propagule to the hymenium. Moreover, the presence of crystals in the outer lobes of G. gelineus is another indication of its relationship with Ostropales, which have characteristic crystalliferous hyphae. The placement of Glomerobolus within the Ostropales further expands the ecological diversity exhibited by this order. It also provides a phylogenetic hypothesis for assessing the homology of the enigmatic hyphomal morphology with apothecia-forming Ascomycota.     

四种栎属青冈亚属植物叶绿体基因组特征及系统发育研究

栎属青冈亚属植物的系统发育地位长期存在着争议，部分种的种间关系不明确。为揭示宁冈青冈(Quercus ningangensis)、曼青冈(Q.oxyodon)、毛曼青冈(Q.gambleana)、竹叶青冈(Q.neglecta)的叶绿体基因组特征及系统发育关系，该研究选择以上4种栎属青冈亚属植物的成熟叶片进行二代测序，对其叶绿体基因组结构和特征进行分析，并结合相关类群进行系统发育研究。结果表明：(1)宁冈青冈、曼青冈、毛曼青冈、竹叶青冈的叶绿体基因组序列长度分别为160 906、160 883、160 832、160 784 bp,均编码133个基因，包括88个蛋白质编码基因、37个tRNA基因、8个rRNA基因。(2)4种栎属青冈亚属植物偏好以A/T结尾的密码子，质体基因组变异区域主要存在于非编码序列。(3)通过IR边界分析得出，4种栎属青冈亚属植物存在ycf1假基因且在IRb/SSC区域发生扩张。(4)系统发育分析显示，在壳斗科中，水青冈属(Fagus)和轮叶三棱栎属(Trigonobalanus)较早分化出来，栎亚属(subg.Quercus)未形成一个单系群，叶绿体基因组建树结...     

Revision and reclassification of three Plasmopara species based on morphological and molecular phylogenetic data

Based on the results of morphological and DNA sequence (partial D1–D3/D7–D8 nuLSU and partial nuSSU-ITS1-5.8S rDNA) data, three species of Plasmopara are revised and reclassified. A species of Plasmopara parasitic on Scorzonera, invalidly published several times, is assigned to a new genus and species under Novotelnova scorzonerae. Plasmopara euphrasiae sp. nov. is segregated from P. densa, and P. centaureae-mollis is revised and relegated to synonymy of Bremia centaureae. All taxa are described and illustrated.     

Phylogenetic relationship of Alexandrium monilatum (Dinophyceae) to other Alexandrium species based on 18S ribosomal RNA gene sequences

The phylogenetic relationship of Alexandrium monilatum to other Alexandrium spp. was explored using 18S rDNA sequences. Maximum likelihood phylogenetic analysis of the combined rDNA sequences established that A. monilatum paired with Alexandrium taylori and that the pair was the first of the Alexandrium taxa to diverge, followed by Alexandrium margalefii. All three are members of the Alexandrium subgenus Gessnerium Halim nov. comb.     

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.