Evolutionary response of Caragana (Fabaceae) to Qinghai–Tibetan Plateau uplift and Asian interior aridification

Caragana is endemic to temperate Asia, with most species distributed on the Qinghai–Tibetan Plateau (QTP) and in Northwestern China. Consequently its biogeography should be hypothesized to have been affected by QTP uplift. To examine the biogeography of Caragana in relation to QTP uplift and consequent interior aridification, we conducted molecular dating analyses based on three genes (ITS, cpDNA trnS-trnG and rbcL). Results from relaxed Bayesian BEAST, relaxed Bayesian Multidivtime, and PL (penalized likelihood) indicate that QTP uplift, especially the onset of Himalayan motion at 21–17 Ma, triggered the origin of Caragana (with estimated ages 16–14 Ma). The subsequent QTP rapid uplift at 8 Ma is inferred to have driven the evolution and diversification of the three major clades of Caragana: section Caragana (northern China and the Junggar–Altai–Sayan region), section Frutescentes (Central Asia), and sections Bracteolatae and Jubatae, centered in the QTP. A rapid and active speciation process occurring in the QTP intense uplift at 3.4–1.8 Ma, is indicated by the chronogram.     

Evolutionary relationships among aquatic anamorphs and teleomorphs: Lemonniera, Margaritispora, and Goniopila

The hypothesis that similar conidial morphologies in aquatic hyphomycetes are a result of convergent evolution was tested using molecular sequence data. Cladistic analyses were performed on partial sequences of 28S rDNA of seven species of Lemonniera, one species of Margaritispora and one species of Goniopila. Lemonniera has tetraradiate conidia with long arms, whereas Margaritispora and Goniopila have typically globose (isodiametric) conidia, with short conical protuberances in a stellate or quadrangular arrangement. Lemonniera and Margaritispora have phialidic conidiogenesis and both produce dark, minute sclerotia in culture whereas Goniopila has holoblastic conidiogenesis and does not produce sclerotia in culture. Goniopila produces a microconidial phialidic synanamorph in culture. All three genera have schizolytic conidial secession. Molecular analyses demonstrate that Lemonniera species are placed in two distinct clades: one within Leotiomycetes; the other within Pleosporales, Dothideomycetes. Margaritispora is placed with Lemonniera species within Leotiomycetes. Goniopila and Lemonniera pseudofloscula are placed within Dothideomycetes. No morphological character was entirely congruent with the molecular derived phylogeny. This suggests that for the group of species studied, conidial shape is not a reliable indicator of phylogeny but more likely the result of convergent evolution in response to the aquatic environment.     

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.     

Carex, subgenus Carex (Cyperaceae) – A phylogenetic approach using ITS sequences

To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed.     

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.     

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.     

Otidea subterranea sp. nov.: Otidea goes below ground

Evidence suggests that truffle-like sporocarp forms have evolved many times in the Pezizales, but primarily from epigeous ancestors within ectomycorrhizal clades. There are several ectomycorrhizal clades, however, that contain no known hypogeous species. We collected specimens of an unusual unidentified truffle from mixed oak woodlands in Iowa. Although clearly a member of the Pezizales (Ascomycota), this hypogeous species did not belong to any of the described truffle genera. Based on a combination of ecological, phylogenetic, and morphological evidence we determined that this new truffle is a hypogeous member of the genus Otidea (Pyronemataceae), a lineage with no described truffle species. We describe it here as a new species, Otidea subterranea.     

Cystobasidiopsis nirenbergiae, a new agaricostilbomycete (Pucciniomycotina)

A new genus, Cystobasidiopsis, and a new species, Cystobasidiopsis nirenbergiae, are described for a fungus isolated from an arable loess soil in Ahlum near Braunschweig, Niedersachsen, Germany. An integrated analysis of morphological, ecological, ultrastructural and molecular data indicates that the new species belongs to the Chionosphaeraceae within the Agaricostilbales. Relevant characteristics of the new species are discussed and compared with those of related taxa.     

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.     

Multi-gene analysis reveals previously unrecognized phylogenetic diversity in Aliivibrio

The “Vibrio fischeri species group” recently was reclassified as a new genus, Aliivibrio, comprising four species, Aliivibrio fischeri, Aliivibrio logei, Aliivibrio salmonicida, and Aliivibrio wodanis. Only limited phylogenetic analysis of strains within Aliivibrio has been carried out, however, and taxonomic ambiguity is evident within this group, especially for phenotypically unusual strains and certain strains isolated from bioluminescent symbioses. Therefore, to examine in depth the evolutionary relationships within Aliivibrio and redefine the host affiliations of symbiotic species, we examined several previously identified and newly isolated strains using phylogenetic analysis based on multiple independent loci, gapA, gyrB, pyrH, recA, rpoA, the luxABE region, and the 16S rRNA gene. The analysis resolved Aliivibrio as distinct from Vibrio, Photobacterium, and other genera of Vibrionaceae, and resolved A. fischeri, A. salmonicida, A. logei, and A. wodanis as distinct, well-supported clades. However, it also revealed that several previously reported strains are incorrectly identified and that substantial unrecognized diversity exists in this genus. Specifically, strain ATCC 33715 (Y-1) and several other strains having a yellow-shifted luminescence were not members of A. fischeri. Furthermore, no strain previously identified as A. logei grouped with the type strain (ATCC 29985^T), and no bona-fide strain of A. logei was identified as a bioluminescent symbiont. Several additional strains identified previously as A. logei group instead with the type strain of A. wodanis (ATCC BAA-104^T), or are members of a new clade. Two strongly supported clades were evident within A. fischeri, a phylogenetic structure that might reflect differences in the host species or differences in the ecological incidence of strains. The results of this study highlight the importance of basing taxonomic conclusions on examination of type strains.     

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.     

Molecular Systematics of Zopfiella and allied genera: evidence from multi-gene sequence analyses

This study aims to reveal the phylogenetic relationships of Zopfiella and allied genera in the Sordariales. Multiple gene sequences (partial 28 S rDNA, ITS/5.8 S rDNA and partial β-tubulin) were analysed using MP and Bayesian analyses. Analyses of different gene datasets were performed individually and then combined to infer phylogenies. Phylogenetic analyses show that currently recognised Zopfiella species are polyphyletic. Based on sequence analyses and morphology, it appears that Zopfiella should be restricted to species having ascospores with a septum in the dark cell. Our molecular analysis also shows that Zopfiella should be placed in Lasiosphaeriaceae rather than Chaetomiaceae. Cercophora and Podospora are also polyphyletic, which is in agreement with previous studies. Our analyses show that species possessing a Cladorrhinum anamorph are phylogenetically closely related. In addition, there are several strongly supported clades, characterised by species possessing divergent morphological characters. It is difficult to predict which characters are phylogenetically informative for delimiting these clades.     

3种锦鸡儿属植物过氧化物酶基因的克隆及表达分析

采用同源克隆技术分离了3种锦鸡儿属植物柠条锦鸡儿(Caragana korshinskii)、小叶锦鸡儿(C.microphylla)和中间锦鸡儿(C.intermedia)的过氧化物酶(POD)基因(分别命名为CkPOD、CmPOD和CiPOD),并对它们在干旱胁迫条件下的表达特征进行了分析。CkPOD、CiPOD、CmPOD基因的cDNA序列均包含有1 074bp的开放阅读框(ORF),编码的蛋白质由357个氨基酸构成,分子量为38.7kD。系统进化分析结果显示:3种锦鸡儿属植物的POD可以和鹰嘴豆等豆科植物的POD聚为一类,且CkPOD和CmPOD具有较近的亲缘关系,CiPOD与CkPOD和CmPOD的亲缘关系相对较远,这一结果与3种锦鸡儿属植物的进化地位一致,显示POD基因较为保守,可以为锦鸡儿属植物的系统分类提供参考。PEG模拟干旱胁迫能够强烈诱导CkPOD、CiPOD和CmPOD基因的表达,显示POD基因在锦鸡儿属植物抵御干旱胁迫过程中发挥着重要作用。研究结果可为解析锦鸡儿属植物的耐旱机理以及利用锦鸡儿属植物进行荒漠改良和生态修复提供理论和实验依据。     

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.     

新疆地图衣属地衣分类学研究

该研究以新疆的地图衣科(Rhizocarpaceae)地图衣属(Rhizocarpon)100余份地衣标本为材料,通过形态解剖学观察、化学成分分析及分子学鉴定的方法了解新疆地图衣属地衣的物种多样性。结果表明:(1)鉴定出7种地图衣属地衣,包括1个中国新记录种,命名为淡黄色地图衣(R.atroflavescens),6个常见种分别是黑红地图衣(R.badioatrum)、灰地图衣(R.disporum)、双孢地图衣(R.geminatum)、地图衣(R.geographicum)、巨地图衣(R.grande)和岩表地图衣(R.superficiale)。(2)编制了新疆22种地图衣属地衣的分种检索表。(3)系统发育分析结果表明,新疆地图衣属地衣的分子鉴定与形态解剖特征结果一致,更准确地证明淡黄色地图衣为中国新记录种。(4)对已报道的新疆22种地图衣属地衣的地区分布及海拔分布统计显示,新疆22种地图衣属地衣在世界各地均有分布,其中亚洲分布最丰富;该22种地图衣属地衣从低海拔到高海拔都有分布,且各海拔高度物种分布不均匀,总体在高海拔地区分布的物种较多。     

Morphology and development of Nigrosabulum globosum, a cleistothecial coprophile in the Bionectriaceae (Hypocreales)

Recent DNA sequence analyses indicated that Nigrosabulum globosum is a cleistothecial representative of the Bionectriaceae in the Hypocreales, but morphological characters supporting this relationship are unknown. Using light and electron microscopy we followed the development of the ascomata of this species, from the formation of gametangia through to the development of mature ascospores, and observed a series of characters that confirmed its hypocrealean affinities. These included the formation of a gel-filled centrum during early stages of ascoma development, the subsequent appearance of hyaline peridial tissue enclosed within a layer we interpret as representing a melanized uniloculate stroma, apically derived paraphyses, and an ascogenous system that gives rise to asci that were both cylindrical to clavate and globose. Ascospores, previously reported to be smooth, were ornamented with a honeycomb-like reticulum and were able to germinate within the ascoma. The carbonaceous outer (stromatic) walls of the mature, grit-like cleistothecia indicate possible resistance to UV radiation and desiccation. Furthermore, the complement of germinated ascospores would enable mature ascomata to function as propagules that could quickly initiate new growth when transferred to fresh substrate. Our reexamination of N. globosum also provides data that support the hypothesized close relationship with other bionectriaceous, cleistothecial coprophiles, i.e., species of Hapsidospora, and Bulbithecium in particular.