A PCR-based method for the identification of important wood rotting fungal taxa within Ganoderma, Inonotus s.l. and Phellinus s.l

Two multiplex PCRs, based on 10 taxon-specific primers designed on rRNA gene regions, were developed for the identification of taxa within the lignivorous genera Ganoderma, Inonotus s.l. and Phellinus s.l., each comprising both secondary and primary aggressive decay fungi. Each multiplex PCR proved to correctly identify 1 x 10(-2) pg of fungal target DNA directly from wood. This method can be helpful in detecting decay in standing trees independent of its stage of advancement, and to identify the associated decay agents.     

Species recognition, geographic distribution and host-pathogen relationships: a case study in a group of lignicolous basidiomycetes, Phellinus s.l

Morphological, phylogenetic (sequencing of the ribosomal ITS region) and, if applicable, biological (pairings of single-spore testers) species recognition have been used to resolve relationships among 69 collections belonging to the Hymenochaetales genera Phellinus s.str. and Fomitiporia. The isolates originate from a variety of host plants in Europe, North America and Asia. Separate application of recognition modes led to differing results concerning the number of species, geographic distribution and host range. Sole application of morphological criteria was of limited value, especially in taxa exhibiting a wide distribution, both in terms of geographic origin and ecological niche. Relationships of putatively con-specific collections originating from different continents preferably should be resolved by using an integrative approach. In this study, application of a strict morphological approach led to the recognition of seven species. When using molecular and pairing test data, at least 12 species were detectable. Two of them, F. hesleri and F. polymorpha, are described as new. The number of Phellinus s.str. and Fomitiporia species supposed to have Northern Hemispheric or cosmopolitan distribution, when morphological characters are applied for species recognition, has been reduced significantly. As firm tendencies within morphological species, genetic divergence was more distinct in uniparental than in biparental taxa. In the latter, a strong correlation was observed between phylogenetic and biological species recognition. Overall length of the ribosomal ITS region clearly separated Phellinus s.str. and Fomitiporia but was of limited value as a diagnostic tool at species level. The level of innerspecific morphological plasticity of fruit bodies differs widely between even closely related species, suggesting that morphological transitions occur quite frequently in this fungal group. Considerable instability of the reproduction mode was evident in strains belonging to Phellinus tremulae and among closely related species of Fomitiporia.     

Phellinus caribaeo-quercicolus sp. nov., parasitic on Quercus cubana: taxonomy and preliminary phylogenetic relationships

Phellinus caribaeo-quercicolus sp. nov. is described from several collections made in western Cuba, so far exclusively on Quercus cubana. The species is characterized by a perennial, resupinate basidiomes, cushion-shaped to nodulose and multi-layered when old, apically hooked to hamate hymenial setae, and ellipsoid to broadly ellipsoid, thin- to thick-walled, hyaline to faintly yellowish basidiospores, 4.5-5.5 x 3.5-4.5 microm. The species is compared to other Phellinus species with hooked setae, especially Phellinus undulatus, also recorded in Cuba. The preliminary phylogenetic relationships of Ph. caribaeo-quercicolus within the poroid Hymenochaetales complex of genera is presented and discussed here.     

Phylogeny of Symphytognathidae s.l. (Araneae, Araneoidea)

The paper presents a phylogenetic analysis of Symphytognathidae sensu lato (= sensu Forster 1959): Anapidae, Micropholcommatidae, Mysmenidae and Symphytognathidae sensu stricto. These taxa include the smallest known spiders. Several authors have suggested that their similarities are merely the convergent result of reduction and loss (simplifications, minimization of organs). The data matrix comprises 80 characters scored for 12 ingroup and two outgroup taxa. The value of reduction characters is discussed in general, and the evidence regarding symphytognathids in particular is reviewed. In this case, homology explains the data better than convergence. Although Symphytognathidae s.l . is, in fact, based mainly on characters that might have accompanied miniaturization, the taxon is most probably monophyletic. Anapidae as currently defined is paraphyletic. As it constitutes, together with Micropholcommatidae, a well supported monophyletic group, the latter is herewith synonymised with the former. Mysmenidae should be relimited by transferring four Old World genera to a new family, Synaphridae. Sympyhtognathidae s.s. is also monophyletic, even though the main synapomorphy, fused chelicerae, also occurs in Mysmenidae.     

Phylogenetic relationships among genera in theLiliaceae-Asparagoideae-Polygonatae s.l. inferred fromrbcL gene sequence data

The chloroplast gene encoding ribulose-1,5-bisphosphate-carboxylase (rbcL) was sequenced for phylogenetic analysis of 13 species (10 genera) in the tribePolygonatae s.l. of theLiliaceae-Asparagoideae. The data were analysed using maximum parsimony and neighbour-joining methods. There were 233 phylogenetically informative sites out of 1368 base pairs compared. The results suggest that there are three monophyletic groups withinPolygonatae s.l. with high bootstrap confidence values. Group A representsPolygonatae s.str., with generaMaianthemum, Smilacina, Convallaria, Disporopsis, andPolygonatum. Group B containsUvularia andDisporum and group C includesStreptopus, Tricyrtis, Clintonia, andProsartes. The study suggests thatPolygonatae s.l. are not a monophyletic group, including at least three groups of different phylogenetic origin. Monophyly of the taxa within groups A, B, and C is supported by the high bootstrap confidence values (85–100%) of the bootstrap replications for both parsimony and neighbour-joining methods. The differences between each group (calculated as 100x base substitutions per site) were 6.99–9.03 for group A and B, 4.92–7.35 for A and C, and 6.66–7.57 for B and C.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

东喜马拉雅地区多孔菌区系和生态习性

对东喜马拉雅地区多孔菌区系和生态习性进行了分析,发现该地区多孔菌极为丰富,共有10目19科101属372种,其中优势科为多孔菌科和锈革孔菌科,优势属为木层孔菌属和多孔菌属。种的区系地理成分可以分为8类,其中北温带类型种类最多,表明东喜马拉雅地区多孔菌具有明显的北温带区系特征。该地区的多孔菌有常见种、偶见种、稀有种和濒危种分别为156、141、54和21个;有腐生菌304种、寄生菌49种、菌根菌19种。在寄主方面,能够生长在被子植物上的有256种,裸子植物上的有137种,既能生长在被子植物,也能生长在裸子植物上的有40种,地上生长的有19种。东喜马拉雅地区的裸子植物,特别是云杉属、松属和冷杉属树木对于多孔菌的生长更重要,因为生长在这些属树木上的多孔菌分别有71、68和51种,高于该地区被子植物其他属树木上的多孔菌。     

Fomitiporia tenuis and Fomitiporia aethiopica (Basidiomycetes, Hymenochaetales), two undescribed species from the Ethiopian highlands: taxonomy and phylogeny

Fomitiporia tenuis sp. nov. and Fomitiporia aethiopica sp. nov. from the Ethiopian highlands are described. Both are characterized by a resupinate habit, globose, dextrinoid basidiospores, cystidioles, and respectively scarcity or absence of hymenial setae. Fomitiporia pseudopunctata and F. robusta are reported also in the same area. The preliminary phylogenetic relationships of F. tenuis, F. aethiopica and F. pseudopunctata are inferred from parsimony analysis based on partial nuclear ribosomal large subunit (nrLSU). A preliminary key to the poroid Hymenochaetales with dextrinoid basidiospores (Fomitiporia, Phellinus s.l., Pseudoinonotus) is proposed.     

Phylogenetic relationships of Thlaspi s.l. (subtribe Thlaspidinae, Lepidieae) and allied genera based on chloroplast DNA restriction-site variation

Chloroplast DNA restriction-site variation was analyzed in 30 accessions representing 20 species from the major lineages in Thlaspi s.l. (previously described as genera by Meyer 1973, 1979) and allied genera from the subtribe Thlaspidinae (Peltaria, Teesdalia, Cochlearia, Ionopsidium, Aethionema). A total of 161 variable restriction sites were detected. Phylogenetic analyses indicated a division of Thlaspi s.l. into three groups consistent with Meyer's genera Thlaspi s. str., Microthlaspi and Noccaea/Raparia. The genus Thlaspi s.l. as currently described proved to be paraphyletic because one of its major lineages, i.e. Thlaspi s. str., appeared to be more closely related to other genera (Peltaria, Teesdalia) than to the remaining lineages of Thlaspi s.l., i.e. Noccaea/Raparia and Microthlaspi. Sequence divergence values (100 x p) between the Thlaspi s.l. lineages were similar to values between these groups and related genera (Teesdalia, Peltaria), respectively. Chloroplast DNA variation was also used to assess subtribal classification of the genera studied. The cpDNA data were inconsistent with the controversial taxonomic classifications based on morphology. The molecular data would suggest that (1) the subtribe Thlaspidinae, as traditionally described, is not monophyletic; (2) the Thlaspidinae should be reduced to a group consisting of Thlaspi s. str., Peltaria, Teesdalia, Microthlaspi, Noccaea/Raparia, and that Aethionema should be excluded from the Thlaspidinae; and (3) Cochlearia and Ionopsidium represent the subtribe Cochleariinae.     

Phylogeny of the bee subtribe Caenohalictina Michener (Hymenoptera,Apidae s.l., Halictinae s.l.)

Gonçalves, R. B. & Melo, G. A. R. (2009). Phylogeny of the bee subtribe Caenohalictina Michener (Hymenoptera, Apidae s.l., Halictinae s.l.). —Zoologica Scripta, 39, 187–197. Recently, Caenohalictina Michener, 1954 was formally proposed as a group within Halictini based on a phylogenetic analysis using DNA data. Morphological synapomorphies for the subtribe are not stabilized and the relationships among its attributed genera were not completely reconstructed. Also, there are different propositions for the scope and classification of the genera. This study investigates the monophyly of Caenohalictina based on morphological characters and presents a hypothesis for the relationships among its genera and subgenera. For this purpose, a matrix of 36 terminals and 96 characters was coded. The cladistic analysis using character equal weighting resulted in one most parsimonious tree with 189 steps. According to this hypothesis, the subtribe is monophyletic with five synapomorphies supporting it. The relationships among Caenohalictina taxa are: Habralictus(Caenohalictus (((Agapostemon s.s. + Notagapostemon) (Agapostemonoides (Rhinetula (Paragapostemon + Dinagapostemon)))) + ((Ruizanthedella (Ruizantheda + Oragapostemon)) + (Brasilagapostemon (Pseudagapostemon s.s. + Neagapostemon))))). The subgenus Habralictus s.s. is paraphyletic with respect to Habralictus (Zikaniella) crassipes, hence both subgenera are not recognized. Comments on alternative generic classifications and biogeographic patterns are presented.     

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.     

Multigene phylogenetic analysis reveals non-monophyly of Anisakis s.l. and Pseudoterranova (Nematoda: Anisakidae)

The nematode genera Anisakis s.l. and Pseudoterranova (Anisakidae) include causative agents of anisakiasis and pseudoterranovosis, parasitic diseases resulting from eating undercooked or raw fish or squid. Species in both genera have thus attracted considerable attention especially in public health and taxonomic studies. The phylogenetic relationships of these genera within the subfamily Anisakinae, however, remain to be investigated with dense taxonomic sampling. In this study, we collected an anisakid third-stage larva, and identified it morphologically and molecularly as Pseudoterranova ceticola. Phylogeny of 15 anisakine species, including the newly collected specimen of Ps. ceticola, was reconstructed based on sequences of three mitochondrial (cox1, cox2, and 12S rRNA) and two nuclear (ITS and 28S rRNA) regions. The obtained tree suggested the non-monophyly of Anisakis s.l. and Pseudoterranova. Anisakis s.l. was divided into two groups, which are distinguished from each other by the shape of the ventriculus. Based on phylogenetic relationships and morphology, three species with a shorter ventriculus (“A.” brevispiculata, “A.” paggiae, and “A.” physeteris) were assigned to the genus Skrjabinisakis, as recently proposed. Pseudoterranova ceticola was distantly related to the monophyletic Ps. decipiens species complex. Although the phylogenetic position of the type species Ps. kogiae has not been investigated due to a lack of sequence data, this species may morphologically and ecologically resemble Ps. ceticola, inferring a close kinship between the two species.     

A molecular phylogenetic study of Cucujidae s.l. (Coleoptera: Cucujoidea)

Of all the superfamilies within the megadiverse order Coleoptera (Insecta), Cucujoidea (Cucujiformia) is arguably the most problematic taxonomically. The families comprising Cucujidae s.l. (Silvanidae, Laemophloeidae, Passandridae and Cucujidae s.s. represent a large portion of cucujoid diversity. Herein we present the results of a rigorous molecular phylogenetic analysis of Cucujidae s.l. using maximum‐likelihood and Bayesian analyses of seven genes. Representatives of over half of the families of Cucujoidea (excluding the cerylonid series), as well as a broad sampling of Silvanidae and Laemophloeidae, were analysed. The monophyly of Cucujidae s.l. is rejected but a subgrouping of taxa that may form the core of a natural cucujoid lineage is recovered. This clade consists of two large monophyletic groups including several families each. Relationships among these smaller cucujoid groups are discussed, including several novel phylogenetic hypotheses, whereas morphological characters considered significant for classification in Cucujidae s.l. are evaluated in light of these phylogenetic hypotheses. Silvaninae, Telephanini, Brontini and Brontinae are recovered as monophyletic in the Bayesian analysis, but the former two are recovered as paraphyletic in the maximum‐likelihood analysis. Our results support the placement of Psammoecus Latreille within Telephanini and also recover a paraphyletic Telephanus Erichson. Silvaninae is divided into three lineages, each representing a potential tribal lineage. Laemophloeidae is rendered paraphyletic in all analyses by Propalticidae and the latter is herein formally transferred to Laemophloeidae stat.n . Several suprageneric laemophloeid clades are recovered and discussed as potential higher‐level groups. Laemophloeus Dejean is not recovered as monophyletic.     

Phylogeny and taxonomy of the genus Phylloporia (Hymenochaetales)

Based on 28 taxa, including six species of Phylloporia, and respectively one representative of 17 genera of the Hymenochaetales, a phylogenetic analysis of a region of the large subunit of the nuclear encoded ribosomal DNA was performed. Molecular sequence data as well as morphological and anatomical features show the genus to be monophyletic. Next related to Phylloporia is Fulvifomes. The phylogenetic relationships of Phylloporia are discussed. In addition the genus Phylloporia is monographed; 12 species are accepted and described with a key.     

Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae s.l.) inferred from five gene regions

Accurate classification systems based on evolution are imperative for biological investigations. The recent explosion of molecular phylogenetics has resulted in a much improved classification of angiosperms. More than five phylogenetic lineages have been recognized from Scrophulariaceae sensu lato since the family was determined to be polyphyletic; however, questions remain about the genera that have not been assigned to one of the segregate families of Scrophulariaceae s.l. Rehmannia Liboschitz and Triaenophora Solereder are such genera with uncertain familial placement. There also is debate whether Triaenophora should be segregated from Rehmannia. To evaluate the phylogenetic relations between Rehmannia and Triaenophora, to find their closest relatives, and to verify their familial placement, we conducted phylogenetic analyses of the sequences of one nuclear DNA (ITS) region and four chloroplast DNA gene regions (trnL-F, rps16, rbcL, and rps2) individually and combined. The analyses showed that Rehmannia and Triaenophora are each strongly supported as monophyletic and together are sister to Orobanchaceae. This relation was corroborated by phytochemical and morphological data. Based on these data, we suggest that Rehmannia and Triaenophora represent the second nonparasitic branch sister to the remainder of Orobanchaceae (including Lindenbergia).     

Molecular systematics of Boraginaceae tribe Boragineae based on ITS1 and trnL sequences, with special reference to Anchusa s.l

BACKGROUND AND AIMS: Boragineae is one of the main tribes of Boraginaceae, but delimitation and intergeneric classification of this group are unclear and have not yet been studied using DNA sequences. In particular, phylogenetic relationships in Anchusa s.l. still need to be elucidated in order to assess its taxonomic boundaries with respect to the controversial segregate genera Hormuzakia, Gastrocotyle, Phyllocara and Cynoglottis. METHODS: Phylogenetic relationships among 51 taxa of tribe Boragineae were investigated by comparative sequencing of the trnL(UAA) intron of the plastid genome and of the ITS1 region of the nuclear ribosomal DNA. Exemplar taxa from 16 genera of Boragineae and all subgenera of Anchusa s.l. were included, along with two selected outgroups from tribes Lithospermeae and Cynoglosseae. KEY RESULTS: Phylogenies generated by maximum parsimony and combined ITS1-trnL sequences support the monophyly of the tribe and a split into two clades, Pentaglottis and the remainder of Boragineae. The latter contains two large monophyletic groups. The first consists of three moderately to well-supported branches, Borago-Symphytum, Pulmonaria-Nonea and Brunnera. In the Pulmonaria-Nonea subclade, the rare endemic Paraskevia cesatiana is sister to Pulmonaria, and Nonea appears to be paraphyletic with respect to Elizaldia. The second main group corresponds to the well-supported clade of Anchusa s.l., with the megaphyllic, polyploid herb Trachystemon orientalis as sister taxon, although with low support. Anchusa s.l. is highly paraphyletic to its segregate genera and falls into four subclades: (1) Phyllocara, Hormuzakia, Anchusa subgenus Buglossum and A. subgenus Buglossoides; (2) Gastrocotyle; (3) A. subgenus Buglossellum and Cynoglottis; and (4) A. subgenus Anchusa, Lycopsis and Anchusella. All species of Anchusa subg. Anchusa, including the South African A. capensis, are included in a single unresolved clade. Anchusa subgenus Limbata is also included here despite marked divergence in floral morphology. The low nucleotide variation of ITS1 suggests a recent partly adaptive radiation within this group. CONCLUSIONS: Molecular data show that nine of the usually accepted genera of the Boragineae consisting of two or more species are monophyletic: Anchusella, Borago, Brunnera, Cynoglottis, Gastrocotyle, Hormuzakia, Nonea, Pulmonaria and Symphytum. In addition, the tribe includes the four monotypic genera Paraskevia, Pentaglottis, Phyllocara and Trachystemon. The morphologically well-characterized segregate genera in Anchusa s.l. are all confirmed by DNA sequences and should be definitively accepted. Most of the traditionally recognized subgenera of Anchusa are also supported as monophyletic groups by both nuclear and plastid sequence data. In order to bring taxonomy in line with phylogeny, the institution of new, independent generic entities for subgenera Buglossum, Buglossellum and Buglossoides and a narrower but more natural concept of Anchusa are advocated.     

Cladistic analysis of Taxaceae s. l.

Taxaceae s. l. is a wider concept of classification treating five genera of Taxaceae s. str. and Cephalotaxus together. Cephalotaxus is morphologically very similar to the five genera of Taxaceae s. str. Various models of classification for six genera have already been published. However, the phylogenetic position and genuine relationships of these genera and species are still confusing. A cladistic analysis of Taxaceae s. l. has been carried out to resolve the problem existing in their phylogeny and to provide a new approach regarding the relationships of these six genera. Parsimony analyses were based on 28 characters and eight genera including two outgroups Agathis and Sciadopitys. The most parsimonious tree retained with branch length 38 and 194 rearrangement trials. Consistency index was 0.68 and retention index was 0.66. Principally, two main clades were found: one represented by Austrotaxus forming the base of the tree and another by the remaining five genera. Taxus + Pseudotaxus clade split after Austrotaxus, and Cephalotaxus was sister to Torreya + Amentotaxus clade. Taxus + Pseudotaxus clade was supported by the highest bootstrap value. Finally, cladistic analysis does not support existence of Cephalotaxaceae. Therefore, it would be better to classify Cephalotaxus within Taxaceae s. l. with the other five genera.