Phylogenetic lineages in the Capnodiales

The Capnodiales incorporates plant and human pathogens, endophytes, saprobes and epiphytes, with a wide range of nutritional modes. Several species are lichenised, or occur as parasites on fungi, or animals. The aim of the present study was to use DNA sequence data of the nuclear ribosomal small and large subunit RNA genes to test the monophyly of the Capnodiales, and resolve families within the order. We designed primers to allow the amplification and sequencing of almost the complete nuclear ribosomal small and large subunit RNA genes. Other than the Capnodiaceae (sooty moulds), and the Davidiellaceae, which contains saprobes and plant pathogens, the order presently incorporates families of major plant pathological importance such as the Mycosphaerellaceae, Teratosphaeriaceae and Schizothyriaceae. The Piedraiaceae was not supported, but resolves in the Teratosphaeriaceae. The Dissoconiaceae is introduced as a new family to accommodate Dissoconium and Ramichloridium. Lichenisation, as well as the ability to be saprobic or plant pathogenic evolved more than once in several families, though the taxa in the upper clades of the tree lead us to conclude that the strictly plant pathogenic, nectrotrophic families evolved from saprobic ancestors (Capnodiaceae), which is the more primitive state.Taxonomic novelties: Brunneosphaerella Crous, gen. nov., B. jonkershoekensis (Marinc., M.J. Wingf. & Crous) Crous, comb. nov., B. protearum (Syd. & P. Syd.) Crous, comb. nov., Devriesia hilliana Crous & U. Braun, sp. nov., D. lagerstroemiae Crous & M.J. Wingf., sp. nov., D. strelitziicola Arzanlou & Crous, sp. nov., Dissoconiaceae Crous & de Hoog, fam. nov., Hortaea thailandica Crous & K.D. Hyde, sp. nov., Passalora ageratinae Crous & A.R. Wood, sp. nov., P. armatae Crous & A.R. Wood, sp. nov., Rachicladosporium cboliae Crous, sp. nov.     

Phylogenetic lineages in Pseudocercospora

Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1α, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general morphology, within the same geographic region, frequently differed phylogenetically, indicating that the application of European and American names to Asian taxa, and vice versa, was often not warranted.

Taxonomic novelties:

New genera - Pallidocercospora Crous, Phaeomycocentrospora Crous, H.D. Shin & U. Braun; New species - Cercospora eucommiae Crous, U. Braun & H.D. Shin, Microcyclospora quercina Crous & Verkley, Pseudocercospora ampelopsis Crous, U. Braun & H.D. Shin, Pseudocercospora cercidicola Crous, U. Braun & C. Nakash., Pseudocercospora crispans G.C. Hunter & Crous, Pseudocercospora crocea Crous, U. Braun, G.C. Hunter & H.D. Shin, Pseudocercospora haiweiensis Crous & X. Zhou, Pseudocercospora humulicola Crous, U. Braun & H.D. Shin, Pseudocercospora marginalis G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora ocimi-basilici Crous, M.E. Palm & U. Braun, Pseudocercospora plectranthi G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora proteae Crous, Pseudocercospora pseudostigmina-platani Crous, U. Braun & H.D. Shin, Pseudocercospora pyracanthigena Crous, U. Braun & H.D. Shin, Pseudocercospora ravenalicola G.C. Hunter & Crous, Pseudocercospora rhamnellae G.C. Hunter, H.D. Shin, U. Braun & Crous, Pseudocercospora rhododendri-indici Crous, U. Braun & H.D. Shin, Pseudocercospora tibouchinigena Crous & U. Braun, Pseudocercospora xanthocercidis Crous, U. Braun & A. Wood, Pseudocercosporella koreana Crous, U. Braun & H.D. Shin; New combinations - Pallidocercospora acaciigena (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora crystallina (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora heimii (Crous) Crous, Pallidocercospora heimioides (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora holualoana (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidocercospora konae (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidoocercospora irregulariramosa (Crous & M.J. Wingf.) Crous & M.J. Wingf., Phaeomycocentrospora cantuariensis (E.S. Salmon & Wormald) Crous, H.D. Shin & U. Braun, Pseudocercospora hakeae (U. Braun & Crous) U. Braun & Crous, Pseudocercospora leucadendri (Cooke) U. Braun & Crous, Pseudocercospora snelliana (Reichert) U. Braun, H.D. Shin, C. Nakash. & Crous, Pseudocercosporella chaenomelis (Y. Suto) C. Nakash., Crous, U. Braun & H.D. Shin; Typifications: Epitypifications - Pseudocercospora angolensis (T. Carvalho & O. Mendes) Crous & U. Braun, Pseudocercospora araliae (Henn.) Deighton, Pseudocercospora cercidis-chinensis H.D. Shin & U. Braun, Pseudocercospora corylopsidis (Togashi & Katsuki) C. Nakash. & Tak. Kobay., Pseudocercospora dovyalidis (Chupp & Doidge) Deighton, Pseudocercospora fukuokaensis (Chupp) X.J. Liu & Y.L. Guo, Pseudocercospora humuli (Hori) Y.L. Guo & X.J. Liu, Pseudocercospora kiggelariae (Syd.) Crous & U. Braun, Pseudocercospora lyoniae (Katsuki & Tak. Kobay.) Deighton, Pseudocercospora lythri H.D. Shin & U. Braun, Pseudocercospora sambucigena U. Braun, Crous & K. Schub., Pseudocercospora stephanandrae (Tak. Kobay. & H. Horie) C. Nakash. & Tak. Kobay., Pseudocercospora viburnigena U. Braun & Crous, Pseudocercosporella chaenomelis (Y. Suto) C. Nakash., Crous, U. Braun & H.D. Shin, Xenostigmina zilleri (A. Funk) Crous; Lectotypification - Pseudocercospora ocimicola (Petr. & Cif.) Deighton; Neotypifications - Pseudocercospora kiggelariae (Syd.) Crous & U. Braun, Pseudocercospora lonicericola (W. Yamam.) Deighton, Pseudocercospora zelkovae (Hori) X.J. Liu & Y.L. Guo.Key words: Capnodiales, Cercospora, cercosporoid, Mycosphaerella, Mycosphaerellaceae, Paracercospora, Pseudocercosporella, Multi-Locus Sequence Typing (MLST), systematics     

Phylogenetic reassessment of Mycosphaerella spp. and their anamorphs occurring on Eucalyptus. II.

Species of Eucalyptus are widely planted as exotics in the tropics and Southern Hemisphere and to some extent in southern Europe, for timber and fibre production. Species of Mycosphaerella are commonly associated with leaves and twigs of Eucalyptus and can result in defoliation, dieback, and even tree death. In the present study, numerous isolates of Mycosphaerella species were collected from leaf litter, living leaves exhibiting leaf spot symptoms or severe Mycosphaerella leaf blotch symptoms. Isolates were compared based on DNA sequence data for the internal transcribed spacer region (ITS1 & ITS2) and the 5.8S gene. These data, together with characteristics of the fungal growth on three different media, morphology of the anamorph and teleomorph structures as well as ascospore germination patterns were used to describe 21 new species.Taxonomic novelties: Colletogloeopsis stellenboschiana Crous sp. nov., Mycosphaerella davisoniellae Crous sp. nov. (anamorph Davisoniella eucalypti H.J. Swart), Mycosphaerella eucalyptorum Crous & M.J. Wingf. sp. nov. Mycosphaerella gamsii Crous sp. nov., Mycosphaerella perpendicularis Crous& M.J. Wingf. sp. nov., Mycosphaerella pluritubularis Crous & J.P. Mansilla sp. nov., Mycosphaerella pseudafricana Crous & T. Coutinho sp. nov., Mycosphaerella pseudocryptica Crous sp. nov. (anamorph Colletogloeopsis sp.), Mycosphaerella pseudoendophytica Crous & G. Hunter sp. nov. (anamorph Pseudocercosporella sp.), Mycosphaerella pseudosuberosa Crous & M.J. Wingf. sp. nov. (anamorph Trimmatostroma sp.), Mycosphaerella quasicercospora Crous & T. Coutinho sp. nov., Mycosphaerella scytalidii Crous & M.J. Wingf. sp. nov. (anamorph Stenella sp., synanamorph, Scytalidium-like.), Mycosphaerella secundaria Crous & A.C. Alfenas sp. nov., Mycosphaerella stramenti Crous & A.C. Alfenas sp. nov., Mycosphaerella stramenticola Crous & A.C. Alfenas sp. nov., Mycosphaerella sumatrensis Crous & M.J. Wingf. sp. nov., Mycosphaerella verrucosiafricana Crous & M.J. Wingf. sp. nov., Septoria eucalyptorum Crous sp. nov., Septoria provencialis Crous sp. nov., Stenella pseudoparkii Crous & M.J. Wingf. sp. nov. (teleomorph Mycosphaerella sp.), Stenella xenoparkii Crous & M.J. Wingf., sp. nov. (teleomorph Mycosphaerella sp.).     

Opportunistic,human-pathogenic species in the Herpotrichiellaceae are phenotypically similar to saprobic or phytopathogenic species in the Venturiaceae

Although morphologically similar, species of Cladophialophora (Herpotrichiellaceae) were shown to be phylogenetically distinct from Pseudocladosporium (Venturiaceae), which was revealed to be synonymous with the older genus, Fusicladium. Other than being associated with human disorders, species of Cladophialophora were found to also be phytopathogenic, or to occur as saprobes on organic material, or in water, fruit juices, or sports drinks, along with species of Exophiala. Caproventuria and Metacoleroa were confirmed to be synonyms of Venturia, which has Fusicladium (= Pseudocladosporium) anamorphs. Apiosporina, based on A. collinsii, clustered basal to the Venturia clade, and appears to represent a further synonym. Several species with a pseudocladosporium-like morphology in vitro represent a sister clade to the Venturia clade, and are unrelated to Polyscytalum. These taxa are newly described in Fusicladium, which is morphologically close to Anungitea, a heterogeneous genus with unknown phylogenetic affinity. In contrast to the Herpotrichiellaceae, which were shown to produce numerous synanamorphs in culture, species of the Venturiaceae were morphologically and phylogenetically more uniform. Several new species and new combinations were introduced in Cladophialophora, Cyphellophora (Herpotrichiellaceae), Exophiala, Fusicladium, Venturia (Venturiaceae), and Cylindrosympodium (incertae sedis).Taxonomic novelties: Cladophialophora australiensis Crous& A.D. Hocking, sp. nov., Cladophialophora chaetospira (Grove) Crous & Arzanlou, comb. nov., Cladophialophora hostae Crous, U. Braun & H.D. Shin, sp. nov., Cladophialophora humicola Crous& U. Braun, sp. nov., Cladophialophora potulentorum Crous & A.D. Hocking, sp. nov., Cladophialophora scillae (Deighton) Crous, U. Braun & K. Schub., comb. nov., Cladophialophora sylvestris Crous& de Hoog, sp. nov., Cylindrosympodium lauri Crous & R.F. Castañeda, sp. nov., Cyphellophora hylomeconis Crous, de Hoog& H.D. Shin, sp. nov., Exophiala eucalyptorum Crous, sp. nov., Fusicladium africanum Crous, sp. nov., Fusicladium amoenum (R.F. Castañeda & Dugan) Crous, K. Schub. & U. Braun, comb. nov., Fusicladium brevicatenatum (U. Braun & Feiler) Crous, U. Braun & K. Schub., comb. nov., Fusicladium fagi Crous & de Hoog, sp. nov., Fusicladium intermedium (Crous & W.B. Kendr.) Crous, comb. nov., Fusicladium matsushimae (U. Braun & C.F. Hill) Crous, U. Braun & K. Schub., comb. nov., Fusicladium pini Crous& de Hoog, sp. nov., Fusicladium ramoconidii Crous & de Hoog, sp. nov., Fusicladium rhodense Crous & M.J. Wingf., sp. nov., Venturia hystrioides (Dugan, R.G. Roberts & Hanlin) Crous & U. Braun, comb. nov.     

Re-evaluating the taxonomic status of Phaeoisariopsis griseola,the causal agent of angular leaf spot of bean

Angular leaf spot of Phaseolus vulgaris is a serious disease caused by Phaeoisariopsis griseola, in which two major gene pools occur, namely Andean and Middle-American. Sequence analysis of the SSU region of nrDNA revealed the genus Phaeoisariopsis to be indistinguishable from other hyphomycete anamorph genera associated with Mycosphaerella, namely Pseudocercospora and Stigmina. A new combination is therefore proposed in the genus Pseudocercospora, a name to be conserved over Phaeoisariopsis and Stigmina. Further comparisons by means of morphology, cultural characteristics, and DNA sequence analysis of the ITS, calmodulin, and actin gene regions delineated two groups within P. griseola, which are recognised as two formae, namely f. griseola and f. mesoamericana.Taxonomic novelties: Pseudocercospora griseola (Sacc.) Crous & U. Braun comb. nov., P. griseola f. mesoamericana Crous & U. Braun f. nov.     

Eucalyptus microfungi known from culture. 1. Cladoriella and Fulvoflamma genera nova,with notes on some other poorly known taxa

A study of microfungi associated with living Eucalyptus leaves and leaf litter revealed several novel and interesting taxa. Cladoriella eucalypti gen. et sp. nov. is described as a Cladosporium-like genus associated with litter collected in South Africa, while Fulvoflamma eucalypti gen. et. sp. nov. is newly described from leaf litter collected in Spain. Beta-conidia are newly reported for species of Pestalotiopsis, namely Pestalotiopsis disseminata in New Zealand, and a Pestalotiopsis sp. from Colombia. Satchmopsis brasiliensis is reported from litter in Colombia and Indonesia, while Torrendiella eucalypti is reported from leaf litter in Indonesia, and shown to have a Sporothrix-like anamorph. Leptospora rubella is reported from living Eucalyptus leaves in Colombia, where it is associated with leaf spots of Mycosphaerella longibasalis, while Macrohilum eucalypti is reported from leaf spots of Eucalyptus in New Zealand.Taxonomic novelties: Cladoriella eucalypti Crous gen. et sp. nov., Fulvoflamma eucalypti Crous gen. et sp. nov.     

Pestalotioid fungi from Restionaceae in the Cape Floral Kingdom

Eight pestalotioid fungi were isolated from the Restionaceae growing in the Cape Floral Kingdom of South Africa. Sarcostroma restionis, Truncatella megaspora, T. restionacearum and T. spadicea are newly described. New records include Pestalotiopsis matildae, Sarcostroma lomatiae, Truncatella betulae and T. hartigii. To resolve generic affiliations, phylogenetic analyses were performed on ITS (ITS1, 5.8S, ITS2) and part of 28S rDNA. DNA data support the original generic concept of Truncatella, which encompasses Pestalotiopsis species having 3-septate conidia. The genus Sarcostroma is retained as separate from Seimatosporium.Taxonomic novelties: Pestalotiopsis matildae (Richatt) S. Lee & Crous comb. nov., Truncatella betulae (Morochk.) S. Lee& Crous comb. nov., Sarcostroma restionis S. Lee & Crous sp. nov., Truncatella megaspora S. Lee & Crous sp. nov., Truncatella restionacearum S. Lee & Crous sp. nov., Truncatella spadicea S. Lee & Crous sp. nov.     

Mycosphaerella is polyphyletic

Mycosphaerella, one of the largest genera of ascomycetes, encompasses several thousand species and has anamorphs residing in more than 30 form genera. Although previous phylogenetic studies based on the ITS rDNA locus supported the monophyly of the genus, DNA sequence data derived from the LSU gene distinguish several clades and families in what has hitherto been considered to represent the Mycosphaerellaceae. Several important leaf spotting and extremotolerant species need to be disposed to the genus Teratosphaeria, for which a new family, the Teratosphaeriaceae, is introduced. Other distinct clades represent the Schizothyriaceae, Davidiellaceae, Capnodiaceae, and the Mycosphaerellaceae. Within the two major clades, namely Teratosphaeriaceae and Mycosphaerellaceae, most anamorph genera are polyphyletic, and new anamorph concepts need to be derived to cope with dual nomenclature within the Mycosphaerella complex.Taxonomic novelties: Batcheloromyces eucalypti (Alcorn) Crous & U. Braun, comb. nov., Catenulostroma Crous & U. Braun, gen. nov., Catenulostroma abietis (Butin & Pehl) Crous& U. Braun, comb. nov., Catenulostroma chromoblastomycosum Crous& U. Braun, sp. nov., Catenulostroma elginense (Joanne E. Taylor& Crous) Crous & U. Braun, comb. nov., Catenulostroma excentricum (B. Sutton & Ganap.) Crous & U. Braun, comb. nov., Catenulostroma germanicum Crous & U. Braun, sp. nov., Catenulostroma macowanii (Sacc.) Crous & U. Braun, comb. nov., Catenulostroma microsporum (Joanne E. Taylor & Crous) Crous & U. Braun, comb. nov., Catenulostroma protearum (Crous & M.E. Palm) Crous & U. Braun, comb. nov., Penidiella Crous & U. Braun, gen. nov., Penidiella columbiana Crous & U. Braun, sp. nov., Penidiella cubensis (R.F. Castañeda) U. Braun, Crous& R.F. Castañeda, comb. nov., Penidiella nectandrae Crous, U. Braun & R.F. Castañeda, nom. nov., Penidiella rigidophora Crous, R.F. Castañeda & U. Braun, sp. nov., Penidiella strumelloidea (Milko & Dunaev) Crous & U. Braun, comb. nov., Penidiella venezuelensis Crous & U. Braun, sp. nov., Readeriella blakelyi (Crous & Summerell) Crous & U. Braun, comb. nov., Readeriella brunneotingens Crous & Summerell, sp. nov., Readeriella considenianae (Crous & Summerell) Crous & U. Braun, comb. nov., Readeriella destructans (M.J. Wingf. & Crous) Crous & U. Braun, comb. nov., Readeriella dimorpha (Crous& Carnegie) Crous & U. Braun, comb. nov., Readeriella epicoccoides (Cooke & Massee) Crous & U. Braun, comb. nov., Readeriella gauchensis (M.-N. Cortinas, Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Readeriella molleriana (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Readeriella nubilosa (Ganap. & Corbin) Crous & U. Braun, comb. nov., Readeriella pulcherrima (Gadgil & M. Dick) Crous & U. Braun, comb. nov., Readeriella stellenboschiana (Crous) Crous & U. Braun, comb. nov., Readeriella toledana (Crous & Bills) Crous & U. Braun, comb. nov., Readeriella zuluensis (M.J. Wingf., Crous & T.A. Cout.) Crous & U. Braun, comb. nov., Teratosphaeria africana (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria alistairii (Crous) Crous & U. Braun, comb. nov., Teratosphaeria associata (Crous & Carnegie) Crous & U. Braun, comb. nov., Teratosphaeria bellula (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria cryptica (Cooke) Crous & U. Braun, comb. nov., Teratosphaeria dentritica (Crous & Summerell) Crous & U. Braun, comb. nov., Teratosphaeria excentrica (Crous& Carnegie) Crous & U. Braun, comb. nov., Teratosphaeria fimbriata (Crous & Summerell) Crous & U. Braun, comb. nov., Teratosphaeria flexuosa (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria gamsii (Crous) Crous & U. Braun, comb. nov., Teratosphaeria jonkershoekensis (P.S. van Wyk, Marasas & Knox-Dav.) Crous & U. Braun, comb. nov., Teratosphaeria maxii (Crous) Crous & U. Braun, comb. nov., Teratosphaeria mexicana (Crous) Crous & U. Braun, comb. nov., Teratosphaeria molleriana (Thüm.) Crous & U. Braun, comb. nov., Teratosphaeria nubilosa (Cooke) Crous & U. Braun, comb. nov., Teratosphaeria ohnowa (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria parkiiaffinis (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria parva (R.F. Park& Keane) Crous & U. Braun, comb. nov., Teratosphaeria perpendicularis (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria pluritubularis (Crous & Mansilla) Crous& U. Braun, comb. nov., Teratosphaeria pseudafricana (Crous & T.A. Cout.) Crous & U. Braun, comb. nov., Teratosphaeria pseudocryptica (Crous) Crous & U. Braun, comb. nov., Teratosphaeria pseudosuberosa (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria quasicercospora (Crous & T.A. Cout.) Crous & U. Braun, comb. nov., Teratosphaeria readeriellophora (Crous & Mansilla) Crous & U. Braun, comb. nov., Teratosphaeria secundaria (Crous & Alfenas) Crous & U. Braun, comb. nov., Teratosphaeria stramenticola (Crous & Alfenas) Crous& U. Braun, comb. nov., Teratosphaeria suberosa (Crous, F.A. Ferreira, Alfenas & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria suttonii (Crous & M.J. Wingf.) Crous & U. Braun, comb. nov., Teratosphaeria toledana (Crous & Bills) Crous& U. Braun, comb. nov., Teratosphaeriaceae Crous & U. Braun, fam. nov.     

Taxonomy and phylogenetic relationships of nine species of Hypocrea with anamorphs assignable to Trichoderma section Hypocreanum

Morphological studies and phylogenetic analyses of DNA sequences from the internal transcribed spacer (ITS) regions of the nuclear ribosomal gene repeat, a partial sequence of RNA polymerase II subunit (rpb2), and a partial sequence of the large exon of tef1 (LEtef1) were used to investigate the taxonomy and systematics of nine Hypocrea species with anamorphs assignable to Trichoderma sect. Hypocreanum. Hypocrea corticioides and H. sulphurea are reevaluated. Their Trichoderma anamorphs are described and the phylogenetic positions of these species are determined. Hypocrea sulphurea and H. subcitrina are distinct species based on studies of the type specimens. Hypocrea egmontensis is a facultative synonym of the older name H. subcitrina. Hypocrea with anamorphs assignable to Trichoderma sect. Hypocreanum formed a well-supported clade. Five species with anamorphs morphologically similar to sect. Hypocreanum, H. avellanea, H. parmastoi, H. megalocitrina, H. alcalifuscescens, and H. pezizoides, are not located in this clade. Protocrea farinosa belongs to Hypocrea s.s.Taxonomic novelties:Hypocrea eucorticioides Overton, nom. nov., Hypocrea victoriensis Overton, sp. nov., Hypocrea parmastoi Overton, sp. nov., Hypocrea alcalifuscescens Overton, sp. nov.     

利用SSR分子标记研究花生属种间亲缘关系

以5份花生栽培种资源和花生属六个区组的19份野生种资源为研究材料，通过SSR分子标记技术分析其DNA多态性并进行聚类分析。大多数从栽培种基因组分离出的SSR引物能在野生种中扩增出DNA片段，共筛选出21对多态性SSR引物；每对引物在花生基因组中扩增出的条带数为1～13条，在供试材料中扩增出的总条带数为5～40条，平均18.1条，其中多态性条带为4～40条，平均18.0条；SSR引物的多态性指数为0.92～9.04；供试材料间的遗传距离为0.33～0.91，平均0.76。结果表明，大多数花生SSR引物为多位点引物，花生属种间种质存在丰富的DNA多态性， A. duranensis是花生栽培种（A. hypogaea L.）的野生种亲本之一，与花生区组野生种亲缘关系最近的是异形花区组，最远的是大根区组。     

艾纳香属系统分类研究进展

回顾自Loureiro以来艾纳香属(Blumea de Candolle)分类和系统发育研究的历史沿革和取得的成就,并提出艾纳香属系统分类研究中亟待解决的问题。     

A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages

Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare rocks. Multigene phylogenetic analyses were used to study relationships of ascomycetes from a variety of substrates, with a dataset including a broad sampling of rock dwellers from different geographical locations. Rock-inhabiting fungi appear particularly diverse in the early diverging lineages of the orders Chaetothyriales and Verrucariales. Although these orders share a most recent common ancestor, their lifestyles are strikingly different. Verrucariales are mostly lichen-forming fungi, while Chaetothyriales, by contrast, are best known as opportunistic pathogens of vertebrates (e.g. Cladophialophora bantiana and Exophiala dermatitidis, both agents of fatal brain infections) and saprophytes. The rock-dwelling habit is shown here to be key to the evolution of these two ecologically disparate orders. The most recent common ancestor of Verrucariales and Chaetothyriales is reconstructed as a non-lichenised rock-inhabitant. Ancestral state reconstructions suggest Verrucariales as one of the independent ascomycetes group where lichenisation has evolved on a hostile rock surface that might have favored this shift to a symbiotic lifestyle. Rock-inhabiting fungi are also ancestral to opportunistic pathogens, as they are found in the early diverging lineages of Chaetothyriales. In Chaetothyriales and Verrucariales, specific morphological and physiological traits (here referred to as extremotolerance) evolved in response to stresses in extreme conditions prevailing on rock surfaces. These factors facilitated colonisation of various substrates including the brains of vertebrates by opportunistic fungal pathogens, as well as helped establishment of a stable lichen symbiosis.     

Multigene phylogeny and mating tests reveal three cryptic species related to Calonectria pauciramosa

Calonectria pauciramosa is a pathogen of numerous plant hosts worldwide. Recent studies have indicated that it included cryptic species, some of which are identified in this study. Isolates from various geographical origins were collected and compared based on morphology, DNA sequence data of the β-tubulin, histone H3 and translation elongation factor-1α regions and mating compatibility. Comparisons of the DNA sequence data and mating compatibility revealed three new species. These included Ca. colombiana sp. nov. from Colombia, Ca. polizzii sp. nov. from Italy and Ca. zuluensis sp. nov. from South Africa, all of which had distinguishing morphological features. Based on DNA sequence data, Ca. brasiliensis is also elevated to species level.Taxonomic novelties: Calonectria brasiliensis (Bat. & Cif.) L. Lombard, M.J. Wingf. & Crous, comb. nov., Calonectria colombiana L. Lombard, Crous & M.J. Wingf., sp. nov., Calonectria polizzii L. Lombard, Crous & M.J. Wingf., sp. nov., Calonectria zuluensis L. Lombard, Crous & M.J. Wingf., sp. nov.     

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

Background  

Science-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the attention focused on the non-coding displacement ("D") loop. We used massively parallel multiplexed sequencing to sequence complete mitochondrial genomes from 40 fishers, a threatened carnivore that possesses low mitogenomic diversity. This allowed us to test a key assumption of conservation genetics, specifically, that the D-loop accurately reflects genealogical relationships and variation of the larger mitochondrial genome.     

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

Background

When a specimen belongs to a species not yet represented in DNA barcode reference libraries there is disagreement over the effectiveness of using sequence comparisons to assign the query accurately to a higher taxon. Library completeness and the assignment criteria used have been proposed as critical factors affecting the accuracy of such assignments but have not been thoroughly investigated. We explored the accuracy of assignments to genus, tribe and subfamily in the Sphingidae, using the almost complete global DNA barcode reference library (1095 species) available for this family. Costa Rican sphingids (118 species), a well-documented, diverse subset of the family, with each of the tribes and subfamilies represented were used as queries. We simulated libraries with different levels of completeness (10-100% of the available species), and recorded assignments (positive or ambiguous) and their accuracy (true or false) under six criteria.

Results

A liberal tree-based criterion assigned 83% of queries accurately to genus, 74% to tribe and 90% to subfamily, compared to a strict tree-based criterion, which assigned 75% of queries accurately to genus, 66% to tribe and 84% to subfamily, with a library containing 100% of available species (but excluding the species of the query). The greater number of true positives delivered by more relaxed criteria was negatively balanced by the occurrence of more false positives. This effect was most sharply observed with libraries of the lowest completeness where, for example at the genus level, 32% of assignments were false positives with the liberal criterion versus < 1% when using the strict. We observed little difference (< 8% using the liberal criterion) however, in the overall accuracy of the assignments between the lowest and highest levels of library completeness at the tribe and subfamily level.

Conclusions

Our results suggest that when using a strict tree-based criterion for higher taxon assignment with DNA barcodes, the likelihood of assigning a query a genus name incorrectly is very low, if a genus name is provided it has a high likelihood of being accurate, and if no genus match is available the query can nevertheless be assigned to a subfamily with high accuracy regardless of library completeness. DNA barcoding often correctly assigned sphingid moths to higher taxa when species matches were unavailable, suggesting that barcode reference libraries can be useful for higher taxon assignments long before they achieve complete species coverage.     

用SSR分子标记研究茶组植物种间亲缘进化关系

本研究利用50对来自茶系的SSR引物对41份茶组资源进行PCR扩增,研究不同类型SSR引物的通用性和多样性指数。研究结果表明,茶系的SSR引物在茶组植物中的通用性高,其中EST-SSR通用性多态位点的比例达到60%。另外,利用SSR标记技术对茶组材料的遗传多样性进行分析。不同位点在种间的等位基因数为2～6个,平均每个位点4.21个等位基因。通过UPGMA方法构建了茶组12个种的遗传进化关系图。