Phenotypic and genotypic identification and phylogenetic characterisation of <Emphasis Type="Italic">Taphrina</Emphasis> fungi on alder

All Taphrina species are dimorphic with a mycelium stage biotrophic on vascular plants and a saprophytic yeast stage. European species of Taphrina on Alnus species (Betulaceae) were identified using morphological, physiological and molecular characteristics, the latter including determination of PCR fingerprints and of nucleotide sequences from selected nuclear ribosomal DNA regions. PCR fingerprinting gives a good overview of species identification, as do nucleotide sequences, which in addition, help to clarify phylogenetic relationships. Taphrina alni is a homogeneous species that exhibited more than 50% similarity in PCR fingerprinting with three different primers. Morphologically, it produces tongue-like outgrowths from female catkins of Alnus incana. Taphrina robinsoniana from A. rugosa and A. serrulata in North America is phylogenetically closely related to T. alni, but the two species could be separated by their PCR fingerprints, partial sequences of 26S rDNA (D1/D2) and ITS1/ITS2 sequences. T. epiphylla and T. sadebeckii are two phylogenetically closely related species. T. epiphylla causes witches brooms in crowns of A. incana. In addition, T. epiphylla forms slightly yellow white-grey leaf spots in midsummer on A. incana. Yellow white-grey leaf spots up to 10 mm on A. glutinosa are characteristic for T. sadebeckii. Both species can be separated well by PCR fingerprinting. Different from T. epiphylla, T. sadebeckii is genotypically more heterogeneous. Only two out of three different primers showed similarity values above 50% in different European strains of T. sadebeckii. Although genetic variability was not detected in complete sequences of the 18S ribosomal DNA of T. sadebeckii, ITS1/ITS2 sequences appeared to be more heterogeneous, too. Taphrina tosquinetii is a genotypically homogeneous species causing leaf curl on Alnus glutinosa. It was not possible to distinguish the yeast phases from different Taphrina species on Alnus using morphological and physiological characteristics only. Dedicated to Prof. Dr. Hanns Kreisel on the occasion of his 70^th birthday     

Description of a new small-sized Synodontis species (Siluriformes: Mochokidae) that is important for local subsistence fisheries in the middle Lufira (upper Congo River,DR Congo)

Synodontis denticulatus sp. nov. is an endemic from the middle Lufira Basin and its associated tributaries and lakes. The species shows close morphological resemblance to Synodontis greshoffi and Synodontis unicolor, which are widespread Congo Basin and Bangweulu-Mweru endemic species, respectively. However, it differs from both S. greshoffi and S. unicolor by its non-villous skin (v. villous skin), strong and numerous serrations on the posterior margin of the dorsal spine (v. weak and fewer serrations), weak and few serrations on the posterior margin of the pectoral spine (v. strong and numerous serrations), relatively short maxillary barbels (v. long) and its small maximum standard length (89.1 mm L_S v. 148.0 and 190.7 mm L_S respectively). A DNA barcoding study (coI, mtDNA) revealed that S. denticulatus forms a distinct genetic clade with a genetic distance of 2.18% with S. greshoffi and 0.84% with S. unicolor. Synodontis denticulatus is caught regularly and abundantly as a by-catch in the gillnet fisheries in the middle Lufira lakes. Owing to its small overall size and large bony head, the species has usually no real commercial value but is an important food fish for the fishermen's families.     

Genetic analysis of Japanese and American specimens of <Emphasis Type="Italic">Scirpus hattorianus</Emphasis> suggests its introduction from North America

Scirpus hattorianus is a possible alien species in Japan, and a clarification of its unclear taxonomy is required to reveal its origin. It is not known whether the plants initially described from Japan represent the same species distributed in North America. To clarify the origin of the species, we attempted to sequence old specimens collected about 80 years ago using newly designed primer pairs specific for short sequences, including the variable sites. Chloroplast sequences of ndhF were compared among Japanese and North American S. hattorianus, and the closely related species, S. atrovirens, S. flaccidifolius, and S. georgianus. We succeeded in sequencing all samples, and two haplotypes were detected in S. hattorianus: one was unique to the species and the other, detected from specimens potentially collected from the same population as the types, was shared by both North American S. hattorianus and two closely related species, S. atrovirens and S. flaccidifolius. Our results suggest that Japanese S. hattorianus is an alien species that was introduced from North America at least twice.     

The coralline genera Sporolithon and Heydrichia (Sporolithales,Rhodophyta) clarified by sequencing type material of their generitypes and other species

Interspecific systematics in the red algal order Sporolithales remains problematic. To re‐evaluate its species, DNA analyses were performed on historical type material and recently collected specimens assigned to the two genera Sporolithon and Heydrichia. Partial rbcL sequences from the lectotype specimens of Sporolithon ptychoides (the generitype species) and Sporolithon molle, both from El Tor, Egypt, are exact matches to field‐collected topotype specimens. Sporolithon crassum and Sporolithon erythraeum also have the same type locality; material of the former appears to no longer exist, and we were unable to PCR amplify DNA from the latter. A new species, Sporolithon eltorensis, is described from the same type locality. We have not found any morpho‐anatomical characters that distinguish these three species. No sequenced specimens reported as S. ptychoides from other parts of the world represent this species, and likely reports of S. ptychoides and S. molle based on morpho‐anatomy are incorrect. A partial rbcL sequence from the holotype of Sporolithon dimotum indicates it is not a synonym of S. ptychoides, and data from the holotype of S. episporum confirm its specific recognition. DNA sequences from topotype material of Heydrichia woelkerlingii, the generitype species, and isotype material of Heydrichia cerasina confirm that these are distinct species; the taxon reported to be H. woelkerlingii from New Zealand is likely an undescribed species. Type specimens of all other Sporolithon and Heydrichia species need to be sequenced to confirm that they are distinct species; morpho‐anatomical studies have proved inadequate for this task.     

Fungal Communities in Decaying Sapwood and Heartwood of a Conifer <Emphasis Type="Italic">Keteleeria evelyniana</Emphasis>

Fungal communities in decaying sapwood and heartwood of K. evelyniana were demonstrated through construction of four 18 S rRNA gene libraries. The 210 sequenced clones were clustered into 11 subgroups, belonging to Basidiomycota (71.9%) and to Ascomycota (22.4%) and unclassified (1 subgroup; 5.7%). The heartwood displayed higher species richness than the sapwood. Basidiomycota were dominant in either the heartwood or the sapwood. Phylogenetically diverse Homobasidiomycetes were detected in the heartwood, contrary to the sapwood, where Heterobasidiomycetes were detected. Clones close to Spongipellis unicolor dominated in the heartwood (21 of 99 clones), while those close to Hydnochaete olivacea dominated in the sapwood (41 of 111 clones). The common species between the two parts were those related to S. unicolor, Calocera cornea, Debaryomyces hansenii, Davidiella tassiana, and Nomuraea rileyi and those from Chaetothyriomycetes.     

Notes on <Emphasis Type="Italic">Swartzia</Emphasis> (Leguminosae) in Central America preliminary to the Flora Mesoamericana,with descriptions of two new species from Costa Rica

In preparation of a treatment of Swartzia (Leguminosae) for the Flora Mesoamericana, recent updates to the taxonomy of the genus in Central America are discussed, and two new species from the Pacific slope and lowlands of central and southern Costa Rica are described and illustrated. One of them, S. picramnioides, is a member of the section Possira and is closely related to S. standleyi of Guatemala and Belize and to the South American species S. myrtifolia. The other, S. zeledonensis, belongs to the Central American apetalous clade of section Terminales. It is probably most closely related to the Panamanian species, S. nuda. We conclude that Swartzia is represented in Mexico and Central America by 14 species and provide a key for their identification.     

A Comparative and Phylogenetic Study of the Ditylenchus dipsaci,Ditylenchus destructor and Ditylenchus gigas Populations Occurring in Poland

The genus Ditylenchus contains more than 80 recognized nematode species with a very wide host range. The most serious species are Ditylenchus dipsaci and Ditylenchus destructor. Populations of D. dipsaci species complex were collected from Allium cepa, Cichorium endivia and Phlox paniculata in Poland. The Ditylenchus gigas population was collected from Vicia faba minor, and populations of D. destructor, from Solanum tuberosum spp. tuberosum. Analyses of the rDNA sequences spanning both ITS1 and ITS2 fragment regions were carried out on the collected populations. The obtained DNA sequences were compared with those DNA sequences deposited in GenBank of populations isolated in other countries. Phylogenetic analysis was performed using the data obtained from the DNA sequence comparisons. The results indicated that there is no clear distinction between European and non‐European populations within D. dipsaci. The results also showed no clear distinction between populations isolated from different host plant species, including populations found in Poland. The populations of D. destructor described here constitute a common group together with American and Chinese populations belonging to the haplotype C of the D. destructor species. On the other hand, the D. gigas population was localized separately from those populations that have been described up until now, from Europe and Africa. This is also the first report on the occurrence of D. gigas in Poland.     

Phylogenetic relationships among Neoechinorhynchus species (Acanthocephala: Neoechinorhynchidae) from North-East Asia based on molecular data

Phylogenetic and statistical analyses of DNA sequences of two genes, cytochrome oxidase subunit 1 (cox 1) of the mitochondrial DNA and 18S subunit of the nuclear ribosomal RNA (18S rRNA), was used to characterize Neoechinorhynchus species from fishes collected in different localities of North-East Asia. It has been found that four species can be clearly recognized using molecular markers—Neoechinorhynchus tumidus, Neoechinorhynchus beringianus, Neoechinorhynchus simansularis and Neoechinorhynchus salmonis. 18S sequences ascribed to Neoechinorhynchus crassus specimens from North-East Asia were identical to those of N. tumidus, but differed substantially from North American N. crassus. We renamed North-East Asian N. crassus specimens to N. sp., although the possibility that they represent a subspecies of N. tumidus cannot be excluded, taking into account a relatively small distance between cox 1 sequences of North-East Asian specimens of N. crassus and N. tumidus. Maximum likelihood, maximum parsimony and Bayesian inference analyses were performed for phylogeny reconstruction. All the phylogenetic trees showed that North-East Asian species of Neoechinorhynchus analyzed in this study represent independent clades, with the only exception of N. tumidus and N. sp. for 18S data. Phylogenetic analysis has shown that the majority of species sampled (N. tumidus + N. sp., N. simansularis and N. beringianus) are probably very closely related, while N. salmonis occupies separate position in the trees, possibly indicating a North American origin of this species.     

<Emphasis Type="Italic">Rhodocollybia</Emphasis> in neotropical montane forests

Traditional concepts of Collybia (Agaricales) have included a variety of morphologically disparate taxa. Reapplication of some characters used in circumscribing Collybia s.l. suggests realignment of well-known North American and European species into three genera, viz. Collybia s.s, Rhodocollybia, and Gymnopus. Rhodocollybia is recognized here at generic rank based on morphological characteristics and phylogenetic signaling. Seven new species epithets under Rhodocollybia, and a new combination under Gymnopus, are proposed. A key to species of Rhodocollybia found in neotropical montane forests is provided.     

Prosthecium species with Stegonsporium anamorphs on Acer

Data from microscopic morphology, single-spore cultures, and DNA analyses of teleomorphs and anamorphs support the recognition of five species of Prosthecium with Stegonsporium anamorphs on Acer: P. acerinum sp. nov., the teleomorph of S. acerinum; P. acerophilum comb. nov., formerly known as Dictyoporthe acerophila; P. galeatum comb. nov., originally described as Massaria galeata; P. opalus sp. nov.; and P. pyriforme sp. nov., the teleomorph of S. pyriforme s. str. The morphology of both type specimens and freshly collected material was investigated. The teleomorphs have brown ellipsoidal ascospores with five distosepta and often a longitudinal distoseptum. The anamorphs of all species described here belong to Stegonsporium; their connection to the Prosthecium teleomorphs was demonstrated by morphology and DNA sequences of single spore cultures derived from both ascospores and conidia. The anamorphs and teleomorphs of all five Prosthecium species are described and illustrated by LM images, and a key to these species is provided. As perceived from this work, S. pyriforme is restricted to Europe and does not occur in North America, whereas S. acerinum is restricted to North America, not found in Europe. The host associations given in the literature are revised and evidence is provided that only A. opalus, A. pseudoplatanus, and A. saccharum are confirmed hosts of Prosthecium with Stegonsporium anamorphs. Molecular phylogenetic analyses of tef1, ITS rDNA, and partial nuLSU rDNA sequences confirm that the species with Stegonsporium anamorphs are closely related to P. ellipsosporum, the generic type species. Stilbospora macrosperma is confirmed as the anamorph of P. ellipsosporum by DNA data of single spore isolates obtained from both ascospores and conidia.     

A critical review on some closely related species of <Emphasis Type="Italic">Tetranychus</Emphasis> sensu stricto (Acari: Tetranychidae) in the public DNA sequences databases

Taxonomic misidentification of the specimens used to obtain DNA sequences is a growing problem reported for different groups of organisms, which threatens the utility of the deposited sequences in public DNA databases. This paper provides new evidence of misidentifications in molecular DNA public databases in phytophagous mites of the Tetranychidae family belonging to the group Tetranychus (Tetranychus). Several species in this group are of economic and quarantine importance in agriculture and among them Tetranychus urticae, a highly polyphagous mite causing outbreaks in many crops worldwide, is certainly the most studied. We analyzed and evaluated the identity of 105 GenBank accessions of ITS2 rDNA and 138 COI mtDNA sequences which were deposited as T. urticae and those of 14 other taxa morphologically closely related to Tetranychus sensu stricto. In addition, ITS2 and COI sequences of 18 T. urticae samples collected for this study and identified by morphological criteria, were generated and included in the analyzed dataset. Among the deposited sequences in the GenBank database, numerous cases of apparently mistaken identities were identified in the group Tetranychus s. str., especially between T. urticae, T. cinnabarinus, T. kanzawai and T. truncatus. Unreliable sequences (misidentified or dubious) were estimated at nearly 30%. In particular the analysis supports the invalidity of the controversial species status of T. cinnabarinus. More generally, it highlights the need of using combined morphological and molecular approaches to guarantee solid species diagnostics for reliable sequence accessions in public databases.     

Genetic Identification of Western Mediterranean Sturgeons and its Implication for Conservation

To date, the only native sturgeon species in Western Europe was believed to be Acipenser sturio. However, this species is currently restricted to the Gironde River (Southern France), and it poses serious difficulties for rearing in captivity and for using in recovery programme. Furthermore, it has been questioned whether A. sturio is in fact the only species within the rivers of Western Europe, as A. naccarii, a species previously considered endemic of the Adriatic region, has been reported from the Iberian Peninsula in recent years. Here, we have used forensic techniques to obtain DNA from several museum specimens of sturgeons caught in the Spanish Guadalquivir River and in other European rivers. We analysed DNA sequences from these specimens for five genetic markers (three nuclear and two mitochondrial regions), which were subsequently compared with sequences obtained from A. sturioand A. naccarii. Our study demonstrates that A. naccarii coexists withA. sturio, from the Adriatic Sea to the Iberian Peninsula, a finding that could be taken into account in future sturgeon recovery programmes in Western Europe.     

Epibiotic <Emphasis Type="Italic">Vibrio</Emphasis> Luminous Bacteria Isolated from Some Hydrozoa and Bryozoa Species

Luminous bacteria are isolated from both Hydrozoa and Bryozoa with chitinous structures on their surfaces. All the specimens of the examined hydroid species (Aglaophenia kirchenpaueri, Aglaophenia octodonta, Aglaophenia tubiformis, Halopteris diaphana, Plumularia setacea, Ventromma halecioides), observed under blue light excitation, showed a clear fluorescence on the external side of the perisarc (chitinous exoskeleton) around hydrocladia. In the bryozoan Myriapora truncata, luminous bacteria are present on the chitinous opercula. All the isolated luminous bacteria were identified on the basis of both phenotypic and genotypic analysis. The isolates from A. tubiformis and H. diaphana were unambiguously assigned to the species Vibrio fischeri. In contrast, the isolates from the other hydroids, phenotypically assigned to the species Vibrio harveyi, were then split into two distinct species by phylogenetic analysis of 16S rRNA gene sequences and DNA–DNA hybridization experiments. Scanning electron microscopy analysis and results of culture-based and culture-independent approaches enabled us to establish that luminous vibrios represent major constituents of the bacterial community inhabiting the A. octodonta surface suggesting that the interactions between luminous bacteria and the examined hydrozoan and bryozoan species are highly specific. These interactions might have epidemiological as well as ecological implications because of the opportunistic pathogenicity of luminous Vibrio species for marine organisms and the wide-distribution of the hydrozoan and bryozoan functioning as carriers.     

Deep‐sea anglerfishes (Lophiiformes: Ceratioidei) from the western North Atlantic: Testing the efficacy of DNA barcodes

The taxonomy of ceratioid fishes is challenging and frequently based on a small number of female specimens described for each species. Twenty ceratioid specimens caught on Flemish Cap and Grand Bank (western North Atlantic), representing 12 species and six families: Ceratias holboelli and Cryptopsaras couesii (Ceratiidae); Himantolophus albinares (Himantolophidae); Melanocetus johnsonii (Melanocetidae); Lophodolos acanthognathus, Oneirodes eschrichtii, Dolopichthys karsteni, and Leptacanthichthys gracilispinis (Oneirodidae); Caulophryne polynema (Caulophrynidae); and Haplophryne mollis, Linophryne brevibarbata, and L. bicornis (Linophrynidae) were identified by examination of morphological characters. DNA barcode sequences, from the 5′ end of the COI mitochondrial gene, were developed for 18 specimens and compared with all ceratioid barcode sequences available in public repositories. The analyses extended the ranges of some quantitative traits for certain species, highlighted the possible existence of cryptic species in C. couesii with distinct ranges in the Atlantic and Pacific oceans, and indicated a close relationship between Bertella and Dolopichthys meriting further attention. The authoritative identification of the 18 voucher specimens made possible detection of erroneous identifications of some sequences extracted from the repositories and highlighting of taxonomic conflicts that should be the subject of future studies.     

On polyphyly of the former section Ochlopoa and the hybridogenic section Acroleucae (Poa,Poaceae): insights from molecular phylogenetic analyses

In this study, sequence data from the inert nuclear region ITS1‐5.8S rDNA‐ITS2 and the chloroplast region trnL–F, as well as a few morphological characters, are analysed to the relationships among known annual Poa (bluegrasses). It is shown that all taxa from the Poa annua aggregate distinguished by lemma characters and growth form have identical ITS and trnL–trnF sequences, all ITS sequences of this aggregate are the same as thethose of P. supina, and all trnL–trnF sequences are homologous with those of P. infirma. Furthermore, no differences were found between unusual morphotypes of P. supina with short spinules on their panicle branches and typical plants, but Siberian samples were found to have a slightly differentiated trnL–trnF region. These results suggest a hybrid origin of the Asian annual bluegrasses. Their maternal genome is close to that of P. sect. Homalopoa, but their ITS sequences are different. Some ITS sequences from annual Asian bluegrasses are resolved among representatives of P. sect. Stenopoa while for other (morphologically closely similar) species they fall in a clade with representatives of P. sect. Malacanthae. The latter group is distant from P. sect. Ochlopoa and is better treated as a separate section, viz P. sect. Acroleucae. The American annual bluegrasses are heterogeneous and also rather distant from P. sect. Ochlopoa. Poa chapmaniana, a species with cleistogamic flowers, is nested among the basal Subantarctic sections, far away from the taxa with which it has previously been considered related. It is indeed closer to P. sect. Ochlopoa than to other annual American bluegrasses. Thus, the studied annual species in fact belong to four independent evolutionary lines (or six including the separate genus Eremopoa and the Turkish Poa jubata), one of which, Acroleucae, has gone through three reticulation events. As in previous studies, our analysis did not support the generic status of P. sect. Ochlopoa.     

Morphological and molecular characterization of <Emphasis Type="Italic">Mariannaea aquaticola</Emphasis> sp. nov. collected from freshwater habitats

Mariannaea aquaticola sp. nov. is described, illustrated, and compared with closely related taxa. Phylogenetic analysis of rDNA ITS and 28S sequences show that Mariannaea aquaticola has affinity with Nectriaceae, which is in agreement with other Mariannaea species. Other morphologically similar genera such as Verticillium and Clonostachys are shown to be phylogenetically distant to Mariannaea. The generic concept of Mariannaea is discussed, and the affinity to Nectriaceous teleomorphs is suggested as additional generic character. A key to Mariannaea species is provided.