Browsing by Subject "GENUS"

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  • Spirin, Viacheslav; Malysheva, Vera; Roberts, Peter; Trichies, Gérard; Savchenko, Anton; Larsson, Karl-Henrik (2019)
    Morphological and DNA data show that effused representatives of the Auriculariales (Basidiomycota) with sphaeropedunculate basidia belong to eleven genera of which seven are dealt with in this study. Among them, Myxarium is the largest genus containing 21 accepted species of which nine are reintroduced below and five are described as new. Protodontia is limited to three species only, P. subgelatinosa (the generic type) and two newly described species from Africa. Protoacia is a new monotypic genus for P. delicata, sp. nov., widely distributed on coniferous hosts in Eurasia. Myxariellum is erected for two new species with smooth hymenophore from northwestern North America while Gelacantha is introduced for G. pura, a new species with hydnoid hymenophore from Caucasus. Our data do not confirm the present synonymy of Sebacina sphaerospora with Tremella glaira, and these species are placed in two separate genera - Hydrophana, gen. nov., and Ofella, gen. nov., respectively. A key to European Myxarium and similar-looking species is included.
  • Howlader, Mohammad Sajid Ali; Nair, Abhilash; Gopalan, Sujith V.; Merilä, Juha (2015)
    A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species - designated here as Microhyla nilphamariensis sp. nov. - forms a clade with M. ornate, it is highly divergent from M. ornata and all of its congeners, with 5.7 - 13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril-snout length, internarial distance is roughly five times greater than nostril-snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermore, inner metacarpal tubercle is small and ovoid-shaped, whereas outer metacarpal tubercle is very small and rounded. Toes have rudimentary webbing, digital discs are absent, inner metatarsal tubercle is small and round, outer metatarsal tubercle is ovoid-shaped, minute, and indistinct.
  • Truong Nguyen, Phuoc; Garcia-Valle, Santiago; Puigbo, Pere (2021)
    Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host-virus relationships.
  • Hokynar, Kati; Salava, Alexander; Vesterinen, Eero; Lauerma, Antti; Ranki, Annamari; Puolakkainen, Mirja (2018)
  • Silva, Ximena; Roux, Jolanda; Asiegbu, Fred O. (2020)
    Background and objectives: The global forest economy is threatened by eucalypt pathogens which are often latent or cryptic species that escape common quarantine and detection methods. Plantation forestry using eucalypts is of considerable importance to Paraguay, but knowledge regarding the pests and diseases affecting these plantations is limited. This study identified fungal diseases present in these plantations. Materials and Methods: We surveyed eucalypt plantations in four provinces in Paraguay and collected material from diseased trees for identification of the causal agents. The samples were analyzed using a combination of morphological and molecular methods. Results: Diseases encountered included Botryosphaeria stem canker, Calonectria leaf blight, Chrysoporthe stem canker, myrtle/eucalypt rust, Coniella leaf spot, heartwood rot and Teratosphaeria stem canker. Contrary to expectations, the causal agent of Teratosphaeria stem canker was identified as Teratosphaeria zuluensis (M.J. Wingf., Crous & T.A. Cout.) M.J. Wingf. & Crous and not Teratosphaeria gauchensis (M.-N. Cortinas, Crous & M.J. Wingf.) M.J. Wingf. & Crous, that is commonly documented for the South American region. Conclusions: This study updates the knowledge on forest fungal pathogens in Paraguayan eucalypt plantations and is the first report of T. zuluensis in Paraguay and in South America.
  • Huemer, Peter; Karsholt, Ole; Aarvik, Leif; Berggren, Kai; Bidzilya, Olexey; Junnilainen, Jari Kalevi; Landry, Jean-Francois; Mutanen, Marko; Nupponen, Kari; Segerer, Andreas; Šumpich, Jan; Wieser, Christian; Wiesmair, Benjamin; Herbert, Paul D. N. D. N. (2020)
    For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.
  • Chen, Chi-Chuan; Hyvönen, Jaakko; Schneider, Harald (2020)
    The microsoroid ferns are one of the largest subfamilies of the Polypodiaceae with over 180 species mainly found in the humid forests of tropical Australasia. The phylogenetic relationships are still unclear, especially the delimitation of the genus Microsorum which has been recognized to be non-monophyletic. We analysed the microsoroid ferns using six chloroplast DNA regions (rbcL, rps4+rps4-trnS, trnL+trnL-trnF, atpA, atpB and matK) in order to present a robust hypothesis of their phylogeny. Our results suggest that they comprise up to 17 genera; of them, 12 agree with a previously accepted generic classification. Five tribes are proposed based on the phylogenetic relationships. Most of the species traditionally included in the genus Microsorum are found in six genera belonging to two tribes. In addition to the commonly used DNA markers, the additional atpA and matK are helpful to provide information about the phylogenetic relationships of the microsoroid ferns.
  • Ahti, Teuvo; Mayrhofer, Helmut; Schultz, Matthias; Tehler, Anders; Fryday, Alan M. (2016)
  • Launis, Annina; Pykälä, Juha; van den Boom, Pieter; Serusiaux, Emmanuel; Myllys, Leena (2019)
    In this study we clarify the phylogeny and reassess the current taxonomy of the Micarea prasina group, focusing especially on the M. byssacea and M. micrococca complexes. The phylogeny was investigated using ITS, mtSSU and Mcm7 regions from 25 taxa belonging to the M. prasina group. A total of 107 new sequences were generated. Data were analyzed using maximum parsimony and maximum likelihood methods. The results reveal five undescribed well-supported lineages. Four of the lineages represent new species described as Micarea pseudomicrococca Launis & Myllys sp. nov., M. czarnotae Launis, van den Boom, Serusiaux & Myllys sp. nov., M. microareolata Launis, Pykala & Myllys sp. nov. and M. laeta Launis & Myllys sp. nov. In addition, a fifth lineage was revealed that requires further study. Micarea pseudomicrococca is characterized by an olive green granular thallus, small cream-white or brownish apothecia lacking the Sedifolia-grey pigment and two types of paraphyses up to 2 mu m wide. Micarea czarnotae forms a granular, densely granular or continuous olive green thallus, convex to hemispherical apothecia often with the Sedifolia-grey pigment and no crystalline granules in the thallus. Micarea microareolata is characterized by a +/- pale green areolate thallus (composed of goniocysts), cream-white apothecia lacking the Sedifolia-grey pigment and narrow spores. Micarea laeta has a vivid to olive green granular thallus, pale apothecia lacking the Sedifolia-grey pigment and wider spores compared to M. microareolata. Descriptions, images and a key are provided for the new species. Crystalline granules are introduced as a novel species-level character for Micarea.
  • Kantelinen, Annina; Hyvärinen, Marko; Kirika, Paul; Myllys, Leena (2021)
    The genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila, M. stellaris, M. taitensis and M. versicolor. Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris, M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one (M. taitensis) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades.
  • Biffignandi, Gherard Batisti; Gibbon, Marjorie J.; Corbella, Marta; Thorpe, Harry A.; Merla, Cristina; Castelli, Michele; Kallonen, Teemu; Pegrum, Katie; Brisse, Sylvain; Corander, Jukka; Marone, Piero; Feil, Edward J.; Sassera, Davide (2021)
    During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50=615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage= 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and "Superficieibacter." An ortholog-based phylogenomic analysis indicated a sister group relationship with "Superficieibacter electus," in a distinct Glade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of "Superficiebacter," average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus "Superficieibacter." We propose for the new species the name "Superficieibacter maynardsmithii."
  • Malysheva, Vera; Schoutteten, Nathan; Verbeken, Annemieke; Spirin, Viacheslav (2021)
    The identity of Achroomyces effusus is re-established with the use of morphological and DNA methods, and a neotype is selected. The species is conspecific with Colacogloea peniophorae, the generic type of Colacogloea, and has a priority over it. A new combination, C. effusa, is proposed.
  • Vesth, Tammi C.; Nybo, Jane L.; Theobald, Sebastian; Frisvad, Jens C.; Larsen, Thomas O.; Nielsen, Kristian F.; Hoof, Jakob B.; Brandl, Julian; Salamov, Asaf; Riley, Robert; Gladden, John M.; Phatale, Pallavi; Nielsen, Morten T.; Lyhne, Ellen K.; Kogle, Martin E.; Strasser, Kimchi; McDonnell, Erin; Barry, Kerrie; Clum, Alicia; Chen, Cindy; LaButti, Kurt; Haridas, Sajeet; Nolan, Matt; Sandor, Laura; Kuo, Alan; Hainaut, Matthieu; Drula, Elodie; Tsang, Adrian; Magnuson, Jon K.; Henrissat, Bernard; Wiebenga, Ad; Simmons, Blake A.; Makela, Miia R.; de Vries, Ronald P.; Grigoriev, Igor V.; Mortensen, Uffe H.; Baker, Scott E.; Andersen, Mikael R. (2018)
    Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter-and intraspecies genomic variation. We further predicted 17,903 carbohydrateactive enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.
  • Mengual, Ximo; Ståhls, Gunilla; Skevington, Jeffrey H. (2020)
    Phylogenetic relationships of theSphaerophorialineage (SphaerophoriaLe Peletier & Audinet-Serville and related genera) were inferred based on molecular characters, with the specific aim to infer the phylogenetic placement of the AfrotropicalSphaerophoriaspecies andLoveridgeana beattieivan Doesburg & van Doesburg. Three molecular markers were used, i.e., the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. TheSphaerophorialineage generaExallandraVockeroth andLoveridgeanawere resolved within the genusSphaerophoria, and the IndomalayanEosphaerophoriaFrey was placed sister toCitrogrammaVockeroth, both related to a large species radiation from the New World.FaziaShannon andAllograptaOsten Sacken were recovered as non-monophyletic. Our results recovered two differentFaziaclades with dissimilar natural history resulted from our analyses, andAllograptaspecies were resolved into two clades, one with Nearctic and Neotropical species and a second clade with species from Oceanian, Indomalayan and Afrotropical Regions.Exallandrais considered a subgenus ofSphaerophoria,S. (Exallandra)stat. rev.,andSphaerophoria cinctifacies(Speiser)n. comb.a member of this subgenus together withS. loewiiZetterstedt. A newSphaerophoriasubgenus is designatedS.(Loveridgeana)stat. rev.to includeS. beattiein. comb.and the South African species, i.e.,S. quadrituberculataBezzi,S. retrocurvaHull, andS. aff.retrocurva. Based on their phylogenetic distinctiveness, functional traits, and ecological relevance we do recommend further ecological study and protection efforts for this Afrotropical group of pollinators.
  • Sasic, Ljiljana; Acanski, Jelena; Vujic, Ante; Ståhls, Gunilla; Radenkovic, Snezana; Milic, Dubravka; Vidakovic, Dragana Obreht; Dan, Mihajla (2016)
    The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Gunz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).
  • Brozzo, Alissa; Harl, Josef; De Mattia, Willy; Teixeira, Dinarte; Walther, Frank; Groh, Klaus; Pall-Gergely, Barna; Glaubrecht, Matthias; Hausdorf, Bernhard; Neiber, Marco T. (2020)
    The Geomitrini is the most species-rich group of land snails in the Madeiran Archipelago. The phylogeny of the group is reconstructed based on mitochondrial and nuclear genetic markers. The timing of diversification, the colonisation history of the islands of the Madeiran Archipelago and the evolution of characters of the dart apparatus are studied. The results of the phylogenetic analyses confirm the sister group relationship of Geomitrini and Cochlicellini, but also show that several previously accepted genus-group taxa are not monophyletic. A new classification for the Geomitrini is proposed, including the description of two new genera, Domunculifex Brozzo, De Mattia, Harl & Neiber, n. gen. and Testudodiscula Brozzo, De Mattia, Harl & Neiber, n. gen. The onset of diversification of Geomitrini was dated in our analysis at 13 Ma, which largely coincides with the emergence of the present-day islands. The ancestral state estimation recovered the presence of two appendiculae in the reproductive system as the ancestral state in Geomitrini. One appendicula was lost three times independently within the tribe and is even missing completely in one group. The ancestral area estimation suggests recurrent colonisations of Madeira (and the Ilhas Desertas) from the older island Porto Santo.
  • Sihvonen, Pasi; Murillo-Ramos, Leidys; Brehm, Gunnar; Staude, Hermann; Wahlberg, Niklas (2020)
    A multigene phylogenetic study was carried out to test current, mostly morphology-based hypotheses on Sterrhinae phylogeny with additional material included from further geographical areas and morphologically different lineages. A maximum likelihood analysis (11 molecular markers and 7665 bp) was conducted on 76 species and 41 genera using iq-tree software. The resulting phylogenetic hypothesis is well resolved and branches have high support values. Results generally agree with earlier hypotheses at tribal levels and support the hypothesis that Sterrhinae comprises two major lineages. Based on the molecular phylogeny and extensive morphological examination, nine tribes are considered valid and the following taxonomic changes are introduced to recognize monophyletic groups: Mecoceratini Guenee, 1858 (= Ametridini Prout, 1910) is transferred from Desmobathrinae to Sterrhinae, and it is considered valid at tribal level new classification; Haemaleini Sihvonen & Brehm is described as a new tribe and deemed sister to Scopulini + Lissoblemmini; Lissoblemmini Sihvonen & Staude is described as a new tribe and sister to Scopulini; Lythriini Herbulot, 1962 is now a junior synonym of Rhodometrini Agenjo, 1952 syn.n.; and Rhodostrophiini Prout, 1935 is now a junior synonym of Cyllopodini Kirby, 1892 syn.n. In addition, 48 taxa are transferred from other geometrid subfamilies to Sterrhinae, or within Sterrhinae from one tribe to another, or they are classified into a tribe for the first time, or a new genus classification is proposed. The results demonstrate the limited explanatory power of earlier classifications, particularly at the tribal level. This is probably a result of earlier classifications being based on superficial characters and biased towards the European and North American fauna. The species richness and distribution of Sterrhinae and its constituent tribes are reviewed, showing that the globally distributed Sterrhinae are most diverse in the Neotropics (31% of global fauna). They are species-rich in the Palaearctic (22%), Afrotropics (19%) and Indo-Malay (16%) regions, whereas they are almost absent in Oceania (1%). In terms of the described fauna, the most species-rich tribes are Scopulini (928 species), Sterrhini (876 species) and Cosymbiini (553 species), all of which have a cosmopolitan distribution. Mecoceratiini and Haemaleini are almost entirely Neotropical. Timandrini and Lissoblemmini, by contrast, are absent in the Neotropics. We present a revised classification of the global Sterrhinae fauna, which includes about 3000 putatively valid species, classified into nine tribes and 97 genera. Four genera are of uncertain position within Sterrhinae. Our results highlight the compelling need to include more genera from a global perspective in molecular phylogenetic studies, in order to create a stable global classification for this subfamily. This published work has been registered on ZooBank, :pub:A66F5DDD-06D6-4908-893E-E8B124BB99B1.
  • Malysheva, Vera; Spirin, Viacheslav; Miettinen, Otto; Kout, Jiří; Savchenko, Anton; Larsson, Karl-Henrik (2019)
    In the present paper, we select a neotype for Tremella cerasi and prove that it is conspecific with Ditangium insigne (the genus type of Ditangium). We argue that Ditangium should be restored as a correct genus for T. cerasi, while the currently used generic name Craterocolla is to be treated as its younger synonym. Morphological, ecological and genetic variability of Ditangium cerasi is discussed, and two other Ditangium species are described—D. altaicum, sp. nov. and D. incarnatum, comb. nov. In addition, Exidia fulva is combined in Globulisebacina.
  • Spirin, Viacheslav; Malysheva, Vera; Larsson, Karl-Henrik (2018)
    As shown by morphological and molecular (ITS, nrLSU and tef1 sequences) evidence, the current concept of Myxarium nucleatum covers four species in the Nordic countries: M. cinnamomescens, M. hyalinum, M. nucleatum s.s. and M. populinum. These species are redescribed here, their nomenclature is discussed and all relevant names are typified. Exidia cartilaginea and E. villosa are typified and shown to be conspecific with the North American species E. candida. Based on morphological differences, E. cartilaginea is retained as a variety of E. candida. Exidia subrepanda is treated as a synomym of E. saccharina, and Heterochaete europaea as a synomym of E. thuretiana.