Browsing by Subject "TAXONOMY"

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  • Cheng, Lu; Walker, Alan W.; Corander, Jukka (2012)
  • Radenkovic, Snezana; Velickovic, Nevena; Ssymank, Axel; Vidakovic, Dragana Obreht; Djan, Mihajla; Ståhls, Gunilla; Veselic, Sanja; Vujic, Ante (2018)
    An ongoing study of the genus Merodon Meigen, 1803 in the Republic of South Africa (RSA) has revealed the existence of new species related to M. melanocerus Bezzi, 1915. The M. melanocerus subgroup belongs to the Afrotropical lineage of the M. desuturinus group. Revision of all available material from museums and detailed analyses of newly -collected specimens from our own expeditions to RSA resulted in delimitation of five species: M. capensis Hurkmans sp. n., M. commutabilis Radenkovic et Vujic sp. n., M. drakonis Vujic et Radenkovic sp. n., M. flavocerus Hurkmans sp. n. and M. melanocerus. In addition to classical morphological characters, sequences of the mitochondrial COI gene are provided for four related taxa. Results of molecular phylogenetic analyses supports monophyly of the M. desuturinus group and confirmed delimitation between species. Links between Palaearctic and Afrotropical faunas of this group, as well as possible evolutionary paths, are discussed. Based on phylogenetic analyses, four lineages (putative subgenera) have been recognized within the genus Merodon; besides the three previously established ones, albifrons+desuturinus, aureus (sensu lato) and avidus-nigritarsis, one new lineage named natans is distinguished.
  • Laiho, Juha; Ståhls, Gunilla (2013)
    A majority of the known Colias species (Lepidoptera: Pieridae, Coliadinae) occur in the mountainous regions of Central-Asia, vast areas that are hard to access, rendering the knowledge of many species limited due to the lack of extensive sampling. Two gene regions, the mitochondrial COI ‘barcode’ region and the nuclear ribosomal protein RpS2 gene region were used for exploring the utility of these DNA markers for species identification. A comprehensive sampling of COI barcodes for Central-Asian Colias butterflies showed that the barcodes facilitated identification of most of the included species. Phylogenetic reconstruction based on parsimony and Neighbor-Joining recovered most species as monophyletic entities. For the RpS2 gene region species-specific sequences were registered for some of the included Colias spp. Nevertheless, this gene region was not deemed useful as additional molecular ‘barcode’. A parsimony analysis of the combined COI and RpS2 data did not support the current subgeneric classification based on morphological characteristics
  • Hakala, Sanja Maria; Seppä, Perttu; Heikkilä, Maria; Punttila, Pekka; Sorvari, Jouni; Helanterä, Heikki (2018)
    Coptoformica Muller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.
  • 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."
  • Spirin, Viacheslav; Malysheva, Vera; Miettinen, Otto; Vlasak, Josef; Mendes Alvarenga, Renato Lucio; Gibertoni, Tatiana Baptista; Ryvarden, Leif; Larsson, Karl-Henrik (2019)
    The taxonomy of Protomerulius and Heterochaetella is revised based on DNA data and morphological evidence, and their type species, P. brasiliensis and H. dubia, are proved to be congeneric. As a consequence, H. dubia and related species, of which four are described as new, are placed in Protomerulius. Heterochaete microspora is also combined in Protomerulius, and the genus concept is redefined to encompass effused species with smooth or spiny hymenophore and monomitic hyphal structure. Psilochaete multifora, gen. and spec. nov. is a distant relative of Protomerulius spp. found in Norway. Heterochaetella cystidiophora is re-collected in Brazil and placed in the synonyms of Heterochaete sanctae-catharinae. This species does not belong to the Protomerulius-Heterochaetella lineage, and it is transferred to Metulochaete, gen. nov.
  • Aivelo, Tuomas; Medlar, Alan (2018)
    Despite metabarcoding being widely used to analyse bacterial community composition, its application in parasitological research remains limited. What interest there has been has focused on previously intractable research settings where traditional methods are inappropriate, for example, in longitudinal studies and studies involving endangered species. In settings such as these, non-invasive sampling combined with metabarcoding can provide a fast and accurate assessment of component communities. In this paper we review the use of metabarcoding in the study of helminth communities in wild mammals, outlining the necessary procedures from sample collection to statistical analysis. We highlight the limitations of the metabarcoding approach and speculate on what type of parasitological study would benefit from such methods in the future.
  • Finn, Robert D.; Bateman, Alex; Clements, Jody; Coggill, Penelope; Eberhardt, Ruth Y.; Eddy, Sean R.; Heger, Andreas; Hetherington, Kirstie; Holm, Liisa; Mistry, Jaina; Sonnhammer, Erik L. L.; Tate, John; Punta, Marco (2014)
  • Runnel, Kadri; Miettinen, Otto; Lohmus, Asko (2021)
    Polyporous fungi, a morphologically delineated group of Agaricomycetes (Basidiomycota), are considered well studied in Europe and used as model group in ecological studies and for conservation. Such broad interest, including widespread sampling and DNA based taxonomic revisions, is rapidly transforming our basic understanding of polypore diversity and natural history. We integrated over 40,000 historical and modern records of polypores in Estonia (hemiboreal Europe), revealing 227 species, and including Polyporus submelanopus and P. ulleungus as novelties for Europe. Taxonomic and conservation problems were distinguished for 13 unresolved subgroups. The estimated species pool exceeds 260 species in Estonia, including at least 20 likely undescribed species (here documented as distinct DNA lineages related to accepted species in, e.g., Ceriporia, Coltricia, Physisporinus, Sidera and Sistotrema). Four broad ecological patterns are described: (1) polypore assemblage organization in natural forests follows major soil and tree-composition gradients; (2) landscape-scale polypore diversity homogenizes due to draining of peatland forests and reduction of nemoral broad-leaved trees (wooded meadows and parks buffer the latter); (3) species having parasitic or brown-rot life-strategies are more substrate-specific; and (4) assemblage differences among woody substrates reveal habitat management priorities. Our update reveals extensive overlap of polypore biota throughout North Europe. We estimate that in Estonia, the biota experienced ca. 3-5% species turnover during the twentieth century, but exotic species remain rare and have not attained key functions in natural ecosystems. We encourage new regional syntheses on long studied fungal groups to obtain landscape-scale understanding of species pools, and for elaborating fungal indicators for biodiversity assessments.
  • Miettinen, Otto; Spirin, Viacheslav; Vlasák, Josef; Rivoire, Bernard; Stenroos, Soili; Hibbett, David (2016)
    We explored whether DNA-phylogeny-based and morphology-based genus concepts can be reconciled in the basidiomycete family Phanerochaetaceae. Our results show that macromorphology of fruiting bodies and hymenophore construction do not reflect monophyletic groups. However, by integrating micromorphology and re-defining genera, harmonization of DNA phylogeny and morphological genus concepts is possible in most cases. In the case of one genus (Phlebiopsis), our genetic markers could not resolve genus limits satisfactorily and a clear morphological definition could not be identified. We combine extended species sampling, microscopic studies of fruiting bodies and phylogenetic analyses of ITS, nLSU and rpb1 to revise genus concepts. Three new polypore genera are ascribed to the Phanerochaetaceae: Oxychaete gen. nov. (type Oxyporus cervinogilvus), Phanerina gen. nov. (type Ceriporia mellea), and Riopa (including Ceriporia metamorphosa and Riopa pudens sp. nov.). Phlebiopsis is extended to include Dentocorticium pilatii, further species of Hjortstamia and the monotypic polypore genus Castanoporus. The polypore Ceriporia inflata is combined into Phanerochaete. The identity of the type species of the genus Riopa, R. davidii, has been misinterpreted in the current literature. The species has been included in Ceriporia as a species of its own or placed in synonymy with Ceriporia camaresiana. The effort to properly define R. davidii forced us to study Ceriporia more widely. In the process we identified five closely related Ceriporia species that belong to the true Ceriporia clade (Irpicaceae). We describe those species here, and introduce the Ceriporia pierii group. We also select a lectotype and an epitype for Riopa metamorphosa and neotypes for Sporotrichum aurantiacum and S. aurantium, the type species of the anamorphic genus Sporotrichum, and recommend that teleomorphic Riopa is conserved against it.
  • Malysheva, Vera; Spirin, Viacheslav; Miettinen, Otto; Motato-Vasquez, Viviana; Hernawati,; Seelan, Jaya Seelan Sathiya; Larsson, Karl-Henrik (2018)
    Three species currently addressed to Protohydnum (Auriculariales) are studied with morphological and DNA methods. The genus Protohydnum is retained for the type species only, P. cartilagineum, recently re-collected in Brazil. The European species, P. piceicola, is not congeneric with P. cartilagineum and, therefore, placed in its own genus, Hyalodon, gen. nov. Another Hyalodon species, H. antui, is described from East Asia. The third member of Protohydnum sensu lato, P. sclerodontium from South-East Asia, is transferred to Elmerina.
  • Fukushima, Caroline Sayuri; Mendoza, Jorge Ivan; West, Rick C.; Longhorn, Stuart; Rivera, Emmanuel; Cooper, Ernst W. T.; Henaut, Yann; Henriques, Sergio; Cardoso, Pedro (2019)
    Background CITES is an international agreement between governments to ensure that international trade in specimens of wild animals and plants does not threaten their survival. Regarding spiders, all species listed in CITES are tarantulas. They are included in Appendix II, meaning that they are species that are not necessarily now threatened with extinction but that they may become so unless trade is closely controlled. Many tarantulas are legally and illegally traded in the pet market and they are one of the most traded invertebrate groups. Originally, the CITES list published in 1995 included all the current species of the genus Brachypelma Simon, 1891 plus Aphonopelma pallidum (F. O. Pickard-Cambridge, 1897) and the so-called Aphonopelma albiceps (Pocock, 1903). After that, some taxonomic changes were done, as well as descriptions of new species in the genus Brachypelma. The objective of this paper is to assess the 21 taxonomically valid spider species listed on CITES according to the IUCN criteria, study the general patterns and trends and advise on possible future conservation actions critical for the survival of endangered species. New information Amongst all 21 species assessed, 16 had sufficient data on their distribution, ecology and threats to properly understand their current status and suggest possible conservation measures. A decline in the area of occupancy (AOO) and extent of occurrence (EOO) was inferred to almost all species, caused mostly by human activities (urbanisation, roads, agricultural and touristic activities), which often lead to the complete loss of subpopulations across their range. Hurricanes and frequent rising water, which are increasing in frequency due to climate change, can cause decline in habitat quality and consequent change in EOO and AOO of some species and should also be considered when planning conservation actions. Severe fragmentation was detected in 13 species and is therefore one of the most relevant threats to the most endangered Brachypelma species and should be made a priority aspect to deal with when proposing conservation actions for the group. Regarding the loss of individuals in wild populations, the main cause seems to be the overharvesting to meet the illegal trade. The most important conservation actions identified across species include preserving their natural habitat through protected areas, establishing management plans for both the species and their habitats and undertaking systematic monitoring to provide information about population recovery and species re-introduction programmes. In general, we propose to prioritise and support research on the population trends and distribution, as well as on the impact of land use and habitat degradation. Special attention regarding conservation actions and research plans has to be given to the central Pacific coastal area of Mexico, particularly around Guerrero State where five species of Brachypelma occur. Critically, for some of the most endangered species, such as B. baumgarteni and B. hamorii, there is no official protected area in their range of occurrence. It would therefore be highly recommended to establish at least one conservation unit which focuses on protecting each of these species in situ. In some cases, basic taxonomic research is needed before development of any appropriate conservation action can be proposed.
  • Gafforov, Yusufjon; Ordynets, Alexander; Langer, Ewald; Yarasheva, Manzura; de Mello Gugliotta, Adriana; Schigel, Dmitry; Pecoraro, Lorenzo; Zhou, Yu; Cai, Lei; Zhou, Li-Wei (2020)
    Uzbekistan, located in Central Asia, harbors high diversity of woody plants. Diversity of wood-inhabiting fungi in the country, however, remained poorly known. This study summarizes the wood-inhabiting basidiomycte fungi (poroid and corticoid fungi plus similar taxa such as Merismodes, Phellodon, and Sarcodon) (Agaricomycetes, Basidiomycota) that have been found in Uzbekistan from 1950 to 2020. This work is based on 790 fungal occurrence records: 185 from recently collected specimens, 101 from herbarium specimens made by earlier collectors, and 504 from literature-based records. All data were deposited as a species occurrence record dataset in the Global Biodiversity Information Facility and also summarized in the form of an annotated checklist in this paper. All 286 available specimens were morphologically examined. For 138 specimens, the 114 ITS and 85 LSU nrDNA sequences were newly sequenced and used for phylogenetic analysis. In total, we confirm the presence of 153 species of wood-inhabiting poroid and corticioid fungi in Uzbekistan, of which 31 species are reported for the first time in Uzbekistan, including 19 that are also new to Central Asia. These 153 fungal species inhabit 100 host species from 42 genera of 23 families. Polyporales and Hymenochaetales are the most recorded fungal orders and are most widely distributed around the study area. This study provides the first comprehensively updated and annotated the checklist of wood-inhabiting poroid and corticioid fungi in Uzbekistan. Such study should be expanded to other countries to further clarify species diversity of wood-inhabiting fungi around Central Asia.
  • Knittle, Keegan; Heino, Matti; Marques, Marta M.; Stenius, Minna; Beattie, Marguerite; Ehbrecht, Franziska; Hagger, Martin S.; Hardeman, Wendy; Hankonen, Nelli (2020)
    Behaviour change techniques describe the content of behaviour change interventions, but do not adequately account for the actions that people must themselves undertake to successfully change or self-manage motivation or behaviour. This paper describes the development of a compendium of self-enactable techniques, combining behaviour- and motivation-regulation techniques across six existing classifications of behaviour change techniques and three scoping reviews. The compendium includes 123 techniques, each of which is labelled, defined and presented with instructive examples to facilitate self-enactment. Qualitative feedback was gathered from intervention developers and the general public to improve the utility, congruence and ease of self-enactability of the techniques. This integrative index of self-enactable techniques can assist intervention developers in selecting appropriate self-directed techniques to help people self-manage their motivation and behaviour. Future research with this compendium can expand on the number of behaviours covered by the instructive examples and link techniques with their potential impacts on factors that influence behaviours.
  • Niemi, Tapio; Nurminen, Jukka K.; Liukkonen, Juha-Matti; Hameri, Ari-Pekka (2018)
    High-energy physics studies collisions of particles traveling near the speed of light. For statistically significant results, physicists need to analyze a huge number of such events. One analysis job can take days and process tens of millions of collisions. Today the experiments of the large hadron collider (LHC) create 10 GB of data per second and a future upgrade will cause a ten-fold increase in data. The data analysis requires not only massive hardware but also a lot of electricity. In this article, we discuss energy efficiency in scientific computing and review a set of intermixed approaches we have developed in our Green Big Data project to improve energy efficiency of CERN computing. These approaches include making energy consumption visible to developers and users, architectural improvements, smarter management of computing jobs, and benefits of cloud technologies. The open and innovative environment at CERN is an excellent playground for different energy efficiency ideas which can later find use in mainstream computing. (C) 2017 Elsevier B.V. All rights reserved.