| 1. |
- Abarenkov, Kessy, et al.
(författare)
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PlutoF—a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences
- 2010
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Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 6, s. 189-196
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Tidskriftsartikel (refereegranskat)abstract
- DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.
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| 2. |
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| 3. |
- Kurina, Olavi, et al.
(författare)
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A Siberian fungus gnat (Diptera: Mycetophilidae) species found in Estonia
- 2009
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Ingår i: Entomologica Fennica. - 0785-8760. ; 20:1, s. 56-60
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Tidskriftsartikel (refereegranskat)abstract
- The first European record of Exechia inaperta Ostroverkhova, 1979 is presented and its morphological difference from the allied E. exigua Lundstrom, 1909 is discussed. Diagnostic characters and detailed figures of male terminalia are given for both species. The new finding of E. inaperta in Estonia indicates a possibly disjunct Euro-Siberian distribution pattern of the South-Taiga, also observed in several other species of fungus gnats.
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| 4. |
- Kurina, Olavi, et al.
(författare)
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Fungus gnats (Diptera: Sciaroidea excl. Sciaridae) in the Swedish boreonemoral forests
- 2004
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Ingår i: Studia dipterologica. ; 11:2, s. 471-488
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Tidskriftsartikel (refereegranskat)abstract
- Fungus gnats in boreonemoral forests of south Sweden are studied using material collected with Malaise and window traps from 17 localities in the years 2001 and 2002. 250 species are recorded including 76 species new to Sweden. 14 of these are found in Fennoscandia for the first time: Docosia setosa Landrock, D. spec. (indet. sensu Hutson et al. 1980), Brevicornu cognatum Ostroverkhova, Mycetophila eppingensis Chandler, M. lobulata A. Zaitzev, M. pyrenaica Matile, M. subsigillata A. Zaitzev, Sceptonia cryptocauda Chandler, S. flavipuncta Edwards, S. longisetosa Ševcik, S. pilosa Bukowski, S. pughi Chandler, Sciophila interrupta (Winnertz) and S. plurisetosa Edwards. One new synonym is proposed: Dynatosoma dihaeta Polevoi, 1995 = Dynatosoma schachti Plassmann, 1999 syn. nov.
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| 5. |
- Kurina, Olavi, et al.
(författare)
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Review of the European Greenomyia Brunetti (Diptera, Mycetophilidae) with new descriptions of females
- 2011
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Ingår i: ZooKeys. - : Pensoft Publishers. - 1313-2970 .- 1313-2989. ; :77, s. 31-50
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Forskningsöversikt (refereegranskat)abstract
- The females of the four continental Greenomyia Brunetti species in Europe are associated with the males, diagnosed and keyed, providing the first association and description of the females of G. baikalica Zaitzev, 1994 and G. stackelbergi Zaitzev, 1982. Colour photographs of their habitus and line drawings of their female terminalia are provided. Greenomyia mongolica Lagtovka & Matile, 1974 is found to be a senior synonym of Greenomyia theresae Matile, 2002. syn. n. The diagnostic characters used to distinguish between Greenomyia and Neoclastobasis Ostroverkhova in keys did not hold up to a closer scrutiny and leave the status of Neoclastobasis as separate genus questionable.
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| 6. |
- Mikryukov, Vladimir, et al.
(författare)
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Connecting the multiple dimensions of global soil fungal diversity
- 2023
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Ingår i: Science advances. - 2375-2548. ; 9:48
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Tidskriftsartikel (refereegranskat)abstract
- How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.
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| 7. |
- Srivathsan, Amrita, et al.
(författare)
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Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing
- 2019
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries.Results: We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.).Conclusions: We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.
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| 8. |
- Tedersoo, Leho, et al.
(författare)
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Global patterns in endemicity and vulnerability of soil fungi.
- 2022
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Ingår i: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
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Tidskriftsartikel (refereegranskat)abstract
- Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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