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 wellequipped, 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 specimenand 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.

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.

1Background: 2More than 80% of all animal species remain unknown to science. Most of these species live in 3 the tropics and belong to animal taxa that combine small body size with high specimen 4abundance and large species richness. For such clades, using morphology for species 5 discovery is slow because large numbers of specimens must be sorted using detailed 6 microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA 7 sequences could be used for sorting specimens to species. Morphological verification of such 8 "molecular Operational Taxonomic Units" (mOTUs) could then be based on dissection of a small 9 subset of specimens. However, this approach requires cost-effective and low-tech DNA 10 barcoding techniques because well equipped, well-funded molecular laboratories are not readily 11 available in many biodiverse countries. 12 Results: 13We here document how MinION sequencing can be used for large-scale species discovery in a 14 specimen-and species-rich taxon like the hyper-diverse fly family Phoridae (Diptera). We 15 sequenced 7,059 specimens collected in a single Malaise trap in Kibale National Park, Uganda 16 over the short period of eight weeks. We discovered >650 species which exceeded the number 17 of phorid species currently described for the entire Afrotropical region. The barcodes were 18 obtained using an improved low-cost MinION pipeline that increased the barcoding capacity 19 sevenfold from 500 to 3,500 barcodes per flowcell. This was achieved by adopting 1D 20 sequencing, re-sequencing weak amplicons on a used flowcell, and improving demultiplexing. 21Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% 22 methods. In insects, one of the most widely used methods is Malaise trapping. Such traps 48 routinely collect thousands, or even tens of thousands, of specimens per site and week; i.e., 49 sorting all specimens to species-level virtually never happens and the world's natural history 50 museums store billions of unsorted specimens. Species-level sorting is usually restricted to a 51 few taxa with small to moderate numbers of specimens. It is accomplished in two stages. The 52 first is grouping specimens into easily identifiable major taxa (e.g., major groups of beetles, flies, 53 wasps). This type of pre-sorting is usually accomplished by parataxonomists with basic training 54 in morphology (e.g., students). The main challenge is the second sorting stage; i.e., sorting to 55 species-level. This work is best carried out by taxonomic experts whose techniques are, 56 however, mostly effective for taxa that have fairly small numbers of specimens and species. In 57 contrast, large, hyperdiverse and abundant taxa are ill-suited because they require dissection 58 and microscopic study of many specimens. An alternative to species-level sorting by 59 taxonomists is a hybrid approach that combines rapid pre-sorting to "morpho-species" by 60 parataxonomists with subsequent verification of morpho-species via DNA barcodes that ar...

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.

BackgroundDeer keds are obligatory haematophagous parasites of large homeothermic animals, particularly cervids. Two of the five known species occurring in Europe—Lipoptena cervi (Linnaeus) and L. fortisetosa Maa—are known to have a relatively wide distribution. Lipoptena fortisetosa is considered to have been introduced into Europe with sika deer from the Eastern Palaearctic and is continuously expanding its range. Little is known about the medical importance of deer keds, but they can cause hair loss in cervids and are suspected to be vectors of several diseases.New informationDetails of the distribution of Lipoptena fortisetosa in Europe, including its northernmost record, are provided. This species has been shown to have a viable population in Southern Estonia. Furthermore, the differences from allied L. cervi are discussed, based on morphological and molecular characters.

Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.

Two new Mycetophilidae species, Neuratelia jabalmoussae sp. n. and Neuratelia salmelai sp. n. are described on the basis of material collected from Lebanon, Estonia and Finland. Detailed figures of male terminalia and photographs of general facies are provided along with discussions of their morphological distinction from sibling species. For the first time molecular characters are used to distinguish new fungus gnat species. Molecular analysis relies on cytochrome oxidase subunit one (COI) but has additionally been corroborated by information from the 28S and ITS2 regions of nuclear ribosomal DNA. Situations where morphological and molecular data provide conflicting evidence for species delimitation are discussed. A new country record from Georgia is provided for Neuratelia caucasica.

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