28 results on '"Nielsen, Ida Broman"'
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2. The biodiversity effect of reduced tillage on soil microbiota
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Frøslev, Tobias Guldberg, Nielsen, Ida Broman, Santos, Susana Silva, Barnes, Christopher James, Bruun, Hans Henrik, and Ejrnæs, Rasmus
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- 2022
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3. Above and Belowground Microbes Are Associated With Variation of the Leaf Metabolome; But Herbivory Has Nominal Effects
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Barnes, Christopher, primary, Hilton, Sally, additional, Nielsen, Ida Broman, additional, Ahlstrand, Natalie Iwanycki, additional, Hansen, Anders Johannes, additional, Frøslev, Tobias Guldberg, additional, Rønsted, Nina, additional, and Bending, Gary D, additional
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- 2023
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4. Holarctic Species in the Pluteus podospileus Clade: Description of Six New Species and Reassessment of Old Names
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Ševčíková, Hana, primary, Malysheva, Ekaterina F., additional, Antonín, Vladimír, additional, Borovička, Jan, additional, Dovana, Francesco, additional, Ferisin, Giuliano, additional, Eyssartier, Guillaume, additional, Grootmyers, Django, additional, Heilmann-Clausen, Jacob, additional, Kalichman, Jacob, additional, Kaygusuz, Oğuzhan, additional, Lebeuf, Renée, additional, González, Guillermo Muñoz, additional, Minnis, Andrew M., additional, Russell, Stephen D., additional, Saar, Irja, additional, Nielsen, Ida Broman, additional, Frøslev, Tobias Guldberg, additional, and Justo, Alfredo, additional
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- 2023
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5. Treated like dirt:Robust forensic and ecological inferences from soil eDNA after challenging sample storage
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Frøslev, Tobias Guldberg, Ejrnæs, Rasmus, Hansen, Anders J., Bruun, Hans Henrik, Nielsen, Ida Broman, Ekelund, Flemming, Vestergård, Mette, Kjøller, Rasmus, Frøslev, Tobias Guldberg, Ejrnæs, Rasmus, Hansen, Anders J., Bruun, Hans Henrik, Nielsen, Ida Broman, Ekelund, Flemming, Vestergård, Mette, and Kjøller, Rasmus
- Abstract
Biodiversity of soil is routinely assessed with environmental DNA—most often by massive parallel sequencing of marker genes (eDNA metabarcoding). Soil biodiversity may be investigated in relation to biodiversity research or as a tool in forensic investigations. After sampling, the taxonomic composition of soil biotic communities may change. In order to minimize community changes, it is desirable to reduce biological activity, e.g., by freezing immediately after sampling. However, this may be impossible due to remoteness of study sites or, in forensic cases, where soil has been attached to an item of interest for protracted periods of time. Here, we investigated the effect of storage duration and conditions on the assessment of the soil biota with eDNA metabarcoding. We extracted eDNA from freshly collected soil samples and again from the same samples after storage under contrasting temperature conditions and contrasting exposure (open/closed tubes). We used four different primer sets targeting bacteria, fungi, protists (cercozoans), and general eukaryotes. We quantified differences in richness, evenness, and community composition. Subsequently, we tested whether we could correctly infer habitat type and original sample identity after storage using a large reference dataset. We found stronger community composition differences with extended storage time and with higher storage temperature, and differences between open and closed tubes. However, for samples stored <28 days at a maximum of 20°C, changes were generally insignificant. Classification models successfully assigned most samples to their exact location of origin and correct habitat type even after 480 days storage. Even samples showing larger changes generally retained the original sample as the best match. For most biodiversity and forensic applications, storage of samples for days and even several weeks may thus not be a problem, if storage temperature does not exceed 20°C.
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- 2023
6. Seawater environmental DNA reflects seasonality of a coastal fish community
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Sigsgaard, Eva Egelyng, Nielsen, Ida Broman, Carl, Henrik, Krag, Marcus Anders, Knudsen, Steen Wilhelm, Xing, Yingchun, Holm-Hansen, Tore Hejl, Møller, Peter Rask, and Thomsen, Philip Francis
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- 2017
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7. Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage
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Frøslev, Tobias Guldberg, primary, Ejrnæs, Rasmus, additional, Hansen, Anders J., additional, Bruun, Hans Henrik, additional, Nielsen, Ida Broman, additional, Ekelund, Flemming, additional, Vestergård, Mette, additional, and Kjøller, Rasmus, additional
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- 2022
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8. Ancient root macropores and fractures in glacial till and their contribution to pesticide vulnerability of groundwater in low- and high-ground agricultural landscape:Pestpore2
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Jørgensen, Peter, Krogh, Paul Henning, Qin, Jiayi, Modesti, Luca, Nielsen, Ida Broman, Seersholm, Frederik Valeur, Wagner, Natascha, Hansen, Anders Johannes, Olsen, Jesper, Strobel, Bjarne W., Hansen, Søren, Gudbjerg, Jacob, Petersen, Carsten Tilbæk, Lacoste, Marine, Cousin, Isabelle, Keaveney, Evelyn, Barrett, Gerard, Jørgensen, Peter, Krogh, Paul Henning, Qin, Jiayi, Modesti, Luca, Nielsen, Ida Broman, Seersholm, Frederik Valeur, Wagner, Natascha, Hansen, Anders Johannes, Olsen, Jesper, Strobel, Bjarne W., Hansen, Søren, Gudbjerg, Jacob, Petersen, Carsten Tilbæk, Lacoste, Marine, Cousin, Isabelle, Keaveney, Evelyn, and Barrett, Gerard
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- 2022
9. Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
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Barnes, Christopher James, Nielsen, Ida Broman, Aagaard, Anne, Ejrnæs, Rasmus, Hansen, Anders Johannes, Frøslev, Tobias Guldberg, Barnes, Christopher James, Nielsen, Ida Broman, Aagaard, Anne, Ejrnæs, Rasmus, Hansen, Anders Johannes, and Frøslev, Tobias Guldberg
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While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast trnL region (10–143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the trnL sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the specificity of assignments made by the trnL primers, and improves the accuracy of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.
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- 2022
10. Ancient Root Macropores and Fractures in Glacial till and Their Contribution to Pesticide Vulnerability of Groundwater in Low and High‐ground Agricultural Landscapes ‐:PESTPORE2
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Jørgensen, Peter R., Krogh, P H, Qin, Jiayi, Modesti, Luca, Nielsen, Ida Broman, Seersholm, Frederik, Wagner, Natascha, Hansen, Anders Johannes, Olsen, Jesper, Strobel, Bjarne W., Hansen, Søren, Gudbjerg, Jacob, Petersen, Carsten Tilbæk, Lacoste, Marine, Cousin, Isabelle, Keaveney, Evelyn, and Barrett, Gerard
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- 2022
11. Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
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Barnes, Christopher James, primary, Nielsen, Ida Broman, additional, Aagaard, Anne, additional, Ejrnæs, Rasmus, additional, Hansen, Anders Johannes, additional, and Frøslev, Tobias Guldberg, additional
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- 2022
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12. Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage
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Frøslev, Tobias Guldberg, primary, Ejrnæs, Rasmus, additional, Hansen, Anders J., additional, Bruun, Hans Henrik, additional, Nielsen, Ida Broman, additional, Ekelund, Flemming, additional, Vestergård, Mette, additional, and Kjøller, Rasmus, additional
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- 2021
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13. Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage.
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Frøslev, Tobias Guldberg, Ejrnæs, Rasmus, Hansen, Anders J., Bruun, Hans Henrik, Nielsen, Ida Broman, Ekelund, Flemming, Vestergård, Mette, and Kjøller, Rasmus
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- 2023
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14. The biodiversity effect of reduced tillage on soil microbiota
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Frøslev, Tobias Guldberg, primary, Nielsen, Ida Broman, additional, Santos, Susana Silva, additional, Barnes, Christopher James, additional, Bruun, Hans Henrik, additional, and Ejrnæs, Rasmus, additional
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- 2021
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15. Systematics of West African Miniopterus with the description of a new species
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Monadjem, Ara, Shapiro, Julie T., Richards, Leigh R., Karabulut, Hatice, Crawley, Wing, Nielsen, Ida Broman, Hansen, Anders, Bohmann, Kristine, and Mourier, Tobias
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Miniopteridae ,Chiroptera ,Mammalia ,Animalia ,Biodiversity ,Chordata ,Taxonomy - Abstract
Monadjem, Ara, Shapiro, Julie T., Richards, Leigh R., Karabulut, Hatice, Crawley, Wing, Nielsen, Ida Broman, Hansen, Anders, Bohmann, Kristine, Mourier, Tobias (2019): Systematics of West African Miniopterus with the description of a new species. Acta Chiropterologica 21 (2): 237-256, DOI: 10.3161/15081109ACC2019.21.2.001
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- 2019
16. Miniopterus nimbae Monadjem & S Hapiro & Richards & Karabulut & Crawley & Nielsen & Hansen & Bohmann & Mourier 2019, sp. nov
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Monadjem, Ara, Shapiro, Julie T., Richards, Leigh R., Karabulut, Hatice, Crawley, Wing, Nielsen, Ida Broman, Hansen, Anders, Bohmann, Kristine, and Mourier, Tobias
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Miniopteridae ,Chiroptera ,Miniopterus nimbae ,Mammalia ,Animalia ,Miniopterus ,Biodiversity ,Chordata ,Taxonomy - Abstract
Miniopterus nimbae sp. nov. Nimba long-fingered bat Holotype DM 12621 (field no. AM2010_12_18_1), an adult male, was collected by Ara Monadjem. The specimen was fixed in formalin and then transferred to 70% alcohol. The skull has been extracted and cleaned. Photograph of the skull and drawing of the tragus of the holotype are illustrated in Figs. 6 and 7. Type locality Liberia, Nimba Province, Mount Gangra, 10 km to the west of Mount Nimba (Fig. 1). The bat was netted on 18 December 2010 exiting from a mine adit mid-way up Mount Gangra (7.55434°N, 8.62902°W) at 720 m a.s.l, in secondary forest. Paratypes No other specimens of this species were captured or collected on the same day at the same site. However, the previous night an adult female (DM 12614) was collected at the Yiti River 9 km to the south-east of Mount Gangra. Photograph of the paratype is illustrated in Fig. 8. Etymology This species is named after Mount Nimba, one of just three localities from which it is known, further highlighting the critical importance of this mountain for bat conservation in Africa (Monadjem et al., 2016). Diagnosis This is a large-sized Miniopterus from Mount Nimba, Liberia, with a mean forearm length of 47.4 mm (n = 26 individuals). The large size of this bat (particularly its forearm length) readily distinguishes M. nimbae from all other African Miniopterus taxa except the M. inflatus / M. africanus group. In external and craniodental measurements, M. nimbae is similar in size to other members of the M. inflatus group (M. inflatus s.s., M. cf. inflatus and M. africanus) (Tables 3–5); however, in multi-dimensional morphospace based on craniodental measurements, it overlaps only with M. inflatus s.s. The taxon M. cf. inflatus from eastern and southern Africa tends to have a light pelage, being more reddish-brown in colour (compared with a deep chocolate brown in M. nimbae). It is not possible, at present to distinguish M. nimbae from M. inflatus s.s. on external characters. However, they can be readily distinguished by cranial features. In particular, the 1st upper premolar has an additional lingual cusp, posterior to the main cusp, that is present in M. nimbae but absent in M. inflatus s.s. (Fig. 9); this feature being clearly visible, even with a low magnification hand lens, and consistently present in all the specimens examined in this study. The lower tooth row (i 1 –m 3) and lower molar (LWMOLS) lengths are also slightly larger in M. nimbae than M. inflatus s.s. In terms of cranial geometry, M. nimbae differs from M. inflatus s.s. as it bears a slightly more gracile skull, less ‘inflated’ braincase, and the point of maximum curvature along the occiput is more elevated in the newly described taxon than in the nominate form. Furthermore, these two taxa, are also distinguishable on molecular grounds (K2P pairwise genetic distance = 1.6%). Additionally, the ranges of the two taxa do not appear to overlap. Miniopterus africanus appears to be restricted to north-eastern Africa and is genetically distinct (K2P pairwise distance = 16.7%) from M. nimbae. Description External characters.— Miniopterus nimbae is large-sized for the genus, but showing typical generic features including a rounded head, an elongated second phalanx of the third digit, rounded ears, and a relatively long and straight tragus. The tail is slightly less than half that of the total length. The pelage is dark chocolate brown above and slightly paler below. Individual hairs are unicoloured. The mass and standard external measurements of the holotype compared with a small sample of other individuals are shown in Table 3. Craniodental characters.—The skull is robust for a Miniopterus species. The rostrum is broad and the braincase is rounded and high, typical for the genus of Miniopterus. The dentition of M. nimbae is I 2/3, C 1/1, P 2/3, M 3/3, which is typical of the genus. In the upper tooth row, the inner incisor is larger than the outer one, and the anterior premolar is relatively well developed. The cranial and dental measurements of the holotype compared with a small sample of other individuals are shown in Tables 4 and 5. Distribution Analysis of genetic samples taken from five specimens with large forearm lengths (range 46.9– 48.2 mm) at Mount Gangra (Nimba, Liberia), group them all as M. nimbae (Figs. 2 and 3). Although not genetically analysed, it is likely that specimens previously collected from northern Liberia or southeastern Guinea and identified as M. inflatus are instead referable to this new species, M. nimbae. Based on this assumption, this taxon is known from just three localities: Mount Nimba (and surrounding uplands), Liberia; Wonegizi Mountains, Liberia; and Mount Béro, Guinea (Wolton et al., 1982; Koopman et al., 1995; Fahr et al., 2006; Monadjem et al., 2016). The closest locality for M. inflatus s.s. is at least 2,000 km away in eastern Nigeria (Happold, 2013 b), and no other large Miniopterus specimens have been collected in the intermediate area, despite extensive surveys in a number of localities e.g., Thaï and Comoé National Parks in Côte d’Ivoire (Fahr and Kalko, 2011), the Simandou Range in eastern Guinea (Decher et al., 2015), the Fouta Djallon mountains in central Guinea (Weber and Fahr, 2007) or anywhere in Ghana or Sierra Leone (Grubb et al., 1998; Happold, 2013 b, 2013 c). Therefore, M. nimbae is probably an endemic to the upland areas of northern Liberia and south-eastern Guinea, and may be shown to also occur in the upland area of western Côte d’Ivoire at and around Mount Nimba. Biology: Practically nothing is known about the biology of this Upper Guinea forest endemic. It has been recorded roosting in mine adits at 720– 970 m above sea level (a.s.l.) at Mount Gangra and Mount Yuelliton (both within 10 km of Mount Nimba). The size of one roosting colony at Mount Gangra was estimated at between 20–30 individuals; the site was shared with large numbers of Myonycteris angolensis and Hipposideros cf. ruber, and a few H. marisae. A second roosting colony was estimated to include> 200 individuals of this species at Mount Yuelliton (which was not inhabited by any other bat species — A. Monadjem, personal observation). It has been netted at various localities in the foothills of Mount Nimba and in the low-lying rainforest region between these three upland areas. This suggests that this species roosts in upland areas (700 m a.s.l.), and then descends to forage in lower lying forested areas (about 500 m a.s.l.). In a sample of 13 females captured at Nimba between late December and end-March, five were pregnant. During the same period, three out of 10 males had scrotal testes. The mean frequency of the knee of handreleased M. nimbae captured at Mount Nimba was 48.4 kHz (range: 47.2–48.9 kHz, n = 4). Other Taxonomic Considerations In addition to the description of the new species, M. nimbae, the phylogeny presented here (Figs. 2 and 3) also identifies two other distinct taxa. The first is the taxon M. villiersi, which does not appear to be closely related to M. schreibersii s.s. and should therefore not be considered a subspecies of the latter mentioned taxon. In fact, M. villiersi is sister to M. nimbae (Figs. 2 and 3), from which it is readily distinguishable based on genetics and size (see Tables 2–5); the pairwise genetic distance between the two species is 9.0%, and there is no overlap between these two species in forearm length or any of the craniodental measurements presented here. The echolocation calls also differ, with the frequency of the knee of M. villiersi calls (based on hand-released individuals that were captured at Mount Nimba — x = 51.6 kHz, range 51.1–52.4 kHz, n = 5) being distinctly higher than that of M. nimbae (x = 48.4 kHz, range 47.2–48.9 kHz, n = 4) with no overlap between the two species. The second taxon refers to the M. inflatus group, which appears to be paraphyletic. Miniopterus inflatus s.s. (based on sequenced specimens from Gabon, and close to the type locality in southern Cameroon) is sister to the taxon M. nimbae and these two are sister to M. villiersi (Figs. 2 and 3). By contrast, the M. cf. inflatus specimens (from Malawi and Mozambique) are sister to M. fraterculus and M. minor. This suggests that the taxon M. inflatus s.l. comprises, in addition to the newly recognised M. nimbae, two distinct and not closely related taxa which we refer to as M. inflatus s.s. (from Gabon), and M. cf. inflatus (from Malawi and Mozambique)., Published as part of Monadjem, Ara, Shapiro, Julie T., Richards, Leigh R., Karabulut, Hatice, Crawley, Wing, Nielsen, Ida Broman, Hansen, Anders, Bohmann, Kristine & Mourier, Tobias, 2019, Systematics of West African Miniopterus with the description of a new species, pp. 237-256 in Acta Chiropterologica 21 (2) on pages 245-248, DOI: 10.3161/15081109ACC2019.21.2.001, http://zenodo.org/record/3944920, {"references":["MONADJEM, A., L. RICHARDS, and C. DENYS. 2016. An African bat hotspot: the exceptional importance of Mount Nimba for bat diversity. Acta Chiropterologica, 18: 359 - 375.","WOLTON, R. J., P. A. ARAK, H. C. J. GODFRAY, and R. P. WILSON. 1982. Ecological and behavioural studies of the Megachiroptera at Mount Nimba, Liberia, with notes on Microchiroptera. Mammalia, 18: 359 - 375.","KOOPMAN, K. F., C. P. KOFRON, and A. CHAPMAN. 1995. The bats of Liberia: systematics, ecology, and distribution. American Museum Novitates, 3148: 1 - 24.","FAHR, J., B. A. DJOSSA, and H. VIERHAUS. 2006. Rapid assessment of bats (Chiroptera) in Dere, Diecke and Mt. Bero classified forests, southeastern Guinea; including a review of the distribution of bats in Guinee Forestiere. Pp. 168 - 180, 245 - 247, in A rapid biological assessment of three classified forests in Southeastern Guinea (H. E. WRIGHT, J. MCCULLOUGH, L. E. ALONSO, and M. S. DIALLO, eds.). RAP Bulletin of Biological Assessment, 40: 1 - 248.","HAPPOLD, M. 2013 b. Miniopterus inflatus Greater long-fingered bat. Pp. 714 - 716, in The mammals of Africa. Volume IV: Hedgehogs, shrews and bats (M. HAPPOLD and D. C. HAP- POLD, eds.). Bloomsbury Publishing, London, 800 pp.","FAHR, J., and E. K. V. KALKO. 2011. Biome transitions as centres of diversity: habitat heterogeneity and diversity patterns of West African bat assemblages across spatial scales. Ecography, 34: 177 - 195.","DECHER, J., A. HOFFMANN, J. SCHAER, R. W. NORRIS, B. KADJO, J. ASTRIN, A. MONADJEM, and R. HUTTERER. 2015. Bat diversity in the Simandou Mountain Range of Guinea, with the description of a new white-winged vespertilionid. Acta Chiropterologica, 17: 255 - 282.","WEBER, N., and J. FAHR. 2007. Survey of endemic and globally threatened bat species in the Fouta Djallon Plateau for","GRUBB, P., T. S. JONES, A. G. DAVIES, E. EDBERG, E. D. STARIN, and J. E. HILL. 1998. Mammals of Ghana, Sierra Leone and The Gambia. Trendine Press, Cornwall, UK, 265 pp.","HAPPOLD, M. 2013 c. Miniopterus schreibersii Schreibers's long-fingered bat. Pp. 721 - 722, in The mammals of Africa. Volume IV: Hedgehogs, shrews and bats (M. HAPPOLD and D. C. D. HAPPOLD, eds.). Bloomsbury Publishing, London, 800 pp."]}
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- 2019
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17. Systematics of West African Miniopterus with the Description of a New Species
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Monadjem, Ara, primary, Shapiro, Julie T., additional, Richards, Leigh R., additional, Karabulut, Hatice, additional, Crawley, Wing, additional, Nielsen, Ida Broman, additional, Hansen, Anders, additional, Bohmann, Kristine, additional, and Mourier, Tobias, additional
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- 2020
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18. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach
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Mollerup, Sarah, Asplund, Maria, Friis-Nielsen, Jens, Kjartansdóttir, Kristín Rós, Fridholm, Helena, Hansen, Thomas Arn, Herrera, José Alejandro Romero, Barnes, Christopher James, Jensen, Randi Holm, Richter, Stine Raith, Nielsen, Ida Broman, Pietroni, Carlotta, Alquezar-Planas, David E, Rey-Iglesia, Alba, Olsen, Pernille V S, Rajpert-De Meyts, Ewa, Groth-Pedersen, Line, von Buchwald, Christian, Jensen, David H, Gniadecki, Robert, Høgdall, Estrid, Langhoff, Jill Levin, Pete, Imre, Vereczkey, Ildikó, Baranyai, Zsolt, Dybkaer, Karen, Johnsen, Hans Erik, Steiniche, Torben, Hokland, Peter, Rosenberg, Jacob, Baandrup, Ulrik, Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, Ole, Mourier, Tobias, Vinner, Lasse, Izarzugaza, Jose M G, Nielsen, Lars Peter, Hansen, Anders Johannes, Mollerup, Sarah, Asplund, Maria, Friis-Nielsen, Jens, Kjartansdóttir, Kristín Rós, Fridholm, Helena, Hansen, Thomas Arn, Herrera, José Alejandro Romero, Barnes, Christopher James, Jensen, Randi Holm, Richter, Stine Raith, Nielsen, Ida Broman, Pietroni, Carlotta, Alquezar-Planas, David E, Rey-Iglesia, Alba, Olsen, Pernille V S, Rajpert-De Meyts, Ewa, Groth-Pedersen, Line, von Buchwald, Christian, Jensen, David H, Gniadecki, Robert, Høgdall, Estrid, Langhoff, Jill Levin, Pete, Imre, Vereczkey, Ildikó, Baranyai, Zsolt, Dybkaer, Karen, Johnsen, Hans Erik, Steiniche, Torben, Hokland, Peter, Rosenberg, Jacob, Baandrup, Ulrik, Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, Ole, Mourier, Tobias, Vinner, Lasse, Izarzugaza, Jose M G, Nielsen, Lars Peter, and Hansen, Anders Johannes
- Abstract
BACKGROUND: Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data.METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads.RESULTS: Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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- 2019
19. Contaminating viral sequences in high-throughput sequencing viromics:a linkage study of 700 sequencing libraries
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Asplund, Maria, Kjartansdóttir, Kristín Rós, Mollerup, Sarah, Vinner, Lasse, Fridholm, Helena, Herrera, José A R, Friis-Nielsen, Jens, Hansen, Thomas Arn, Jensen, Randi Holm, Nielsen, Ida Broman, Richter, Stine Raith, Rey-Iglesia, Alba, Matey-Hernandez, Maria Luisa, Alquezar-Planas, David E, Olsen, Pernille V S, Sicheritz-Pontén, Thomas, Willerslev, Eske, Lund, Ole, Brunak, Søren, Mourier, Tobias, Nielsen, Lars Peter, Izarzugaza, Jose M G, Hansen, Anders Johannes, Asplund, Maria, Kjartansdóttir, Kristín Rós, Mollerup, Sarah, Vinner, Lasse, Fridholm, Helena, Herrera, José A R, Friis-Nielsen, Jens, Hansen, Thomas Arn, Jensen, Randi Holm, Nielsen, Ida Broman, Richter, Stine Raith, Rey-Iglesia, Alba, Matey-Hernandez, Maria Luisa, Alquezar-Planas, David E, Olsen, Pernille V S, Sicheritz-Pontén, Thomas, Willerslev, Eske, Lund, Ole, Brunak, Søren, Mourier, Tobias, Nielsen, Lars Peter, Izarzugaza, Jose M G, and Hansen, Anders Johannes
- Abstract
OBJECTIVES: Sample preparation for High-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences.METHODS: A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed by different protocols. In total 712 sequencing libraries were investigated for viral sequence contamination.RESULTS: Among sequences showing similarity to viruses, 493 were significantly associated to the use of laboratory components. Each of these viral sequences showed sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control (NTC) samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components.CONCLUSIONS: We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover we show that detection can be problematic due to stochastic appearance and limited NTCs. Although the exact origin of these viral sequences requires further research, our results support laboratory component linked viral sequence contamination of both biological and synthetic origin.
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- 2019
20. Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries
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Asplund, Maria, Kjartansdóttir, Kristín Rós, Mollerup, Sarah, Vinner, Lasse, Fridholm, Helena, Herrera, José A. R., Friis-Nielsen, Jens, Hansen, Thomas Arn, Jensen, Randi Holm, Nielsen, Ida Broman, Richter, Stine Raith, Rey-Iglesia, Alba, Matey-Hernandez, Maria Luisa, Alquezar-Planas, David E., Olsen, Pernille V. S., Sicheritz-Pontén, Thomas, Willerslev, Eske, Lund, Ole, Brunak, Søren, Mourier, Tobias, Nielsen, Lars Peter, Izarzugaza, Jose M. G., Hansen, Anders Johannes, Asplund, Maria, Kjartansdóttir, Kristín Rós, Mollerup, Sarah, Vinner, Lasse, Fridholm, Helena, Herrera, José A. R., Friis-Nielsen, Jens, Hansen, Thomas Arn, Jensen, Randi Holm, Nielsen, Ida Broman, Richter, Stine Raith, Rey-Iglesia, Alba, Matey-Hernandez, Maria Luisa, Alquezar-Planas, David E., Olsen, Pernille V. S., Sicheritz-Pontén, Thomas, Willerslev, Eske, Lund, Ole, Brunak, Søren, Mourier, Tobias, Nielsen, Lars Peter, Izarzugaza, Jose M. G., and Hansen, Anders Johannes
- Abstract
Sample preparation for High-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences. A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed by different protocols. In total 712 sequencing libraries were investigated for viral sequence contamination. Among sequences showing similarity to viruses, 493 were significantly associated to the use of laboratory components. Each of these viral sequences showed sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control (NTC) samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components. We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover we show that detection can be problematic due to stochastic appearance and limited NTCs. Although the exact origin of these viral sequences requires further research, our results support laboratory component linked viral sequence contamination of both biological and synthetic origin.
- Published
- 2019
21. High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach
- Author
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Mollerup, Sarah, Asplund, Maria, Friis-Nielsen, Jens, Kjartansdóttir, Kristín Rós, Fridholm, Helena, Hansen, Thomas Arn, Herrera, José Alejandro Romero, Barnes, Christopher James, Jensen, Randi Holm, Richter, Stine Raith, Nielsen, Ida Broman, Pietroni, Carlotta, Alquezar-Planas, David E., Rey-Iglesia, Alba, Olsen, Pernille V. S., Rajpert-De Meyts, Ewa, Groth-Pedersen, Line, von Buchwald, Christian, Jensen, David H., Gniadecki, Robert, Høgdall, Estrid, Langhoff, Jill Levin, Pete, Imre, Vereczkey, Ildikó, Baranyai, Zsolt, Dybkaer, Karen, Johnsen, Hans Erik, Steiniche, Torben, Hokland, Peter, Rosenberg, Jacob, Baandrup, Ulrik, Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, Ole, Mourier, Tobias, Vinner, Lasse, Izarzugaza, Jose M. G., Nielsen, Lars Peter, Hansen, Anders Johannes, Mollerup, Sarah, Asplund, Maria, Friis-Nielsen, Jens, Kjartansdóttir, Kristín Rós, Fridholm, Helena, Hansen, Thomas Arn, Herrera, José Alejandro Romero, Barnes, Christopher James, Jensen, Randi Holm, Richter, Stine Raith, Nielsen, Ida Broman, Pietroni, Carlotta, Alquezar-Planas, David E., Rey-Iglesia, Alba, Olsen, Pernille V. S., Rajpert-De Meyts, Ewa, Groth-Pedersen, Line, von Buchwald, Christian, Jensen, David H., Gniadecki, Robert, Høgdall, Estrid, Langhoff, Jill Levin, Pete, Imre, Vereczkey, Ildikó, Baranyai, Zsolt, Dybkaer, Karen, Johnsen, Hans Erik, Steiniche, Torben, Hokland, Peter, Rosenberg, Jacob, Baandrup, Ulrik, Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, Ole, Mourier, Tobias, Vinner, Lasse, Izarzugaza, Jose M. G., Nielsen, Lars Peter, and Hansen, Anders Johannes
- Abstract
Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Here we applied a diverse selection of pre-sequencing enrichment methods targeting all major viral groups, to characterise the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing we generated 710 datasets constituting 57 billion sequencing reads. Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveals a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained one or more viruses, however, no link between specific viruses and cancer types were found. Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
- Published
- 2019
22. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach
- Author
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Mollerup, Sarah, primary, Asplund, Maria, additional, Friis-Nielsen, Jens, additional, Kjartansdóttir, Kristín Rós, additional, Fridholm, Helena, additional, Hansen, Thomas Arn, additional, Herrera, José Alejandro Romero, additional, Barnes, Christopher James, additional, Jensen, Randi Holm, additional, Richter, Stine Raith, additional, Nielsen, Ida Broman, additional, Pietroni, Carlotta, additional, Alquezar-Planas, David E, additional, Rey-Iglesia, Alba, additional, Olsen, Pernille V S, additional, Rajpert-De Meyts, Ewa, additional, Groth-Pedersen, Line, additional, von Buchwald, Christian, additional, Jensen, David H, additional, Gniadecki, Robert, additional, Høgdall, Estrid, additional, Langhoff, Jill Levin, additional, Pete, Imre, additional, Vereczkey, Ildikó, additional, Baranyai, Zsolt, additional, Dybkaer, Karen, additional, Johnsen, Hans Erik, additional, Steiniche, Torben, additional, Hokland, Peter, additional, Rosenberg, Jacob, additional, Baandrup, Ulrik, additional, Sicheritz-Pontén, Thomas, additional, Willerslev, Eske, additional, Brunak, Søren, additional, Lund, Ole, additional, Mourier, Tobias, additional, Vinner, Lasse, additional, Izarzugaza, Jose M G, additional, Nielsen, Lars Peter, additional, and Hansen, Anders Johannes, additional
- Published
- 2019
- Full Text
- View/download PDF
23. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA
- Author
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Sigsgaard, Eva Egelyng, Nielsen, Ida Broman, Bach, Steffen Sanvig, Lorenzen, Eline, Robinson, David Philip, Knudsen, Steen Wilhelm, Pedersen, Mikkel Winther, Al Jaidah, Mohammed, Orlando, Ludovic Antoine Alexandre, Willerslev, Eske, Møller, Peter Rask, Thomsen, Philip Francis, Sigsgaard, Eva Egelyng, Nielsen, Ida Broman, Bach, Steffen Sanvig, Lorenzen, Eline, Robinson, David Philip, Knudsen, Steen Wilhelm, Pedersen, Mikkel Winther, Al Jaidah, Mohammed, Orlando, Ludovic Antoine Alexandre, Willerslev, Eske, Møller, Peter Rask, and Thomsen, Philip Francis
- Published
- 2016
24. First record of Vespertilio murinus from the Arabian Peninsula
- Author
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Monadjem, Ara, Joubert, Christiaan, Richards, Leigh, Nielsen, Ida Broman, Nielsen, Martin, Kjartansdóttir, Kristín Rós, Bohmann, Kristine, Mourier, Tobias, Hansen, Anders Johannes, Monadjem, Ara, Joubert, Christiaan, Richards, Leigh, Nielsen, Ida Broman, Nielsen, Martin, Kjartansdóttir, Kristín Rós, Bohmann, Kristine, Mourier, Tobias, and Hansen, Anders Johannes
- Abstract
A specimen of Vespertilio murinus was captured on 13 May 2014 on the grounds of the Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates. The species was unambiguous-ly identified based on molecular (cytochrome b gene) and morphological characters. This represents the first record of V. murinus from the Arabian Peninsula. A revised checklist of the Vespertilionidae is presented for the Arabian Peninsula which includes 27 species belonging to 13 genera. A phylogeny for the Arabian vespertilionid species is also presented showing the paraphyly of Eptesicus and the position of Nyctalus within Pipistrellus.
- Published
- 2016
25. Identification of known and novel recurrent viral sequences in data from multiple patients and multiple cancers
- Author
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Friis-Nielsen, Jens, Kjartansdóttir, Kristin Rós, Mollerup, Sarah, Asplund, Maria, Mourier, Tobias, Jensen, Randi Holm, Hansen, Thomas Arn, Rey de la Iglesia, Alba, Richter, Stine Raith, Nielsen, Ida Broman, Alquezar Planas, David Eugenio, Olsen, Pernille Vibeke Selmer, Vinner, Lasse, Fridholm, Eva Marie Helena, Nielsen, Lars Peter, Willerslev, Eske, Sicheritz-Pontén, Thomas, Lund, Ole, Hansen, Anders Johannes, Izarzugaza, Jose M. G., Brunak, Søren, Friis-Nielsen, Jens, Kjartansdóttir, Kristin Rós, Mollerup, Sarah, Asplund, Maria, Mourier, Tobias, Jensen, Randi Holm, Hansen, Thomas Arn, Rey de la Iglesia, Alba, Richter, Stine Raith, Nielsen, Ida Broman, Alquezar Planas, David Eugenio, Olsen, Pernille Vibeke Selmer, Vinner, Lasse, Fridholm, Eva Marie Helena, Nielsen, Lars Peter, Willerslev, Eske, Sicheritz-Pontén, Thomas, Lund, Ole, Hansen, Anders Johannes, Izarzugaza, Jose M. G., and Brunak, Søren
- Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
- Published
- 2016
26. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA
- Author
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Sigsgaard, Eva Egelyng, primary, Nielsen, Ida Broman, additional, Bach, Steffen Sanvig, additional, Lorenzen, Eline D., additional, Robinson, David Philip, additional, Knudsen, Steen Wilhelm, additional, Pedersen, Mikkel Winther, additional, Jaidah, Mohammed Al, additional, Orlando, Ludovic, additional, Willerslev, Eske, additional, Møller, Peter Rask, additional, and Thomsen, Philip Francis, additional
- Published
- 2016
- Full Text
- View/download PDF
27. Nielsen, Ida Broman
- Author
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Nielsen, Ida Broman and Nielsen, Ida Broman
- Published
- 2014
28. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.
- Author
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Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JM, and Brunak S
- Subjects
- Computational Biology, Conserved Sequence, High-Throughput Nucleotide Sequencing, Humans, RNA, Viral genetics, Viruses classification, Neoplasms virology, Viruses genetics, Viruses isolation & purification
- Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
- Published
- 2016
- Full Text
- View/download PDF
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