A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

Ratnasingham, Sujeevan; Hebert, Paul D. N.

doi:10.1371/journal.pone.0066213

Cited by 1,760 publications

(1,900 citation statements)

References 61 publications

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“…In total, 122 parasitoid BINs were found by DNA barcoding. For further species‐level analyses, we treated these BINs as species (Ratnasingham & Hebert, 2013). In addition, 21 distinct morphospecies, which were not successfully barcoded, were also considered as species, altogether resulting in 143 putative parasitoid species.…”

Section: Methodsmentioning

confidence: 99%

Vertical canopy gradient shaping the stratification of leaf‐chewer–parasitoid interactions in a temperate forest

Šigut

Šigutová

Šipoš

et al. 2018

Ecology and Evolution

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Knowledge about herbivores and their parasitoids in forest canopies remains limited, despite their diversity and ecological importance. Thus, it is important to understand the factors that shape the herbivore–parasitoid community structure, particularly the effect of vertical gradient. We investigated a quantitative community dataset of exposed and semiconcealed leaf‐chewing larvae and their parasitoids along a vertical canopy gradient in a temperate forest. We sampled target insects using an elevated work platform in a 0.2 ha broadleaf deciduous forest plot in the Czech Republic. We analyzed the effect of vertical position among three canopy levels (first [lowest], second [middle], and third [highest]) and tree species on community descriptors (density, diversity, and parasitism rate) and food web structure. We also analyzed vertical patterns in density and parasitism rate between exposed and semiconcealed hosts, and the vertical preference of the most abundant parasitoid taxa in relation to their host specificity. Tree species was an important determinant of all community descriptors and food web structure. Insect density and diversity varied with the vertical gradient, but was only significant for hosts. Both host guilds were most abundant in the second level, but only the density of exposed hosts declined in the third level. Parasitism rate decreased from the first to third level. The overall parasitism rate did not differ between guilds, but semiconcealed hosts suffered lower parasitism in the third level. Less host‐specific taxa (Ichneumonidae, Braconidae) operated more frequently lower in the canopy, whereas more host‐specific Tachinidae followed their host distribution. The most host‐specific Chalcidoidea preferred the third level. Vertical stratification of insect density, diversity, and parasitism rate was most pronounced in the tallest tree species. Therefore, our study contradicts the general paradigm of weak arthropod stratification in temperate forest canopies. However, in the network structure, vertical variation might be superseded by variation among tree species.

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Section: Methodsmentioning

confidence: 99%

Vertical canopy gradient shaping the stratification of leaf‐chewer–parasitoid interactions in a temperate forest

Šigut

Šigutová

Šipoš

et al. 2018

Ecology and Evolution

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“…Depressaria sp. and the subfamily Olethreutinae were made by comparing the COI sequences with DNA barcodes in BOLD through their Barcode Index Number (BIN) assignments (Ratnasingham and Hebert 2013). The remaining specimens were identified using the identification tool in BOLD, an approach which led to uncertainty in species assignments only for Bucculatrix sp.…”

Section: Methodsmentioning

confidence: 99%

“…DNA barcoding (Hebert et al 2003) can overcome this hurdle if a high quality reference library is available to permit specieslevel matches. Moreover, even if a specific match cannot be made at the time of data acquisition, the deposition of the DNA barcode in BOLD (Ratnasingham and Hebert 2007) allows its assignment to a Barcode Index Number (Ratnasingham and Hebert 2013) and its subsequent assignment to a species when the barcode reference library gains coverage for that taxon. Further efficiency in the analysis of Malaise trap samples can be achieved if combined with high-throughput sequencing technologies, since presorting of the samples then can be reduced to a minimum (Morinière et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Investigating suburban micromoth diversity using DNA barcoding of malaise trap samples

Aagaard

Berggren²,

Hebert

et al. 2016

Urban Ecosyst

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Micromoths can be challenging to identify based on morphology and are frequently omitted in assessments of moth diversity. However, their species richness and biology make them important components of terrestrial ecosystems. In this study we identified 1227 micromoths from a suburban garden at 63°north using DNA barcoding of Malaise trap samples. We recorded 78 different species with the 11 most abundant taxa accounting for 82 % of the catch. The remaining 67 species were represented by fewer than 14 specimens, but the number was often sufficient to provide a good idea of phenology. The larvae of these 78 species all feed on plants common in suburban environments. We show that when facilitated by identifications through DNA barcoding, Malaise traps provide interesting insights into the micromoth communities of suburban environments that might otherwise be overlooked. The use of Malaise traps is beneficial for investigations at high latitudes where light trapping is inefficient for sampling moths due to bright summer nights.

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“…Although the bulk of the world's sequence data is available in the INSDC, this is not the case for DNA barcodes, most of which reside in the Barcode of Life Data System (BOLD) [34,35]. Since 2009 BOLD has released nearly 2.5 million DNA barcodes, with updates every few months.…”

Section: Genomicsmentioning

confidence: 99%

“…6b shows a geophylogeny [26] for DNA barcodes from BOLD for Morethia obscura which reveals considerable phylogenetic structure within "Morethia obscura". Specimens of this species are assigned several distinct Barcode Index Numbers (BINs) [35] implying that "Morethia obscura" comprises more than one species.…”

Section: Integrating Biodiversity Informationmentioning

confidence: 99%

DNA barcoding and taxonomy: dark taxa and dark texts

Page

2016

Preprint

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Both classical taxonomy and DNA barcoding are engaged in the task of digitising the living world. Much of the taxonomic literature remains undigitised. The rise of open access publishing this century, and the freeing of older literature from the shackles of copyright has greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid-to late twentieth century remains offline ("dark texts"). DNA barcoding is generating a wealth of computable data that in many ways is much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These "dark taxa" hamper the classical method of integrating biodiversity data using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature, and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global "digital dashboard" to assess the extent to which biodiversity data is available online.

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A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

Cited by 1,760 publications

References 61 publications

Vertical canopy gradient shaping the stratification of leaf‐chewer–parasitoid interactions in a temperate forest

Vertical canopy gradient shaping the stratification of leaf‐chewer–parasitoid interactions in a temperate forest

Investigating suburban micromoth diversity using DNA barcoding of malaise trap samples

DNA barcoding and taxonomy: dark taxa and dark texts

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