A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys)

Schmidt, Olga; Hausmann, Axel; Araújo, Bruno Cancian de; Sutrisno, Hari; Peggie, Djunijanti; Schmidt, Stefan

doi:10.3897/bdj.5.e20006

Cited by 13 publications

(13 citation statements)

References 33 publications

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“…However, the coverage for the Madagascan lepidopteran fauna is very sparse. Nevertheless, the use of Barcode Index Numbers (BINs) (Ratnasingham and Hebert 2013) as proxies for species allows the assessment of hyperdiverse groups that are taxonomically poorly known, such as micromoths (Schmidt et al 2017;Aagaard et al 2017;Lees et al 2013;Lopez-Vaamonde et al 2012). As of 29 June 2018 (including the current study) there were 2852 DNA barcode BINs for Madagascar out of a total of 113 161 lepidopteran BINS, according to a search of the BIN database in the public portal of BOLD.…”

Section: Introductionmentioning

confidence: 97%

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

Lopez‐Vaamonde

Sire

Rasmussen

et al. 2019

Genome

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Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar. In total, we DNA barcoded 2956 specimens belonging to 1537 Barcode Index Numbers (BINs), 88.4% of which are new to BOLD. Only 1.7% of new BINs were assigned to species. Of 47 different families found, Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae, and Blastobasidae are newly reported for Madagascar and the recently recognized Tonzidae is confirmed. For test faunas of Canada and Australia, 98.9%-99.4% of Macroheterocera BINs exhibited the molecular synapomorphy of a phenylalanine in the 177th complete DNA barcode codon. Non-macroheteroceran BINs could thus be sifted out efficiently in the Malaise sample. The Madagascar micromoth fauna shows highest affinity with the Afrotropics (146 BINs also occur in the African continent). We found 22 recognised pests or invasive species, mostly occurring in disturbed habitats. Malaise trap samples show high temporal turnover and alpha diversity with as many as 507 BINs collected; of these, astonishingly, 499 (98.4%) were novel to BOLD and 292 (57.6%) were singletons. Our results provide a baseline for future surveys across the island.

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Section: Introductionmentioning

confidence: 97%

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

Lopez‐Vaamonde

Sire

Rasmussen

et al. 2019

Genome

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“…The latter was a short Malaise trapping exercise with one trap that was operated for three weeks. For more details about the field and lab protocols see Schmidt et al (2015) , Schmidt et al (2017) and below. The specimen data are accessible on BOLD through the following doi: 10.5883/DS-INWPAPUA and through GenBank (Accession nos MH094885-MH095566),…”

Section: Methodsmentioning

confidence: 99%

“…They serve mainly the purpose of demonstrating sampling, preparation and identification methods for insects and other arthropods. The scientific value of insect collecting during student courses can be dramatically increased if the specimens are adequately preserved and/or mounted for long-term storage in a scientific collection ( Lopez-Vaamonde et al 2012 , Schmidt et al 2017 ). This applies even more if samples are then utilised for more sustainable methods of biodiversity assessment, such as DNA barcode analysis and if sequence and associated collecting data are generally accessible for researchers nationally and internationally (see Hebert et al 2003 , Hajibabaei et al 2005 , Janzen et al 2009 , Gwiazdowski et al 2015 , Wirta et al 2015 , Miller et al 2016 ).…”

Section: Introductionmentioning

confidence: 99%

From field courses to DNA barcoding data release for West Papua - making specimens and identifications from university courses more sustainable

Araújo

Schmidt

et al. 2018

BDJ

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“…A summary of fieldwork and laboratory procedures employed in the IndoBioSys project were presented by Schmidt et al 2017. Methodological steps specific for the work package presented here are described below.…”

Section: Methodsmentioning

confidence: 99%

The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia

Araújo¹,

Schmidt²,

Schmidt³

et al. 2018

BDJ

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The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.

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A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys)

Cited by 13 publications

References 33 publications

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

From field courses to DNA barcoding data release for West Papua - making specimens and identifications from university courses more sustainable

The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia

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