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)

Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology – Indonesian Institute of Sciences (RCB-LIPI, Bogor)

Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix

The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5' fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage >10;CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples;whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming pre-sorting process will yield approximately 30% more high score BINs compared to the nonsorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline

INDOBIOSYS – DNA BARCODING AS A TOOL FOR THE RAPID ASSESSMENT OF HYPERDIVERSE INSECT TAXA IN INDONESIA: A STATUS REPORT

A status report with preliminary results for the IndoBioSys project is presented and the impact of the project results for our knowledge of the Indonesian fauna is discussed. Using the REST API available on the Barcode of Life Data System we recover 21,153 public records (3,390 BINs) from Indonesia and compare against the 21,813 records (3,580 BINs) generated by the IndoBioSys project. From all IndoBioSys BINs, 3,366 (94%) are new to Indonesia. IndoBioSys is responsible for a BIN increase of 36.5% in Lepidoptera, 62.6% in Trichoptera, 986% in Coleoptera, and 1,086% in Hymenoptera. After two years of the IndoBioSys project, the Museum Zoologicum Bogoriense became the depository institution of 51.9% of Lepidoptera records, 95.8% of Coleoptera records, 97.6% of Hymenoptera records and 59.4% of Trichoptera records for Indonesia available on Barcode of Life Data System (BOLD). Now, with 55% of all Indonesian records available on BOLD, it is the most important depository for records of Indonesian genetic biodiversity, housing more than 23,000 new voucher specimens in their collections. Before IndoBioSys, the Museum Zoologicum Bogoriense was responsible for only 9% of all records available in the Barcode of Life Data System for Indonesia, showing the importance of those pipelines in empowering the local institutions in becoming the reference depository of the local fauna

DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project

We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. A total of 3,750 specimens were assigned a Barcode Index Number (BIN), including 2,013 specimens from Cikaniki and 1,737 specimens from Gunung Botol. The 747 BINs, that were obtained, represented 39 families of Coleoptera. The distribution of specimens with BINs per tree was quite heterogeneous in both sites even in terms of the abundance of specimens or diversity of BINs. The specimen distribution per taxon was heterogeneous as well. Some 416 specimens could not be identified to family level, corresponding to 72 BINs that lack a family level identification. The data have shown a large heterogeneity in terms of abundance and distribution of BINs between sites, trees and families of Coleoptera. From the total of 747 BINs that were recovered, 421 (56%) are exclusive from a single tree. Although the two study sites were in close proximity and separated by a distance of only about five kilometres, the number of shared BINs between sites is low, with 81 of the 747 BINs. With this data release, we expect to shed some light on the largely hidden diversity in the canopy of tropical forests in Indonesia and elsewhere

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

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

Figure 2 from: Cancian de Araujo B, Schmidt S, Schmidt O, von Rintelen T, Kilmaskossu A, Panjaitan R, Balke M () From field courses to DNA barcoding data release for West Papua - making specimens and identifications from university courses more sustainable. . https://doi.org/

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

DNA barcoding data release for the Phoridae (Insecta, Diptera) of the Halimun-Salak National Park (Java, Indonesia)

Launched in 2015, the large-scale initiative Indonesian Biodiversity Discovery and Information System (IndoBioSys) is a multidisciplinary German-Indonesian collaboration with the main goal of establishing a standardised framework for species discovery and all associated steps. One aspect of the project includes the application of DNA barcoding for species identification and biodiversity assessments. In this framework, we conducted a large-scale assessment of the insect fauna of the Mount Halimun-Salak National Park which is one of the largest tropical rain-forest ecosystems left in West Java. In this study, we present the results of processing 5,034 specimens of Phoridae (scuttle flies) via DNA barcoding. Despite limited sequencing success, we obtained more than 500 clusters using different algorithms (RESL, ASAP, SpeciesIdentifier). Moreover, Chao statistics indicated that we drastically undersampled all trap sites, implying that the true diversity of Phoridae is, in fact, much higher. With this data release, we hope to shed some light on the hidden diversity of this megadiverse group of flies

DNA barcoding data release for the Phoridae (Insecta, Diptera) of the Halimun-Salak National Park (Java, Indonesia)

Launched in 2015, the large-scale initiative Indonesian Biodiversity Discovery and Information System (IndoBioSys) is a multidisciplinary German-Indonesian collaboration with the main goal of establishing a standardized framework for species discovery and all associated steps. One aspect of the project includes the application of DNA barcoding for species identification and biodiversity assessments. In this framework, we conducted a large-scale assessment of the insect fauna of the Mount Halimun-Salak National Park which is one of the largest tropical rain-forest ecosystems left in West Java. In this study, we present the results of processing 5,034 specimens of Phoridae (scuttle flies) via DNA barcoding. Despite limited sequencing success, we obtained more than 500 clusters using different algorithms (RESL, ASAP, SpeciesIdentifier). Moreover, Chao statistics indicated that we drastically undersampled all trap sites, implying that the true diversity of Phoridae is in fact much higher. With this data release, we hope to shed some light on the hidden diversity of this megadiverse group of flies