Biodiversity Data Journal :
Research Article
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Corresponding author: Bruno Cancian de Araujo (chalcididae@gmail.com)
Academic editor: John-James Wilson
Received: 06 Nov 2018 | Accepted: 19 Dec 2018 | Published: 15 Jan 2019
© 2019 Bruno Cancian de Araujo, Stefan Schmidt, Olga Schmidt, Thomas von Rintelen, Kristina von Rintelen, Andreas Floren, Rosichon Ubaidillah, Djunijanti Peggie, Michael Balke
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Cancian de Araujo B, Schmidt S, Schmidt O, von Rintelen T, von Rintelen K, Floren A, Ubaidillah R, Peggie D, Balke M (2019) DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project. Biodiversity Data Journal 7: e31432. https://doi.org/10.3897/BDJ.7.e31432
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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.
Beetles, BIN, biodiversity, BOLD, Cikaniki, collecting methods, databasing, DNA barcoding, Gunung Botol, Insecta, inventory, Java, monitoring
Insects and other invertebrates account for over 97% of multicellular animal species diversity (
Here we focus on Indonesia, one of the most biodiversity rich countries on Earth, with its diversity, however, largely undiscovered and not described scientifically (Fig.
Heat map showing the worldwide distribution of occurrence records provided by the Global Biodiversity Information Facility (GBIF, www.gbif.org, accessed on 15-Dec-2018). Only 0.19% of the approximately one billion occurrence records that are accessible through GBIF are from Indonesia (blue ellipse), despite Indonesia's being amongst the top global biodiversity hotspots.
The Indonesian archipelago comprises two of the world’s biodiversity hotspots, i.e. areas with a high degree of endemic species that are highly threatened by loss of habitats (see
To accelerate the biodiversity discovery process, as well as to increase our knowledge about the archipelago fauna, the German-Indonesian IndoBioSys project (IndoBioSys, Indonesian Biodiversity Discovery and Information System) combines species discovery and species characterisation using morphology and DNA sequence data (e.g.
Here, we present the results of a DNA barcoding pipeline to provide the first objective diversity assessment of Indonesian forest canopy Coleoptera. This is based on the canopy fogging workpackage of the German-Indonesian IndoBioSys project (IndoBioSys) that combined extensive fieldwork in the Gunung Halimun-Salak National Park in West Java with databasing, molecular species delineation and joint release of results in support of further analysis. A project outline was provided by
Data are stored in and were analysed with the Barcode of Life Data Systems (BOLD). A summary of fieldwork and laboratory procedures related to this study are given in
Canopy fogging was performed at two different sites, Cikaniki and Gunung Botol, in the south-eastern part of the Gunung Halimun-Salak National Park in West Java, Indonesia (Fig.
Family | Species | Cikaniki | Gunung Botol |
Annonaceae | Polyalthia subcordata | 2 | |
Elaeocarpaceae | Sloanea sigun | 4 | 2 |
Fagaceae | Litocarpus indutus | 6 | 3 |
Fagaceae | Castanopsis javanica | 3 | |
Hamamelidiaceae | Altingia excelsa | 1 | |
Lauraceae | Litsea sp. | 2 | |
Melastomataceae | Memecylongar cinioides | 1 | |
Theaceae | Schima wallichii | 4 |
Specimens were collected using an insecticidal fogging technique (
The samples were processed at the ZSM in Munich, Germany where they were sorted to ordinal level. All Coleoptera that were used for molecular biodiversity assessment were mounted on card labels and labelled. All specimens will be repatriated to MZB at the end of the project. This research was conducted under the foreign research permit granted by the Ministry of Research and Higher Education of the Republic of Indonesia number 2B/TKPIPA/E5/Dit.KI/II/2016.
The terms used to refer to BINs abundance and diversity when presenting and discussing the data are as follows. The term "specimen with sequence" refers to specimens processed that had sequences with a length of least 300 bp, "specimen with BIN" refers to specimens processed that were assigned a BIN by the BOLD system and "exclusive BINs" refers to the number of BINs (pre-existing and new to BOLD) that are unique for a specific site, tree or taxon, in other words, the BINs that are not shared with any other site, tree or taxon.
Collection and molecular data were downloaded from the BOLD IndoBioSys campaign projects. The records recovered were filtered by insect order and collecting method, those being the records corresponding to "Coleoptera" collected by "fogging", individualised in separate Excel worksheets for data release and descriptive analysis of spatial and diversity distribution.
All specimen data are accessible in BOLD as a single citable dataset (dx.doi.org/10.5883/DS-INFOGCOL). The data include the record identifier, collecting locality, geographic coordinates, elevation, collector and specimen image. Sequence data can be obtained through BOLD and include a detailed LIMS report, primer informationand access to trace files. The sequences are also available on GenBank (accession numbers MK080571-MK084473).
Most specimens were identified at the family level before submission to the molecular analysis pipeline and to the BOLD platform. After BIN assignment by the BOLD system, specimens that were not identified at the family level and which succeed in receiving a BIN were identified by using the BOLD identification system (BOLD taxonomy match). The BIN-based identification was double-checked by comparing images with images of previously identified specimens and, if necessary, using a tree-based identification approach (NJ-trees).
In total, 7,447 specimens of Coleoptera were processed. From those, 3,836 specimens produced CO1-5P sequences longer than 300 base pairs, representing a success rate of 50.35%, with 3,750 of those specimens receiving a BIN. In total, it corresponded to 747 BINs, distributed heterogeneously over 39 families of Coleoptera. The total amount of specimens with BINs was evenly distributed between the two sites being 2,013 specimens (53.68%) for Cikaniki and 1,737 specimens (46.32%) for Gunung Botol. Despite that, the diversity of BINs found in both sites was not as even as that, with 557 BINs found in Cikaniki and 271 BINs found in Gunung Botol corresponding, respectively, to 67.27% and 32.73% of the BINs diversity. The distribution of specimens with BINs per tree was quite heterogeneous in both sites (especially in Cikaniki) even in terms of the abundance of specimens or diversity of BINs. In terms of abundance, tree 25 from Cikaniki contributed only 10 specimens with BINs when tree 29, at the same site, contributed 448 specimens with BINs, a difference of 44.8 times (Fig.
The specimen distribution per taxon was heterogeneous as well, with only one family (Chrysomelidae) revealing 961 specimens with BINs, more than a quarter of the total found. The two families with most specimens (Chrysomelidae and Staphylinidae) contributed more to the total of specimens with BINs than all other families together with the 25 families with fewer specimens contributing with less than 1% of the total each (Fig.
Part of the Coccinellidae morphological diversity and its correspondent BINs: A. BOLD:ADG7156, B. BOLD:ADG0348 C. BOLD:ADG7156 D. BOLD:ADH1869 E. BOLD:ADG7156 F. BOLD:ADG7156 G. BOLD:ADG3219 H. BOLD:ADG3219 I. BOLD:ADH0801 J. BOLD:ADG3219 K. BOLD:ADC1473 L. BOLD:ADC1743 M. BOLD:ADG8109 N. BOLD:ADG0348 O. BOLD:ADG0348 P. BOLD:ADG7156 Q. BOLD:ADA5666 R. BOLD:ADD3008 S. BOLD:ADH3343 T. BOLD:ADG0264.
The data show a large heterogeneity in terms of abundance and distribution of BINs across sites, trees and families of Coleoptera. From the total of 747 BINs found, 421 (56.4%) are exclusive to a single tree. The low amount of BINs shared between Cikaniki and Gunung Botol sites (81 of the 747 BINs) is impressive considering that those sites are separated by only five kilometres of continuous forest. This might suggest a high altitudinal stratification since Cikaniki is on average 600 metres lower than Gunung Botol. This diversity is also not evenly distributed per tree, with the exclusivity of BINs per tree varying between 2.3% to 20.4% of the total of BINs. Tree 29 from Cikaniki site exemplifies the complex distribution of the Coleoptera diversity over this area. Despite being the tree with the largest contribution in terms of specimens and sequences (972 specimens, 448 producing BINs), most of those specimens share the same BIN ending in a diversity of only 185 BINs for this tree, which indicates an ambient with high abundance and low diversity of beetles. Despite that, 74 of those 185 BINs (16.5%) were found exclusively at this tree, showing that this relatively low diversity is potentially endemic.
At the same time, abundance and diversity were not necessarily related when analysing the families of Coleoptera. The family Coccinellidae has shown to be both diverse and abundant (Fig.
Four putative species (e.g. BOLD:ADG3219 Fig.
With this data release, we expect to highlight the diversity hidden in the canopy of the tropical forests, as well as support and encourage future robust analysis that will help to better understand the processes involved in such an impressive speciation.
The data released here are also an invitation to expert taxonomists to screen the species pages and contribute with further identification, where possible, based on the voucher images.
We thank the Ministry of Research and Higher Education of the Republic of Indonesia for providing a foreign research permit to BCA, SS and OS (number 2B/TKPIPA/E5/Dit.KI/II/2016). The IndoBioSys project was funded by the German Federal Ministry of Education and Research (BMBF) within the bilateral "Biodiversity and Health" funding programme (Project numbers: 16GW0111K, 16GW0112); the Indonesian counterpart institutions were funded by DIPA PUSLIT Biologi LIPI 2015-2016. Many thanks to Dr. Iva Njunjić, Dr. Alexander Riedel and Dr. John James Wilson for their constructive insights and very helpful comments on the manuscript.