Biodiversity Data Journal :
Research Article
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Corresponding author: Bruno Cancian de Araujo (chalcididae@gmail.com)
Academic editor: Gergin Blagoev
Received: 20 Sep 2018 | Accepted: 28 Nov 2018 | Published: 19 Dec 2018
© 2018 Bruno Cancian de Araujo, Stefan Schmidt, Olga Schmidt, Thomas von Rintelen, Rosichon Ubaidillah, 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, Ubaidillah R, Balke M (2018) The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia. Biodiversity Data Journal 6: e29927. https://doi.org/10.3897/BDJ.6.e29927
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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.
Biodiversity, BOLD, Chalcidoidea, Coleoptera, Diptera, Hymenoptera, IndoBioSys, Inventory, Java, Lepidoptera
The Indonesian archipelago features an extraordinarily rich biota that is, amongst other factors, derived from its sheer size and geographic position, basically linking the Oriental and Australian regions. This transition was first described in detail by
The Indonesian and German ministries of Research and Education have therefore provided funding to establish a biodiversity information system (IndoBioSys), that integrates occurrence databasing, species discovery and species characterisation, using morphology and DNA sequence data, specimen vouchering, as well as integrated tools for the discovery of substances of potential use for society. IndoBioSys is, therefore, a case study and foundation for the large-scale exploration of Indonesian species diversity. Moreover, IndoBioSys could be a foundation for the empirical and objective,scientific assessment of species distribution patterns across the archipelago, for example, needed for conservation priority setting.
One work package of the IndoBioSys project was an assessment of the species diversity of the hyperdiverse insect fauna of the Mount Halimun-Salak National Park in West Java, with a focus on sampling with Malaise traps. The National Park has been recognised as one of the largest tropical rain-forest ecosystems left in Java, being designated as a National Park in 2003 with a present area of about 113,357 hectares. Malaise trapping (
Subsets of the samples obtained were submitted to a well-established pipeline employing DNA barcoding (
Here, we release these data with an analysis of their taxonomic content, an approximation of the species diversity encountered and an evaluation of the novelty of the data with respect to publicly available data from the Barcode of Life Data Systems (BOLD).
A summary of fieldwork and laboratory procedures employed in the IndoBioSys project were presented by
From September 2015 until April 2016, 34 Malaise traps (Townes style,
The traps were run for about 120 days in total and the collecting bottles changed monthly. Collecting liquid was 300 ml of 96% Ethanol in each bottle.
The samples were taken to the IndoBioSys Indonesian laboratory at the Museum Zoologicum Bogoriense (MZB) in Cibinong, West Java. Using a 3 mm mesh sieve, they were broken down into two fractions, according to the size of the animals with the smaller samples passing the sieve into a collecting tray.
This fractioning is important for optimising the sorting process as well as for separating the specimens that will be sent entirely for molecular laboratory processing ("voucher recovery pipeline") from the ones that are large enough for a procedure where only one or more legs are removed from the voucher for laboratory use ("leg picking pipeline"). Most of the fractions were sent to the IndoBioSys laboratory at SNSB-ZSM in Munich, where they were sorted to order and family level.
Given the enormous number of specimens (we estimated over 300,000 specimens of invertebrates collected during the project), the orders Coleoptera and Hymenoptera were chosen as the main target groups for the present analysis. Selected groups of Diptera, in particular Syrphidae and Phoridae, will be dealt with in a separate data release. Here, we present the results of a few specimens randomly picked from the samples. For Coleoptera and Hymenoptera, specimens were taken quantitatively from the samples except in case of a long series of morphologically similar individuals, in which case we took only representatives. In these cases, a smaller amount of specimens that represents the morphological diversity of the series was chosen in order to prevent cryptic species bias. The number of specimens taken was determined on a case by case basis.
Lepidoptera, another target group of the IndoBioSys project, were collected using a different method, as described earlier (
All specimens that were not further processed were repatriated to the MZB as ethanol samples. All processed specimens were returned to MZB as dry mounted and labelled voucher specimens (Fig.
All specimen data are accessible in BOLD as a single citable dataset (dx.doi.org/10.5883/DS-IDBMTP). The data include collecting locality, geographic coordinates, elevation, collector, one or more digital images, identifier and voucher depository. Sequences data can be obtained through BOLD and include a detailed LIMS report, primer information and access to trace files. The sequences are also available on GenBank (accession numbers MH926363-MH929079).
Locality information and molecular data from the Malaise trapping programme were downloaded from the BOLD IndoBioSys campaign projects. The records downloaded were individualised by trap and by insect order in separate excel worksheets for analysis of spatial and diversity distribution. Here, we only focus on the orders Hymenoptera, Coleoptera, Diptera and Lepidoptera.
A total of 4,531 specimens were prepared for DNA barcoding. Of these, we obtained cox1-5P sequences from 2,732 individuals. Sequences from 2,598 of these individuals were longer than 300 base pairs. In total, 2,380 individuals produced barcode compliant records (Table
Order | Total indiv. | % |
Indiv. with sequence |
% | BINs | % | Proccessed indiv. per BIN |
Indiv. w sequence per BIN |
Diptera | 108 | 2.4 | 67 | 62.0 | 53 | 4.4 | 2.2 | 1.1 |
Lepidoptera | 169 | 3.7 | 132 | 78.1 | 34 | 2.8 | 5.0 | 3.9 |
Coleoptera | 1,174 | 25.9 | 835 | 71.1 | 398 | 33.2 | 2.9 | 2.1 |
Hymenoptera | 3,080 | 68.0 | 1,702 | 55.3 | 712 | 59.5 | 4.3 | 2.4 |
These 2,380 individuals represent 1,197 exclusive BINs or putative species. They could be assigned to 98 different insect families (Table
COLEOPTERA |
HYMENOPTERA |
||||||
Family |
spp w/ BINs |
Unique BINs |
spp/BIN |
Family |
spp w/ BINs |
Unique BINs |
spp/BIN |
Brentidae |
1 |
1 |
1.0 |
Agaonidae |
5 |
1 |
5.0 |
Buprestidae |
1 |
1 |
1.0 |
Aphelinidae |
36 |
29 |
1.2 |
Erotylidae |
1 |
1 |
1.0 |
Braconidae |
223 |
139 |
1.6 |
Ptiliidae |
1 |
1 |
1.0 |
Chalcididae |
2 |
2 |
1.0 |
Tetratomidae |
1 |
1 |
1.0 |
Crabronidae |
20 |
1 |
20.0 |
Anthicidae |
2 |
1 |
2.0 |
Encyrtidae |
12 |
8 |
1.5 |
Carabidae |
2 |
1 |
2.0 |
Eucharitidae |
8 |
2 |
4.0 |
Cerambycidae |
2 |
2 |
1.0 |
Eulophidae |
133 |
71 |
1.9 |
Melandryidae |
2 |
2 |
1.0 |
Eupelmidae |
2 |
1 |
2.0 |
Limnichidae |
3 |
1 |
3.0 |
Ichneumonidae |
881 |
370 |
2.4 |
Attelabidae |
3 |
3 |
1.0 |
Mymaridae |
32 |
22 |
1.5 |
Leiodidae |
3 |
3 |
1.0 |
Perilampidae |
2 |
2 |
1.0 |
Mycetophagidae |
3 |
3 |
1.0 |
Pteromalidae |
50 |
15 |
3.3 |
Nitidulidae |
3 |
3 |
1.0 |
Sphecidae |
3 |
1 |
3.0 |
Ptinidae |
3 |
3 |
1.0 |
Tenthredinidae |
3 |
1 |
3.0 |
Eucnemidae |
4 |
2 |
2.0 |
Torymidae |
6 |
2 |
3.0 |
Tenebrionidae |
4 |
3 |
1.3 |
Unknown |
63 |
44 |
1.5 |
Throscidae |
7 |
4 |
1.8 |
Vespidae |
7 |
1 |
7.0 |
Melyridae |
7 |
6 |
1.2 |
TOTAL |
1,488 |
712 |
2.2 |
Anthribidae |
9 |
7 |
1.3 |
||||
Scarabaeidae |
11 |
5 |
2.2 |
LEPIDOPTERA |
|||
Scirtidae |
11 |
5 |
2.2 |
Family |
spp w/ BINs |
Unique BINs |
spp/BIN |
Cleridae |
14 |
4 |
3.5 |
Geometridae |
25 |
17 |
1.5 |
Latridiidae |
15 |
3 |
5.0 |
Noctuidae |
1 |
1 |
1 |
Curculionidae |
15 |
11 |
1.4 |
Erebidae |
1 |
1 |
1 |
Lampyridae |
16 |
3 |
5.3 |
Uraniidae |
1 |
1 |
1 |
Lycidae |
16 |
11 |
1.5 |
Unknown |
23 |
14 |
1.6 |
Aderidae |
19 |
6 |
3.2 |
TOTAL |
51 |
34 |
1.2 |
Phalacridae |
20 |
8 |
2.5 |
||||
Elateridae |
20 |
11 |
1.8 |
DIPTERA |
|||
Mordellidae |
22 |
15 |
1.5 |
Family |
spp w/ BINs |
Unique BINs |
spp/BIN |
Corylophidae |
24 |
11 |
2.2 |
Phoridae |
5 |
5 |
1.0 |
Hydrophilidae |
28 |
3 |
9.3 |
Muscidae |
3 |
2 |
1.5 |
Scraptiidae |
37 |
7 |
5.3 |
Cecidomyiidae |
1 |
1 |
1.0 |
Cantharidae |
42 |
15 |
2.8 |
Tipulidae |
1 |
1 |
1.0 |
Chrysomelidae |
69 |
36 |
1.9 |
Syrphidae |
1 |
1 |
1.0 |
Coccinellidae |
71 |
35 |
2.0 |
Asilidae |
2 |
2 |
1.0 |
Staphylinidae |
114 |
35 |
3.3 |
Tachinidae |
1 |
1 |
1.0 |
Unknown |
154 |
126 |
1.2 |
Unknown |
47 |
40 |
1.2 |
TOTAL |
780 |
398 |
2.2 |
TOTAL |
61 |
53 |
1.2 |
The highest diversity of BINs was found in Hymenoptera (712 BINs), followed by Coleoptera (398), Diptera (53) and Lepidoptera (34). The diversity per order was always high, with two or less individuals per BIN on average. The diversity per family was also impressive with 50% of the families being composed by BINs represented by singletons or doubletons.
Given the discrepancy in the sampling effort, it was not possible to compare taxonomic disparities amongst the four sampling areas. The sampling was focused on Cikaniki due to the better conservation of the forest in this area and the presence of the research station that provided better infrastructure to the scientific staff.
Even collecting at four different locations in one nature reserve, the IndoBioSys Malaise trap project alone has added 1,149 new BINs to BOLD. It shows how fast molecular pipelines contribute substantially to objectively inventorying the fauna of megadiverse areas. It also allows us to estimate the enormous diversity of tropical areas like the Halimun-Salak National Park. The astonishing heterogeneity of BINs (See Fig.
The supraspecific taxonomic diversity was relatively high considering the number of specimens analysed. As a comparison, Hendrich and collaborators in their release of a comprehensive DNA barcode database for Central European beetles (
The diversity of Chalcidoidea, a superfamily of Hymenoptera, gives us a clear picture of the diversity uncovered at Halimun-Salak National Park. The Universal Chalcidoidea Database (
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 is funded by the Bundesministerium für Bildung und Forschung 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.