Biodiversity Data Journal : Short Communications
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Short Communications
From field courses to DNA barcoding data release for West Papua - making specimens and identifications from university courses more sustainable
expand article infoBruno Cancian de Araujo, Stefan Schmidt, Olga Schmidt, Thomas von Rintelen§, Agustinus Kilmaskossu|, Rawati Panjaitan|, Michael Balke
‡ SNSB-Zoologische Staatssammlung München, Munich, Germany
§ Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| Department of Biology, Faculty of Sciences and Mathematics, State University of Papua (UNIPA), Jalan Gunung Salju Amban, Manokwari, Indonesia
Open Access

Abstract

The diversity of insects collected during entomological field courses at the University of West Papua (UNIPA), Indonesia, is studied using DNA barcoding tools. The results were compared with public data available for West Papua in the Barcode of Life Data System. During two training courses in 2013 and 2015, 1,052 specimens of insects were collected at eight sites near Manokwari in northern West Papua. The DNA sequences obtained from these specimens were assigned to 311 Barcode Index Numbers (BINs) and represent species in 27 families of Lepidoptera, Hymenoptera and Coleoptera. Of those BINs, 294 (95%) were new to West Papua. The study suggests that DNA barcoding applied to university courses achieves several goals, including capacity building and hands-on experience in molecular biodiversity assessment. In addition, it can provide valuable biodiversity data that are globally available to researchers for further studies.

Introduction

Carrying out field courses for students is a central aspect of any capacity building effort at universities, including and perhaps especially so in tropical countries (see Basset et al. 2000, Basset et al. 2004, Novotny et al. 2012, Tänzler et al. 2012, Rintelen et al. 2017). 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).

The present study makes an attempt to use specimens of insects collected during student courses in a more sustainable way. In particular, we tried to maximise the potential benefit of field and entomological training courses at the University of West Papua (UNIPA) on the western part of the island of New Guinea. The courses were conducted by a team of entomologists from the Zoologische Staatssammlung (ZSM) in Munich, Germany, which was followed up by a repeated staff exchange from UNIPA to the ZSM.

Material and Methods

The methods were described in Cancian de Araujo et al. (2017), with the following differences:

Specimen collecting and processing

In 2013 and 2015, 1,052 specimens of insects were collected during capacity building courses by lecturers and students of the State University of Papua (UNIPA) in Manokwari. The collections mainly served as a vehicle to demonstrate field survey methods and subsequent laboratory procedures for sustainable biodiversity inventory and discovery. Targeted field work was coordinated by RP and AK and part of the laboratory work was conducted by RP during her stay at the SNSB-Zoologische Staatssammlung München (ZSM, Bavarian State Collection of Zoology) in 2014 under the supervision of MB, SS and OS.

Samples were collected at eight sites in the Indonesian province West Papua, viz. Fumato, Kebar Village, Minyambo, Mubrani, Syoubri, Senopi, Gunung Meja and the Papua University Campus in Manokwari (Fig. 1). 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),

Figure 1.  

Specimens distribution per site and Order.

Data acquisition

The specimen data and result files generated for the present study were downloaded directly from the Barcode of Life Data Systems (BOLD, http://www.boldsystems.org) workbench. In addition, all other public records from the province West Papua and other Indonesian areas from the western half of the island of New Guinea present in BOLD were obtained through the REST API of the BOLD platform on 31-Jan-2018. We applied the “Full Data Retrieval” parameters geo=Papua|West%20Papua|Papua%20Barat and marker=COI–5P in order to gather all public records from West Papua with the standard DNA barcoding marker (COI–5P).

Data processing

The files that were downloaded contained information on each record including the Barcode Index Number (BIN), collection data and taxonomy. The data were evaluated in terms of BIN diversity, spatial distribution of specimens, taxonomic identification depth and taxonomic diversity. The results were compared in terms of diversity of BINs, exclusive and shared BINs and BIN distribution. Analyses and comparisons were made using Microsoft Excel. The number of BINs shared by the two sources was evaluated and after that, the shared BINs were subtracted from our West Papua list in order to highlight the contribution of our case study for West Papuan records in general. The map with collecting records was created using Quantum GIS (vers. 2.8).

Results

Between 2013 and 2015, 1,052 specimens from West Papua were processed. The records are distributed in six areas in West Papua and were collected at altitudes between 80 and 1,555 meters above sea level. The taxa belong to three insect orders: Coleoptera (108), Hymenoptera (217) and Lepidoptera (727). The geographic distribution per site and taxon are presented in Fig. 1. Out of these 1,052 specimens, the CO1-5P barcode sequence was recovered from 686 specimens, corresponding to 311 BINs from at least 27 families of insects (Fig. 2).

Figure 2.  

BINs distribution per Order and Family.

When searching for public data of arthropods from West Papua in BOLD, we recovered 1,268 records that were assigned to 584 BINs. The records belong to 10 orders with the most common being Lepidoptera (910 records, 441 BINs), Coleoptera (214 records, 68 BINs) and Decapoda (60 records, 30 BINs). When comparing our records with the public data available on BOLD, only 17 BINs (5%) had been recorded before from West Papua, whereas 294 BINs (95%) were new records for this area in BOLD.

A comparison of BINs recorded in our study that were also recorded from elsewhere showed that 74 BINs (24%) were already present in BOLD from regions outside of West Papua, mainly from Australia (39 BINs), Papua New Guinea (23 BINs), French Polynesia (6 BINs) and Indonesian locations other than West Papua (23 BINs) (Table 1). The species is given if the BIN was associated with a species (or genus) name in BOLD, but it should be stressed that, for many species, the barcode-based species level identification require verification based on morphology by a specialist.

Taxa with BOLD records from locations outside West Papua. Given are insect order, family, Barcode Index Number (BIN) and species (or genus) in case of a BOLD BIN match and country from where the species was recorded.

Order Family BIN / Species Country
Coleoptera Chrysomelidae BOLD:ADG9196 Indonesia (West Sumatera)
Coleoptera Coccinellidae

BOLD:AAH3306

(Scymnus mitior)

Australia
Coleoptera Coccinellidae BOLD:ADC0638 Indonesia (West Sumatera)
Coleoptera Mordellidae BOLD:ADC2466 Malaysia
Coleoptera Nitidulidae

BOLD:ADG5133

(Epuraea ocularis)

Indonesia (West Sumatera), French Polynesia
Hymenoptera Aphelinidae BOLD:ADD0593 Indonesia (West Java)
Hymenoptera Braconidae

BOLD:AAH1084

(Cotesia sp.)

Australia, French Polynesia, Indonesia (West Sumatera), Pakistan, Papua New Guinea, United Arab Emirates
Hymenoptera Braconidae BOLD:AAH1349 Indonesia (West Java), South Korea
Hymenoptera Braconidae BOLD:ADJ6741 Indonesia (West Java)
Hymenoptera Chalcididae BOLD:AAW0748 Australia
Hymenoptera Crabronidae BOLD:ACV0318 Indonesia (West Sumatera)
Hymenoptera Encyrtidae BOLD:ACP0359 Indonesia (Bali, West Sumatera), Australia
Hymenoptera Eulophidae BOLD:ADE0821 Indonesia (West Java)
Hymenoptera Ichneumonidae

BOLD:AAH2022

(Enicospilus sp.)

Australia, Indonesia (West Sumatera)
Hymenoptera Ichneumonidae BOLD:ADG2435 Indonesia (West Java)
Hymenoptera Ichneumonidae BOLD:ADK3119 Indonesia (West Java)
Hymenoptera Sphecidae BOLD:AAH3486 Australia
Lepidoptera Crambidae

BOLD:AAA3666

(Spoladea recurvalis)

Australia, Canada, China, French Polynesia, Israel, Japan, Pakistan, Seychelles, South Africa, South Korea, United States
Lepidoptera Crambidae

BOLD:AAB5972

(Prophantis adusta)

Australia, Papua New Guinea
Lepidoptera Crambidae

BOLD:AAC4723

(Cnaphalocrocis poeyalis)

Australia, French Polynesia
Lepidoptera Crambidae

BOLD:AAD1174

(Eurrhyparodes bracteolalis)

Australia
Lepidoptera Crambidae

BOLD:AAD7675

(Tabidia insanalis)

Australia, Papua New Guinea
Lepidoptera Crambidae

BOLD:AAE0808

(Agrioglypta eurytusalis)

French Polynesia, Australia, Indonesia (West Java)
Lepidoptera Crambidae

BOLD:AAE5257

(Herpetogramma hipponalis)

Australia
Lepidoptera Crambidae

BOLD:AAI4942

(Palpita uedai)

Australia
Lepidoptera Crambidae

BOLD:AAL8459

(Parotis sp.)

Papua New Guinea
Lepidoptera Crambidae BOLD:ABU8109 Indonesia (West Sumatera)
Lepidoptera Drepanidae

BOLD:AAD3754

(Tridrepana lunulata)

Australia
Lepidoptera Erebidae

BOLD:AAB3896

(Cyme nr pyraula)

Australia
Lepidoptera Erebidae

BOLD:AAF0763

(Polypogon fractalis)

Australia
Lepidoptera Erebidae

BOLD:AAZ1754

(Harita nodyna)

Australia
Lepidoptera Erebidae

BOLD:ACE6049

(Pogonia umbrifera)

Australia
Lepidoptera Euteliidae

BOLD:AAK0923

(Anigraea cinctipalpis)

Australia, Malaysia
Lepidoptera Euteliidae

BOLD:ABA5144

(Anigraea deleta)

Malaysia
Lepidoptera Geometridae

BOLD:AAA9837

(Eucyclodes pieroides)

Australia
Lepidoptera Geometridae

BOLD:AAA9900

(Hyposidra talaca)

Indonesia (West Java), Australia, China, Papua New Guinea
Lepidoptera Geometridae

BOLD:AAB0565

(Idaea simplex)

Australia
Lepidoptera Geometridae

BOLD:AAB1570

(Comostola leucomerata)

Australia
Lepidoptera Geometridae

BOLD:AAB8518

Australia, French Polynesia
Lepidoptera Geometridae

BOLD:AAC1659

(Pingasa chlora)

Papua New Guinea
Lepidoptera Geometridae

BOLD:AAD4641

(Symmacra ochrea or S. solidaria)

Papua New Guinea
Lepidoptera Geometridae

BOLD:AAE2192

(Chloroclystis cissocosma)

Indonesia (West Java, East Java), Australia
Lepidoptera Geometridae

BOLD:AAE7089

(Agathiopsis basipuncta)

Australia
Lepidoptera Geometridae

BOLD:AAF3254

(Krananda extranotata)

Australia
Lepidoptera Geometridae BOLD:AAF9464 Papua New Guinea
Lepidoptera Geometridae

BOLD:AAF9570

(Episothalma obscurata)

Australia
Lepidoptera Geometridae

BOLD:AAF9586

(Aeolochroma sp.)

Papua New Guinea
Lepidoptera Geometridae BOLD:AAF9622 Indonesia (West Java, East Java)
Lepidoptera Geometridae BOLD:AAI6447 Australia
Lepidoptera Geometridae

BOLD:AAI7614

(Idaea elaphrodes)

Australia
Lepidoptera Geometridae

BOLD:AAL8324

(Thalassodes sp.)

Papua New Guinea
Lepidoptera Geometridae

BOLD:AAR3997

(Chloroclystis semiscripta)

Indonesia (West Java)
Lepidoptera Geometridae

BOLD:ABW8597

(Paradromulia rufibrunnea)

Papua New Guinea
Lepidoptera Geometridae

BOLD:ABX5389

(Cleora illustraria or C. repetita)

Australia, Papua New Guinea
Lepidoptera Geometridae

BOLD:ABX6387

(Craspedosis aurigutta)

Papua New Guinea
Lepidoptera Geometridae

BOLD:ABY7397

(Aeolochroma sp.)

Papua New Guinea
Lepidoptera Geometridae

BOLD:ABZ2247

(Iridobapta argostola)

Australia
Lepidoptera Geometridae

BOLD:ACB0570

(Dioscore meeki)

Papua New Guinea
Lepidoptera Geometridae

BOLD:ACB8931

(Gymnoscelis sp.)

Papua New Guinea
Lepidoptera Geometridae

BOLD:ACE7174

(Nadagarodes duplicipuncta or N. mysolata)

Australia
Lepidoptera Geometridae

BOLD:ACK8229

(Thalassodes umbrimedia)

Papua New Guinea
Lepidoptera Geometridae BOLD:ACM4629 Papua New Guinea
Lepidoptera Geometridae BOLD:ACP9799 Papua New Guinea
Lepidoptera Geometridae BOLD:ACZ0473 Indonesia (East Java)
Lepidoptera Geometridae BOLD:ACZ0547 Indonesia (Bali)
Lepidoptera Geometridae BOLD:ACZ0867 Indonesia (West Java)
Lepidoptera Geometridae BOLD:ACZ1181 Indonesia (West Java)
Lepidoptera Noctuidae

BOLD:AAO8880

(Argyrolepidia thoracophora)

Australia
Lepidoptera Thyrididae

BOLD:AAA8776

(Mellea ordinaria species complex)

Papua New Guinea
Lepidoptera Thyrididae

BOLD:AAG6033

(Canaea hyalospila or C. rusticata)

Australia, Papua New Guinea
Lepidoptera Tortricidae

BOLD:AAA9084

(Adoxophyes templana species comples)

Australia, Papua New Guinea
Lepidoptera Tortricidae

BOLD:AAB4056

(Homona trachyptera)

Australia, Papua New Guinea
Lepidoptera Uraniidae

BOLD:AAC9235

(Cathetus euthysticha)

Australia
Lepidoptera Uraniidae

BOLD:AAD1023

(Phazaca mutans)

Australia

Two taxa, Spoladea recurvalis (Lepidoptera, Crambidae) and a species of Cotesia (Hymenoptera, Braconidae), had a wider distribution with records from five or more countries (Table 1). The remaining 237 BINs (76%) were recorded excusively from West Papua.

Discussion

The high number of BINs that are exclusive to an area with comparatively well studied surroundings, highlights the urgency of studying the biodiversity of tropical regions. Analysis of 1,052 specimens increased the diversity of known species in this particular area 1.5-fold, from 583 to 877 species, as expressed by BINs that have been shown to closely relate to biological species. This was achieved by analysing a handful of randomly collected samples obtained by students during field courses under the supervision of entomologists from the ZSM (Munich).

Even for well studied groups like Lepidoptera, the study led to an increase of 205 BINs, corresponding to nearly one third (32%) of all species known so far for this insect order from West Papua. For less well known groups like Hymenoptera and Coleoptera, all BINs were new to West Papua. It is important to stress that nearly all Coleoptera and Hymenoptera specimens of the present study were collected at one site, the campus of the Papua University at Manokwari, showing the potential for a significantly higher number of discoveries with a broader sampling regime across different elevations and actually investigating primary forest areas. The Geometridae (Lepidoptera) was a target group for collecting which explains the predominance of geometrid moths, representing nearly half (48%) of the BINs.

Our study suggests that DNA barcoding applied to university courses achieves several goals, including capacity building, hands-on experience in molecular biodiversity assessment and it provides valuable data that are globally available by researchers for further studies (see also Vernooy et al. 2010). Specimens that would usually only be identified to order or perhaps genus level (and then often forgotten) can now serve to provide data in a sustainable manner. The data have become a community resource and are available for local researchers to benefit their research. Ideally, the next steps would include more focussed and specific project orientated field- and laboratory work that could strongly support the analysis of large scale patterns of diversity as outlined by Tänzler et al. (2012).

In a very similar context, DNA barcoding applied to samples obtained through activities of citizen scientists in remote localities (Janzen and Hallwachs 2011, Miller et al. 2014, Wilson et al. 2015, Jisming-See et al. 2016, Loos et al. 2015, Schilthuizen et al. 2017, Suprayitno et al. 2017, Freitag et al. 2018) could make significant, objective contributions to our understanding of the patterns of global biodiversity.

Finally, this simple experiment provided additional occurrence records for virtually cosmopolitan species like the Lepidoptera, Crambidae: Spoladea recurvalis and a widespread species of braconid wasps (Hymenoptera, Braconidae, Cotesia sp.), confirming the usefulness of DNA barcoding for the large scale assessment of global distribution patterns and also for monitoring the distribution and spread of invasive species.

Acknowledgements

We warmly thank BKSDA Manokwari for fieldwork permission and the permission to transfer samples from West Papua province to West Java. Local landowners are thanked for granting access to their gardens and the Museum Zoologicum Bogoriense (MZB) for housing the samples in their collections and for issuing loan permits. The training courses conducted at UNIPA in Manokwari were funded by the Deutscher Akademischer Austauschdienst (DAAD) as part of the Indonesian-German Network for Teaching, Training and Research Collaborations (IGN-TTRC), initiated by W. Nellen (Malang, Indonesia) through the University of Kassel, Germany. Participation of MB and TvR was made possible with support from Bundesministerium für Bildung und Forschung within the bilateral "Biodiversity and Health" funding programme (Project numbers: 16GW0111K, 16GW0112). Logistic support during the field trips was provided by Hengky Lukas (UNIPA) and also by Shita Prativi, Jordan Mencher and Zeth Wonggor (Papua Bird Club, Manokwari). David Lees (NHM, London, UK) participated in the field work and some specimens collected at his light trap were used in the present analysis.

References