Author: Pedro Sousa
Keywords: Diptera, Species, Occurrence, Cytochrome c oxidase I (COI), DNA barcode, Portugal, Azores, Madeira, Craneflies, Occurrence

The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae

Sónia Ferreira^1, Pjotr Oosterbroek^2, Jaroslav Starý^3, Vanessa Alves Mata^1, Luís P. da Silva^1, Pedro Sousa^1, Pedro Beja^1, Pjotr Oosterbroek^4, Jaroslav Starý^5

1 CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal; 2 Naturalis Biodiversity Center, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands; 3 Silesian Museum, Nádražní okruh 31, 746 01, Opava, Czechia; 4 Naturalis Biodiversity Center, aturalis Biodiversity Center, Darwinweg 2. Leiden, The Netherlands, 2333 CR, Leiden, Netherlands; 5 Silesian Museum, Opava, Czechia

Corresponding author(s): Sónia Ferreira (hiporame@gmail.com)Pjotr Oosterbroek (p.oosterbroek@chello.nl)Jaroslav Starý (stary.cranefly@gmail.com)Vanessa Alves Mata (vanessamata@cibio.up.pt)Luís P. da Silva (lfpascoals@gmail.com)Pedro Sousa (psousa@cibio.up.pt)Pedro Beja (pbeja@cibio.up.pt), Pjotr Oosterbroek (p.oosterbroek@chello.nl), Jaroslav Starý (stary.cranefly@gmail.com)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Ferreira, S., Oosterbroek, P., Starý, J., Mata, V.A., Silva, L.P., Sousa, P., Beja, P. (2021): The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae. v1.0. CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. Dataset/Occurrence. http://ipt.gbif.pt/ipt/resource?r=ibi_diptera_02&amp;v=1.6

Abstract

The dataset contains 412 records of Diptera species from the families Limoniidae, Pediciidae and Tipulidae, collected between 2003 to 2019 in Portugal, including the Azores and Madeira archipelagos (Ferreira et al., 2021; Oosterbroek et al., 2020; Starý, 2014). Specimens have been identified to species or subspecies level, in a total of 83 species representing 58% of the Craneflies known for Portugal. Specimens were captured during fieldwork directed specifically for the sampling of Diptera using different methodologies and the majority was stored in 96% ethanol. A tissue sample, usually a leg, was collected from each individual, from which DNA was extracted. The DNA barcoding of these specimens was conducted within the InBIO Barcoding Initiative (IBI), funded by the EnvMetaGen and PORBIOTA projects. The dataset “DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae” is part of a group of Diptera datasets published by IBI, the first of which, “The InBIO Barcoding Initiative Database: Diptera 01” (https://doi.org/10.15468/q1bvt3) has already been made available through GBIF. DNA barcode sequences were deposited in BOLD (Barcode of Life Data System) and GenBank databases. All DNA extracts are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources).

Keywords: Diptera, Species, Occurrence, Cytochrome c oxidase I (COI), DNA barcode, Portugal, Azores, Madeira, Craneflies, Occurrence

General description

Purpose: The InBIO Barcoding Initiative (IBI) aims to develop a reference collection of DNA barcoding sequences primarily covering Portuguese invertebrate taxa providing a tool in ecological studies.

Project details

Project title: The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae
Personnel: Sónia Ferreira, Pjotr Oosterbroek, Jaroslav Starý, Vanessa Alves Mata, Luis Pascoal da Silva, Pedro Sousa, Pedro Beja
Funding: The InBIO Barcoding Initiative was funded by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 668981 and by the project PORBIOTA - Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). The fieldwork benefited from EDP Biodiversity Chair, the project “Promoção dos serviços de ecossistemas no Parque Natural Regional do Vale do Tua: Controlo de Pragas Agrícolas e Florestais por Morcegos” funded by the Agência de Desenvolvimento Regional do Vale do Tua, and includes research conducted at the Long Term Research Site of Baixo Sabor (LTER_EU_PT_002). LPdS and SF were supported by individual research contracts (CEECIND/02064/2017, 2020.03526.CEECIND) funded by FCT. JS was funded by the Ministry of Culture of the Czech Republic through institutional financing of long-term conceptual development of the Silesian Museum research institution (MK000100595).
Study area descriptions/descriptor: Specimens were collected in 14 continental Portugal administrative districts and in the Azores and Madeira archipelagos. Eighty-three different localities were sampled. Collection occurred between 2003 and 2019, although most specimens were collected in 2018 (32%) and 2019 (50%).
Design description: Specimens in this dataset were collected in field work carried out between 2003 and 2019, directed specifically for the sampling of Diptera using different methodologies. Specimens were morphologically identified and DNA barcoded.

Data published through GBIF: http://ipt.gbif.pt/ipt/resource?r=ibi_diptera_02

Taxonomic coverage

General taxonomic coverage description: This dataset is composed of data relating to 412 Diptera specimens. All specimens were determined to species level except for seven specimens. Overall, 83 species are represented in the dataset. Two species have been further identified to subspecies level, Nephrotoma suturalis wulpiana (Bergroth, 1888) and Nephrotoma appendiculata pertenua Oosterbroek, 1978. These species belong to 31 genera unevenly distributed among three Craneflies families, Limoniidae (21 genera), Tipulidae (4 genera) and Pediciidae (2 genera). The families Limoniidae and Tipulidae account for a similar number of collected specimens, 197 and 211, respectively. However, Limoniidae has a higher proportion of recorded species, 45, when compared with Tipulidae, with 36 species.
Taxonomic ranks
Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Diptera
Superfamily: Tipuloidea
Family: Limoniidae, Pediciidae, Tipulidae

Spatial coverage

General spatial coverage: Continental Portugal, Autonomous Regions of the Azores and of Madeira.
Coordinates: 32°38'60''N and 41°58'12''N Latitude; 25°30'36''W and 6°20'24''W Longitude 

Temporal coverage: September 8, 2003 - October 14, 2019

Natural collections description

Collection name: InBIO Barcoding Initiative
Collection identifier: 4ec2b246-f5fa-4b90-9a8d-ddafc2a3f970
Specimen preservation method: Alcohol
Curatorial unit: Between 1 and 381 (Voucher tube)
Curatorial unit: Between 1 and 412 (DNA extractions)

Methods

Method step description: 
- . 	Specimens were collected in 83 different Portuguese localities. Field work was carried out between 2003 and 2019, with 82% of the records made in the years 2018 and 2019.
- . 	Specimens were collected during fieldwork by direct search and individual netting of specimens, by sweeping the vegetation or were directly collected at light traps (using both UV and mercury vapor lights) and preserved in 96% alcohol. The majority of captured specimens were deposited in the IBI reference collection at CIBIO (Research Center in Biodiversity and Genetic Resources).
- . 	All specimens were morphologically identified using the available literature except seven that were identified using the BOLD Identification Engine . For some specimens it was necessary to prepare and then exam their terminalia.
- . 	All specimens were DNA barcoded. For these, one leg was removed from each individual, DNA was then extracted, and a 658 bp COI DNA barcode fragment was amplified and sequenced. All DNA extracts were deposited in the IBI collection.
- . 	All sequences in the dataset were submitted to BOLD and GenBank databases and to each sequenced specimen the morphological identification was contrasted with the results of the BLAST of the newly generated DNA barcodes in BOLD Identification Engine.
- . 	Prior submission to GBIF, data was checked for errors and inconsistencies with OpenRefine 3.4 (http://openrefine.org/).
Study extent description: Portugal, including the Autonomous Regions of the Azores and of Madeira.
Sampling description: The studied material was collected in 83 different Portuguese localities. Sampling was conducted between 2003 and 2019, although 82% of the records were made in the years 2018 and 2019. Specimens were collected by direct search and individual netting of specimens, by sweeping the vegetation with a net or were directly collected at light traps, using both UV and mercury vapor lights. Captured specimens deposited in the IBI reference collection were preserved in 96% alcohol.
Quality control description: For all DNA barcoded specimens, their morphological identification was contrasted with the results of the Blast of the newly generated DNA barcodes in BOLD Identification Engine. Prior submission to GBIF, data was checked for errors and inconsistencies with OpenRefine 3.4 (http://openrefine.org/).

Datasets

Dataset description
Object name: Darwin Core Archive The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.gbif.pt/ipt/archive.do?r=ibi_diptera_02
Publication date of data: 2021-09-24
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2019-12-13
Hierarchy level: Dataset

References
Ferreira, S., Oosterbroek, P., Starý, J., Sousa, P., Mata, V.A., da Silva, L.P., Paupério, J., Beja, P. (2021). The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae. Biodiversity Data Journal 9: e69841. https://doi.org/10.3897/BDJ.9.e69841
Oosterbroek, P., Starý, J., Andrade, R., Hancock, E.G. & Ferreira, S. (2020). The Craneflies of continental Portugal (Diptera, Limoniidae, Pediciidae, Tipulidae) including 28 species new for Portugal. Boletín de la Asociación española de Entomología 44 (3-4): 317-358.
Starý, J. (2014). Some records of Limoniidae and Pediciidae (Diptera) from Portugal and Spain. Acta Musei Silesiae, Scientiae Naturales, 63(1): 83-95. https://doi.org/10.2478/cszma-2014-0010