Integrated Publishing Toolkit(IPT)

free and open access to biodiversity data

The InBIO Barcoding Initiative Database: Diptera 01

Latest version published by CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal on Mar 20, 2020 CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal

The dataset contains 203 records of Diptera species collected from 2014 to 2018 in continental Portugal. All specimens were identified to species level, belonging to 154 species belonging to 41 different fly families. Specimens were captured during fieldwork directed specifically for the sampling of Diptera using different methodologies and 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 EnvMetaGen and PORBIOTA projects. DNA barcode sequences were deposited in BOLD (Barcode of Life Data System) online database. Preserved specimens and DNA extracts are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources).

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 203 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 203 records in English (28 KB) - Update frequency: as needed
Metadata as an EML file download in English (29 KB)
Metadata as an RTF file download in English (14 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Ferreira S, Andrade R, Gonçalves A R, Sousa P, Beja P (2019): The InBIO Barcoding Initiative Database: Diptera 01. v1. CIBIO-InBIO (Research Center in Biodiversity and Genetic Resources), Portugal. Dataset/Occurrence. http://ipt.gbif.pt/ipt/resource?r=ibi_diptera_i&v=1.0

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 21feb87f-62f2-4765-8aa6-6953ee5e09d6.  CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Portugal.

Keywords

Diptera; Species; Occurrence; Cytochrome c oxidase I (COI); DNA barcode; Continental Portugal

Contacts

Who created the resource:

Sónia Ferreira
Post-Doc Researcher
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 Porto PT +351 252660411
Rui Andrade
Researcher
Rua Calouste Gulbenkian, 237, 4H3 4050-145 Porto Porto PT
Ana Rita Gonçalves
Master student
Computational Biology and Population Genomics Group, cE3c, Faculdade de Ciências, Universidade de Lisboa Campo Grande 1749-016 Lisboa Lisboa PT
Pedro Sousa
Post-Doc Researcher
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 Porto PT +351 252660411
Pedro Beja
Coordinating Researcher
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 Porto PT +351 252660411

Who can answer questions about the resource:

Pedro Beja
Coordinating Researcher
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 Porto PT +351 252660411
Sónia Ferreira
Post-Doc Researcher
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 Porto PT +351 252660411

Who filled in the metadata:

Sónia Ferreira
Post-Doc Researcher
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 Porto PT +351 252660411
Rui Andrade
Researcher
Rua Calouste Gulbenkian, 237, 4H3 4050-145 Porto Porto PT
Ana Rita Gonçalves
Master student
Computational Biology and Population Genomics Group, cE3c, Faculdade de Ciências, Universidade de Lisboa Campo Grande 1749-016 Lisboa Lisboa PT
Pedro Sousa
Post-Doc Researcher
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 Porto PT +351 252660411
Pedro Beja
Coordinating Researcher
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 Porto PT +351 252660411

Geographic Coverage

Continental Portugal

Bounding Coordinates South West [40.054, -8.774], North East [42.002, -6.274]

Taxonomic Coverage

This dataset is composed of data relating to 203 Diptera specimens. All specimens were determined to species level. Overall, 154 species are represented in the dataset. These species belong to 41 families. Five families account for 56% of the total collected specimens, Syrphidae, Muscidae, Tachinidae, Calliphoridae and Chloropidae. These five families account for 54% of the total species represented. Nineteen families are represented by a single species.

Kingdom  Animalia
Phylum  Arthropoda
Class  Insecta
Order  Diptera
Family  Anisopodidae,  Anthomyiidae,  Asilidae,  Bibionidae,  Bombyliidae,  Calliphoridae,  Canacidae,  Chloropidae,  Conopidae,  Diastatidae,  Dolichopodidae,  Drosophilidae,  Ephydridae,  Fanniidae,  Heleomyzidae,  Hippoboscidae,  Hybotidae,  Lauxaniidae,  Lonchaeidae,  Micropezidae,  Muscidae,  Nemestrinidae,  Opetiidae,  Opomyzidae,  Pallopteridae,  Periscelididae,  Platystomatidae,  Psychodidae,  Ptychopteridae,  Rhiniidae,  Rhinophoridae,  Sarcophagidae,  Scathophagidae,  Sciomyzidae,  Stratiomyidae,  Syrphidae,  Tabanidae,  Tachinidae,  Tephritidae,  Trichoceridae,  Ulidiidae

Temporal Coverage

Start Date / End Date 2014-05-27 / 2018-07-07

Project Data

The InBIO Barcoding Initiative aims to develop a reference collection of DNA barcoding sequences covering Portuguese invertebrate taxa. Within the project, a special focus is afforded to insects, given their relevance to food webs, ecosystems functioning, high diversity and limited number of DNA barcoding sequences of interest.

Title The InBIO Barcoding Initiative Database: Diptera 01
Identifier InBIO Barcoding Initiative
Funding This project is 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), by EDP Biodiversity Chair, and is part of research conducted at the Long Term Research Site of Baixo Sabor (LTER_EU_PT_002). P.S. was funded by the project ECOLIVES – Fostering sustainable management in Mediterranean olive farms: pest control services provided by wild species as incentives for biodiversity conservation (PTDC/AAG-REC/6480/2014/) supported by Portuguese national funds by FCT/MCTES and co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) throughout COMPETE – Programa Operacional Factores de Competitividade (POFC).
Study Area Description Specimens were collected in eight continental Portugal districts. Fifty-nine different localities were sampled encompassing a great variety of habitats. Sampling was conducted from 2014 to 2018, with more than half of the specimens (62.6%) collected in the year 2017.
Design Description Specimens in this dataset were collected in field work carried out between 2014 and 2018. Specimens resulted from field work directed specifically for the sampling of Diptera using different methodologies.

The personnel involved in the project:

Author
Sónia Ferreira
Author
Rui Andrade
Author
Ana Rita Gonçalves
Originator
Pedro Sousa

Sampling Methods

The studied material was collected in 59 different localities from the northern half of continental Portugal (Fig. 1, Table 1). Sampling was conducted between 2014 and 2018 on a wide range of habitats, using mainly hand-held sweep nets or direct search of specimens. Collected specimens were examined both dry and in alcohol using a binocular stereoscopic microscope (Optika ST-30-2LR, 20x-40x) and stored in 96% ethanol for downstream molecular analysis. Morphological identification was performed based on keys and descriptions from literature (Suppl. material 1)

Study Extent Specimens were collected in 59 different localities of continental Portugal. Sampling was conducted from 2014 to 2018, in several field work expeditions. More than half of the specimens (62.6%) were collected in the year 2017.
Quality Control To each specimen the morphological identification was contrasted with the results of the Blast of the newly generated DNA barcodes in BOLD Identification Engine.

Method step description:

  1. Specimens were collected in 59 different localities of continental Portugal. Sampling was conducted from 2014 to 2018, and consisted of direct search of specimens, the use of entomological nets to intercept specimens flight or to sweep the vegetation. Specimens collected were stored in 96% ethanol. A tissue sample was removed from which DNA was extracted and COI DNA barcode fragment was sequenced. Prior submission to GBIF, data was checked for errors and inconsistencies with OpenRefine 3.2 (http://openrefine.org/).

Collection Data

Collection Name InBIO Barcoding Initiative
Collection Identifier 4ec2b246-f5fa-4b90-9a8d-ddafc2a3f970
Specimen preservation methods Alcohol
Curatorial Units Between 1 and 203 Voucher tube ,  Between 1 and 203 DNA extractions

Additional Metadata

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.
Alternative Identifiers http://ipt.gbif.pt/ipt/resource?r=ibi_diptera_i