The InBIO Barcoding Initiative Database: Portuguese Stick Insects (Phasmatodea)

Daniel Oliveira; Sónia Ferreira; Pedro Sousa; Pedro Beja

doi:10.15468/wppjdk

The InBIO Barcoding Initiative Database: Portuguese Stick Insects (Phasmatodea)

Citation

Oliveira D, Ferreira S, Sousa P, Beja P (2020). The InBIO Barcoding Initiative Database: Portuguese Stick Insects (Phasmatodea). Version 1.4. CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. Occurrence dataset https://doi.org/10.15468/wppjdk accessed via GBIF.org on 2020-09-16.

Description

The dataset contains 18 records of Stick insects (Phasmatodea) species collected from 2006 to 2019 in continental Portugal. All captured specimens were identified to species level, belonging to the two species of Phasmatodea present in Portugal. Specimens were detected and captured by direct search of the environment. Captured specimens were preserved in 96% ethanol. From each specimen one leg (tissue sample) was removed to be used for DNA extraction. Preserved specimens and DNA extracts are deposited in the InBIO Barcoding Initiative (IBI) collection at the CIBIO (Research Center in Biodiversity and Genetic Resources). Samples of each species were selected for DNA sequencing based on geographic provenance of the corresponding specimen. Sequencing of the 658 bp DNA barcodes was conducted within the InBIO Barcoding Initiative (IBI) and all DNA sequences were submitted to BOLD (Barcode of Life Data System) and GenBank databases.

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.

Sampling Description

Study Extent

Specimens of Phasmatodea were captured in ten sites distributed across the country, despite a concentration of records in the NE regions. Sampling was conducted from 2006 to 2019, in several field work expeditions.

Sampling

Specimens were captured from 2006 to 2019 by direct search of ten sampling sites in continental Portugal. Captured insects were preserved in 96% ethanol and stored at the InBIO Barcoding Initiative reference collection.

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. Prior submission to GBIF, data was checked for errors and inconsistencies with OpenRefine 3.2 (http://openrefine.org/).

Method steps

Specimens of Phasmatodea were captured in continental Portugal from 2006 and 2019 by direct search of vegetation. Collected specimens were preserved in 96% ethanol prior to storage.
The specimens were morphologically identified resorting to available literature (Scali, Milani and Passamonti, 2012, 2013).
Six specimens from each species (or all specimens, when less than six available) were selected for DNA extraction and sequencing, based on geographical location. For this, one leg was removed from each individual from which a 658 bp COI DNA barcode fragment was extracted, amplified and sequenced.
All obtained sequences 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 3.2 (http://openrefine.org/).

Taxonomic Coverages

This dataset is composed of data relating to 18 Phasmatodea specimens belonging to the two species present in Portugal, Leptynia attenuata and Clonopsis gallica. These species belong to two different families, Diapheromeridae and Bacillidae, respectively.

Animalia
rank: kingdom
Arthropoda
rank: phylum
Insecta
rank: class
Phasmatodea
rank: order
Diapheromeridae
rank: family
Bacillidae
rank: family

Geographic Coverages

Continental Portugal.

Bibliographic Citations

Scali, V., Milani, L. and Passamonti, M. (2012) ‘Revision of the stick insect genus Leptynia: Description of new taxa, speciation mechanism and phylogeography’, Contributions to Zoology, 81(1), pp. 25–42. doi: 10.1163/18759866-08101002. - doi: 10.1163/18759866-08101002.
Scali, V., Milani, L. and Passamonti, M. (2013) ‘Description and ecology of new Pijnackeria stick insects: Four bisexual species and a triploid parthenogen with their phyletic relationships’, Journal of Zoological Systematics and Evolutionary Research, 51(3), pp. 213–226. doi: 10.1111/jzs.12018. - doi: 10.1111/jzs.12018.

Contacts

Daniel Oliveira
originator
position: Master’s Student
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
Campus Agrário de Vairão, Rua Padre Armando Quintas, nº 7
Vairão
4485-661
Porto
PT
email: daniel.jet100@gmail.com
userId: http://orcid.org/0000-0002-8733-4104

Sónia Ferreira
originator
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: hiporame@gmail.com
userId: http://orcid.org/0000-0002-6884-3966

Pedro Sousa
originator
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: psousa@cibio.up.pt
userId: http://orcid.org/0000-0002-5859-9656

Pedro Beja
originator
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: pbeja@cibio.up.pt
userId: http://orcid.org/0000-0001-8164-0760

Daniel Oliveira
metadata author
position: Master’s Student
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
email: daniel.jet100@gmail.com
userId: http://orcid.org/0000-0002-8733-4104

Sónia Ferreira
metadata author
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: hiporame@gmail.com
userId: http://orcid.org/0000-0002-6884-3966

Pedro Sousa
metadata author
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: psousa@cibio.up.pt
userId: http://orcid.org/0000-0002-5859-9656

Pedro Beja
metadata author
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: pbeja@cibio.up.pt
userId: http://orcid.org/0000-0001-8164-0760

Pedro Beja
administrative point of contact
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: pbeja@cibio.up.pt
userId: http://orcid.org/0000-0001-8164-0760

Sónia Ferreira
administrative point of contact
position: 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
Vairão
4485-661
Porto
PT
Telephone: +351 252660411
email: hiporame@gmail.com
userId: http://orcid.org/0000-0002-6884-3966