Corresponding author: Vanessa A. Mata (
Academic editor: Ricardo Moratelli
The advent and boom of DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present the InBIO Barcoding Initiative Database: Portuguese Bats (
We added four new Barcoding Index Numbers (BINs) to existing
The barcoding of life is a booming initiative to catalogue worldwide biodiversity (
In Portugal, the InBIO Barcoding Initiative was recently launched under the scope of EnvMetaGen ERA-Chair, aiming to contribute for building a DNA barcoding library for the country’s biodiversity of terrestrial and freshwater ecosystems (
This dataset aims to provide a first contribution to an authoritative DNA barcode sequences library for Portuguese bats. Such a library should facilitate DNA-based identification of species for both traditional molecular studies and DNA-metabarcoding studies and constitute a valuable resource for taxonomic and ecological studies.
We obtained the full barcode sequence (COI – 658 bp) for 63 specimens (Fig.
This work provides a clear example on how the DNA barcoding of collections may unveil unexpected results and reveal hidden diversity. In this case, a sample collected in 2005 and sequenced in 2018 provided the first record of
Our take-home message is that the screening of current and older collections, either museum or private, may withhold surprises that will further complete acknowledged species lists. With the ever-decreasing costs of barcoding techniques, it is expected that many researchers may afford this approach. Barcoding will most likely become an essential tool for the managing of collections. Additionally, vouchering of specimens, especially from regions with large knowledge gaps like tropical Africa and Southeast Asia, might help future studies aiming for pathogen discovery, integrative taxonomy, climate change, environmental pollution and other topics that might not constitute the initial focus of the sampling.
The name “The InBIO Barcoding Initiative Database: Portuguese Bats (
Pedro Beja (project coordinator), Sónia Ferreira (IBI manager), Hugo Rebelo (
Continental Portugal (Fig.
Chiropteran specimens were collected in the field, morphologically identified and DNA barcoded.
FCT - Fundação para Ciência e Tecnologia, I.P. funded V.M. (PD/BD/113462/2015) and F.A. (PD/BD/52606/2014). S.F. was funded 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). This research also received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 668981. Fieldwork and sample collection were funded under the scope of the FCT projects PTDC/BIA-BIC/110587/2009, LTER/BIA-BEC/0004/2009 and PTDC/BIA-ECO/31731/2017 and from EDP – Energias de Portugal.
Continental Portugal (Fig.
Bat samples were collected under the scope of several projects spanning from 2005 to 2018 (
Up to five specimens of each species were sequenced in the laboratory. DNA was extracted from wing punches, using the E.Z.N.A. Tissue Kit (Omega Bio-tek). Two partially overlapping fragments of the COI gene were amplified using the primers FwhF1 x Ind_C_R (325bp;
All DNA barcodes sequences were compared against the BOLD database and the 99 top hits were inspected in order to detect possible issues due to contaminations or misidentifications. Prior to GBIF submission, data were checked for errors and inconsistencies with OpenRefine 3.2 (
Samples were collected from bats captured using mist-nets or harp-traps at roost exits and identified morphologically by experts. A non-lethal 3 mm wing punch was collected from each individual and stored in 96% ethanol from where DNA was extracted and the COI DNA barcode fragment was sequenced. Prior to GBIF submission, data were checked for errors and inconsistencies with OpenRefine 3.2 (
Continental Portugal (Fig.
37.4° and 41.9° Latitude; 9.3° and 6.9° Longitude.
This dataset is composed entirely of data relating to 63
Overall, 26 species are represented in the dataset (100% of the ones existing in continental Portugal and 83.8% of the ones existing in Iberia). These species belong to four families, the majority of which belong to the
Rank | Scientific Name | Common Name |
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species |
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Western barbastelle |
species |
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Meridional serotine |
species |
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Common serotine |
species |
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Savi's pipistrelle |
species |
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Common bent-wing |
species |
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Alcathoe |
species |
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Bechstein's |
species |
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Lesser mouse-eared |
species |
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Daubenton's |
species |
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Geoffroy's |
species |
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Escalera's |
species |
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Greater mouse-eared |
species |
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Whiskered |
species |
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Greater noctule |
species |
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Lesser noctule |
species |
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Common noctule |
species |
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Kuhl's pipistrelle |
species |
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Common pipistrelle |
species |
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Soprano pipistrelle |
species |
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Brown long-eared |
species |
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Grey long-eared |
species |
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Mediterranean horseshoe |
species |
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Greater horseshoe |
species |
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Lesser horseshoe |
species |
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Mehely's horseshoe |
species |
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European free-tailed |
Samples were collected in the period from 27 June 2005 to 22 August 2018.
InBIO Barcoding Initiative
4ec2b246-f5fa-4b90-9a8d-ddafc2a3f970
DNA extractions - 1 to 63
Creative Commons Public Domain Waiver (CC-Zero)
The InBIO Barcoding Initiative Database: Portuguese Bats (
1
DS-IBICH IBI -
dwc, xml, tsv, fasta
1
The InBIO Barcoding Initiative Database: Portuguese Bats (
All data are available in the BioStudies database (
Column label | Column description |
---|---|
processid | Unique identifier for the sample |
sampleid | Identifier for the sample being sequenced, i.e. IBI catalogue number at Cibio-InBIO, Porto University. Often identical to the "Field ID" or "Museum ID" |
recordID | Identifier for specimen assigned in the field |
catalognum | Catalogue number |
fieldnum | Field number |
institution_storing | The full name of the institution that has physical possession of the voucher specimen |
bin_uri | Barcode Index Number system identifier |
phylum_taxID | Phylum taxonomic numeric code |
phylum_name | Phylum name |
class_taxID | Class taxonomic numeric code |
class_name | Class name |
order_taxID | Order taxonomic numeric code |
order_name | Order name |
family_taxID | Family taxonomic numeric code |
family_name | Family name |
subfamily_taxID | Subfamily taxonomic numeric code |
subfamily_name | Subfamily name |
genus_taxID | Genus taxonomic numeric code |
genus_name | Genus name |
species_taxID | Species taxonomic numeric code |
species_name | Species name |
identification_provided_by | Full name of primary individual who assigned the specimen to a taxonomic group |
identification_method | The method used to identify the specimen |
voucher_status | Status of the specimen in an accessioning process (BOLD controlled vocabulary) |
tissue_type | A brief description of the type of tissue or material analysed |
collectors | The full or abbreviated names of the individuals or team responsible for collecting the sample in the field |
lifestage | The age class or life stage of the specimen at the time of sampling |
lat | The geographical latitude (in decimal degrees) of the geographic centre of a location |
lon | The geographical longitude (in decimal degrees) of the geographic centre of a location |
country | The full, unabbreviated name of the country where the organism was collected |
province_state | The full, unabbreviated name of the province ("Distrito" in Portugal) where the organism was collected |
region | The full, unabbreviated name of the municipality ("Concelho" in Portugal) where the organism was collected |
exactsite | Additional name/text description regarding the exact location of the collection site relative to a geographic relevant landmark |
We would like to thank our lab technicians Cátia Chaves and Joana Pinto for the lab processing of the samples, as well as Pedro Sousa for the upload of the GBIF data.
Samples were collected by H.R., F.A., P.H., H.R., H.S. and V.A.M. Data analysis was conducted by S.F. Writing of the manuscript was led by H.R., S.F. and V.A.M. with substantial contributions from the remaining authors.
Phylogenetic tree obtained by Maximum Likelihood (ML) analysis of 26 species of bats, based on 63 newly-sequenced cytochrome c oxidase I gene (COI – 658 bp) Portuguese samples (codes started by MB) and representative sequences of all 26 species publicly available on BOLD (
Geographic location of the analysed samples in this study.
Picture of the
Vegetation structure of where
List of species that were collected and DNA barcoded within this project. * Indicate species with new BINs.
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MB12 |
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MB13 |
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MB14 |
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MB60 |
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MB56 |
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MB57 |
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MB58 |
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MB59 |
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MB64 |
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MB65 |
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MB01 |
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MB02 |
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MB03 |
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MB06 |
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MB04 |
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MB05 |
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MB07 |
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MB08 |
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MB09 |
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MB10 |
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MB11 |
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MB33 |
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MB15 |
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MB16 |
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MB17 |
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MB18 |
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MB19 |
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MB20 |
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MB21 |
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MB22 |
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MB23 |
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MB25 |
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MB24 |
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MB26 |
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MB27 |
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MB28 |
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MB29 |
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MB30 |
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MB31 |
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MB32 |
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MB61 |
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MB62 |
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MB63 |
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MB35 |
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MB36 |
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MB37 |
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MB38 |
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MB39 |
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MB40 |
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MB41 |
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MB43 |
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MB44 |
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MB45 |
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MB46 |
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MB47 |
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MB48 |
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MB51 |
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MB49 |
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MB50 |
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MB52 |
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MB53 |
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MB54 |
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MB55 |
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IBI-
Record information - specimen data
The file includes information about all records in BOLD for the IBI-
File: oo_411218.txt
IBI-
Record information - specimen data in Darwin Core Standard format
The file includes information about all records in BOLD for the IBI-
File: oo_411282.txt
IBI-
Genomic data, DNA sequences
COI sequences in fasta format. Each sequence is identified by the BOLD ProcessID, species name, marker and GenBank accession number, separated by pipe. The data are as downloaded from BOLD.
File: oo_411203.txt