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Data Paper (Biosciences)
The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01
expand article infoSonia A Ferreira, Rui Andrade§, Ana R Gonçalves|, Pedro Sousa, Joana Paupério, Nuno A Fonseca, Pedro Beja‡,
‡ CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Vila do Conde, Portugal
§ Rua Calouste Gulbenkian 237 4H3, 4050-145, Porto, Portugal
| Computational Biology and Population Genomics Group, cE3c, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
¶ CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
Open Access

Abstract

Background

The InBIO Barcoding Initiative (IBI) Diptera 01 dataset contains records of 203 specimens of Diptera. All specimens have been morphologically identified to species level, and belong to 154 species in total. The species represented in this dataset correspond to about 10% of continental Portugal dipteran species diversity. All specimens were collected north of the Tagus river in Portugal. Sampling took place from 2014 to 2018, and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

New information

This dataset contributes to the knowledge on the DNA barcodes and distribution of 154 species of Diptera from Portugal and is the first of the planned IBI database public releases, which will make available genetic and distribution data for a series of taxa. All specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

Keywords

Diptera, occurrence records, continental Portugal, DNA barcode, COI

Introduction

Diptera is one of the most diverse, abundant and widespread insect orders, with more than 158 000 described species, and many more still to be described (Pape et al. 2009; Evenhuis and Pape 2019). Dipterans are ubiquitous in many terrestrial ecosystems and larval stages of some species can also been found in aquatic ecosystems. They play important ecological roles in ecosystems, including those of pollinators, detritivores and parasites. Some species are also important disease vectors (Merritt et al. 2009) and crop pests (Skuhravá et al. 2010).

In continental Portugal, 1 475 species of Diptera were recorded, a sizable diversity, but small when compared to the 5 800 species known to occur in continental Spain (Carles-Tolrá 2002). Since the seminal work of Carles-Tolrá (2002), further increments to the Portuguese dipteran fauna have been made (e.g. Andrade and Gonçalves 2014; Ebejer and Andrade 2015; Pollet et al. 2019), but much remains to be known about its diversity and distribution patterns in the country. The huge diversity of this order, the shortage of specialised taxonomists and the difficulties in identifying many species are the main obstacles to overcome this lack of knowledge.

DNA barcoding is a method that aims to identify organisms based on a short DNA sequence previously sequenced from morphologically identified specimens (Hebert et al. 2003). This requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity (Baird et al. 2011, Kress et al. 2005, Ferreira et al. 2018). DNA barcoding can also be used as a first step in new species discovery and, as such, can be used as a tool to help address the taxonomic impediment problem (e.g. Kekkonen and Hebert 2014).

The striking scarcity of genetic data associated with the high biodiversity found in Portugal instigated the creation of a DNA barcoding initiative by the Research Network in Biodiversity and Evolutionary Biology - InBIO (Associate Laboratory). The InBIO Barcoding Initiative (IBI) makes use of Next Generation Sequencing technologies (NGS) to develop a reference collection of DNA barcoding sequences, focusing on Portuguese invertebrate taxa. Within the project, a special focus is afforded to insects, given their relevance to food webs and ecosystems functioning (e.g., Weisser and Siemann 2004; Mata et al. 2016; Silva et al. 2019). Furthermore, for many insect species occurring in Portugal, there are no barcodes available in public databases (Corley and Ferreira 2017; Corley et al. 2017; Weigand et al. 2019), and those that exist often show high distances to sequences obtained in Portugal, which may indicate cryptic diversity (Corley et al. 2019, Corley et al. 2019; Ferreira et al. 2018).

The IBI Diptera 01 dataset contains records of 203 specimens of Diptera collected in continental Portugal, all of which were morphologically identified to species level, for a total of 154 species. This is the first IBI dataset to be released to the Global Biodiversity Information Facility (GBIF) and all specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD). We have included in this dataset the barcodes of all identified Diptera specimens in IBI up to December 2019, except those from the families Tipulidade and Limoniidae, for which we will provide a more detailed treatment in a future paper, due to the detection of new species and the need for further research. Overall, this paper is a contribution to sharing and publicly disseminating the distribution records and DNA barcodes of specimens from our reference collection to increase the available information on Portuguese Diptera fauna.

General description

Purpose: 

This dataset aims to provide a first contribution to an authoritative DNA barcode sequences library for Portuguese Diptera. 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 research on Portuguese Diptera and its distribution.

Additional information: 

A total of 203 specimens of dipterans were collected and DNA barcoded (Suppl. material 2). Fig. 1 illustrates examples of the diversity of species that are part of the dataset of distribution data and DNA barcodes of Portuguese Diptera 01. All sequences of cytochrome c oxidase I (COI) DNA barcodes are 658 bp long. From the 154 species barcoded, twenty nine (19%) from 16 families are new to the DNA barcode database BOLD at the moment of the release (marked with * in Species field of Table 2). Forty-two additional species (27%) from 24 families were previously represented in BOLD, but with less than 10 DNA barcode sequences at the moment of the release (marked with '' in Species field of Table 2). Therefore, this dataset represents a significant contribution to enhance the species and genetic diversity of Diptera fauna represented in public libraries.

Number of specimens collected per Portuguese district and corresponding percentage. The number of recorded specimens also corresponds to the number of species recorded per district, as each species was collected only once in each district.

District

Specimens (n)

Specimens (%)

Bragança

79

38.9%

Aveiro

51

25.1%

Porto

38

18.7%

Braga

21

10.3%

Vila Real

6

3.0%

Castelo Branco

4

2.0%

Viana do Castelo

2

1.0%

Guarda

1

0.5%

not known

1

0.5%

Total

203

100%

List of species that were collected and DNA barcoded within this project. * Indicate species without DNA barcode prior to this study, '' indicates species with less than 10 sequences prior to this study.

Family Species IBI code BOLD code BOLD BIN GenBank
Anisopodidae Sylvicola cinctus (Fabricius, 1787) INV04902 IBIDP034-19 BOLD:AAG1996 MN868840
Anthomyiidae Anthomyia imbrida Rondani, 1866'' INV00551 IBIDP006-19 BOLD:ABX9294 MN868736
Anthomyiidae Anthomyia pluvialis (Linnaeus, 1758) INV00817 IBIDP144-19 BOLD:ADH9310 MN868903
Anthomyiidae Subhylemyia longula (Fallen, 1824)'' INV00555 IBIDP007-19 BOLD:AAP8836 MN868762
Asilidae Molobratia teutonus (Linnaeus, 1767)'' INV07407 IBIDP391-19 BOLD:ADF9805 MN868906
Bibionidae Dilophus febrilis (Linnaeus, 1758) INV04935 IBIDP055-19 BOLD:ACI4790 MN868809
Bombyliidae Anthrax anthrax (Schrank, 1781)'' INV04944 IBIDP063-19 BOLD:ADR8193 MN868791
Bombyliidae Exhyalanthrax afer (Fabricius, 1794)* INV04951 IBIDP151-19 BOLD:ADU1899 MN868734
Bombyliidae Hemipenthes morio (Linnaeus, 1758)'' INV04959 IBIDP070-19 BOLD:ACS6268 MN868882
Calliphoridae Calliphora vicina Robineau-Desvoidy, 1830 INV00609, INV01920, INV05001, INV05029 IBIDP009-19, IBIDP018-19, IBIDP087-19, IBIDP167-19 BOLD:AAB6579 MN868831, MN868732, MN868823, MN868797
Calliphoridae Calliphora vomitoria (Linnaeus, 1758) INV00176, INV02884, INV05036, INV07378 IBIDP001-19, IBIDP024-19, IBIDP107-19, IBIDP381-19 BOLD:AAA8931 MN868884, MN868856, MN868898, MN868853
Calliphoridae Chrysomya albiceps (Wiedemann, 1819) INV05008, INV05075 IBIDP092-19, IBIDP125-19 BOLD:ABX6432 MN868731, MN868796
Calliphoridae Lucilia caesar (Linnaeus, 1758) INV04986 IBIDP083-19 BOLD:AAA7470 MN868868
Calliphoridae Lucilia sericata (Meigen, 1826) INV04987, INV05048 IBIDP084-19, IBIDP112-19 BOLD:AAA6618 MN868905, MN868854
Canacidae Canace nasica (Haliday, 1839)* INV04995 IBIDP161-19 BOLD:ADT0044 MN868786
Canacidae Tethina illota (Haliday, 1838)'' INV05007 IBIDP091-19 BOLD:ABA8670 MN868899
Chloropidae Camarota curvipennis (Latreille, 1805)* INV04955 IBIDP152-19 BOLD:ACP6247 MN868844
Chloropidae Cryptonevra flavitarsis (Meigen, 1830)'' INV04994 IBIDP086-19 BOLD:ACB6675 MN868783
Chloropidae Diplotoxa messoria (Fallen, 1820)'' INV05017, INV05081 IBIDP098-19, IBIDP127-19 BOLD:ACD3417 MN868807, MN868793
Chloropidae Elachiptera bimaculata (Loew, 1845)* INV04990 IBIDP158-19 BOLD:ADU0665 MN868888
Chloropidae Elachiptera megaspis (Loew, 1858) INV05080, INV07368 IBIDP174-19,IBIDP374-19 BOLD:ADU0581 MN868842, MN868711
Chloropidae Eutropha albipilosa (Becker, 1908)* INV04991 IBIDP159-19 BOLD:ADS5005 MN868764
Chloropidae Eutropha fulvifrons (Haliday, 1833)* INV04992 IBIDP160-19 BOLD:ADT0252 MN868855
Chloropidae Lasiochaeta pubescens Thalhammer, 1898* INV05082 IBIDP175-19 BOLD:ACP6247 MN868876
Chloropidae Polyodaspis sulcicollis (Meigen, 1838)* INV04989 IBIDP157-19 BOLD:ADS6761 MN868863
Chloropidae Thaumatomyia elongatula (Becker, 1910)* INV05083 IBIDP176-19 BOLD:ADV5221 MN868862
Chloropidae Trachysiphonella ruficeps (Macquart, 1835)'' INV04996 IBIDP162-19 BOLD:ACP4572 MN868766
Conopidae Conops flavipes Linnaeus, 1758'' INV05010 IBIDP164-19 BOLD:AAJ7146 MN868871
Diastatidae Diastata adusta Meigen, 1830* INV05066 IBIDP172-19 BOLD:ADS5309 MN868880
Dolichopodidae Campsicnemus scambus (Fallen, 1823)'' INV04938 IBIDP058-19 BOLD:ACP5225 MN868902
Dolichopodidae Campsicnemus umbripennis Loew, 1856 INV07394 IBIDP387-19 BOLD:ACQ9843 MN868739
Dolichopodidae Gymnopternus cupreus (Fallen, 1823)* INV04909 IBIDP147-19 BOLD:AAZ8613 MN868838
Dolichopodidae Machaerium maritimae Haliday, 1832* INV05105 IBIDP179-19 BOLD:ADT1791 MN868724
Dolichopodidae Sciapus platypterus (Fabricius, 1805) INV04907 IBIDP037-19 BOLD:ABU9505 MN868817
Drosophilidae Drosophila suzukii (Matsumura, 1931) INV05107 IBIDP135-19 BOLD:AAC2499 MN868726
Drosophilidae Leucophenga maculata (Dufour, 1839) INV05006 IBIDP090-19 BOLD:ACC9004 MN868775
Drosophilidae Phortica variegata (Fallen, 1823)'' INV04906 IBIDP036-19 BOLD:ADP2209 MN868851
Ephydridae Discomyza incurva Fallen, 1823 INV04956 IBIDP069-19 BOLD:ABA8754 MN868839
Ephydridae Hecamede albicans (Meigen, 1830)'' INV04993 IBIDP085-19 BOLD:ABA8686 MN868716
Ephydridae Psilopa nitidula (Fallen, 1813)'' INV04984 IBIDP081-19 BOLD:AAG6948 MN868834
Fanniidae Fannia canicularis (Linnaeus, 1761) INV00177, INV04943 IBIDP002-19, IBIDP062-19 BOLD:AAF7101 MN868723, MN868818
Fanniidae Fannia lustrator (Harris, 1780) INV07364 IBIDP372-19 BOLD:ACB3656 MN868758
Heleomyzidae Suillia variegata (Loew, 1862) INV00970, INV04948 IBIDP011-19, IBIDP065-19 BOLD:ABY1201 MN868749, MN868727
Hippoboscidae Hippobosca equina Linnaeus, 1758'' INV07388 IBIDP385-19 BOLD:AAX0882 MN868873
Hybotidae Hybos culiciformis (Fabricius, 1775) INV01283, INV01808, INV05078 IBIDP013-19, IBIDP014-19, IBIDP173-19 BOLD:ACD8518 MN868781, MN868800, MN868846
Lauxaniidae Calliopum simillimum (Collin, 1933) INV07387 IBIDP384-19 BOLD:ACP8933 MN868801
Lauxaniidae Minettia longipennis (Fabricius, 1794) INV04908 IBIDP038-19 BOLD:ACB3141 MN868788
Lauxaniidae Prosopomyia pallida Loew, 1856* INV04946 IBIDP150-19 BOLD:ADV2313 MN868794
Lauxaniidae Trigonometopus frontalis (Meigen, 1830)'' INV05019 IBIDP099-19 BOLD:ACS3478 MN868881
Lonchaeidae Lamprolonchaea smaragdi (Walker, 1849)'' INV05120 IBIDP184-19 BOLD:ACO9728 MN868843
Lonchaeidae Silba fumosa (Egger, 1862)* INV04985 IBIDP082-19 BOLD:ACQ9578 MN868841
Micropezidae Micropeza lateralis Meigen, 1826'' INV01282 IBIDP145-19 BOLD:ADC0694 MN868910
Muscidae Coenosia atra Meigen, 1830 INV04968, INV05090 IBIDP075-19, IBIDP131-19 BOLD:ACP3222 MN868737, MN868850
Muscidae Coenosia attenuata Stein, 1903 INV05122 IBIDP142-19 BOLD:AAD7633 MN868861
Muscidae Coenosia tigrina (Fabricius, 1775) INV04928 IBIDP052-19 BOLD:AAB5609 MN868826
Muscidae Dasyphora albofasciata (Macquart & Berthelot, 1839)* INV05100 IBIDP178-19 BOLD:ADS1325 MN868827
Muscidae Graphomya maculata (Scopoli, 1763) INV04919 IBIDP046-19 BOLD:ABV4895 MN868806
Muscidae Helina evecta (Harris, 1780) INV05054 IBIDP115-19 BOLD:ACB3279 MN868729
Muscidae Hydrotaea dentipes (Fabricius, 1805) INV05110 IBIDP136-19 BOLD:AAI8769 MN868883
Muscidae Lispe kowarzi Becker, 1903'' INV04975 IBIDP155-19 BOLD:ACA1246 MN868872
Muscidae Lispocephala mikii (Strobl, 1893)'' INV04918 IBIDP148-19 BOLD:ADT6256 MN868912
Muscidae Musca autumnalis De Geer, 1776 INV04936 IBIDP056-19 BOLD:AAA3187 MN868877
Muscidae Musca domestica Linnaeus, 1758 INV05087 IBIDP130-19 BOLD:AAA6020 MN868773
Muscidae Musca tempestiva Fallen, 1817* INV04974 IBIDP154-19 BOLD:ACO3332 MN868751
Muscidae Muscina levida (Harris, 1780) INV04940 IBIDP059-19 BOLD:AAB8817 MN868769
Muscidae Muscina pascuorum (Meigen, 1826) INV04941 IBIDP060-19 BOLD:AAG1714 MN868746
Muscidae Muscina stabulans (Fallen, 1817) INV05015, INV05106 IBIDP096-19, IBIDP134-19 BOLD:AAF6582 MN868720, MN868760
Muscidae Neomyia cornicina (Fabricius, 1781) INV04922 IBIDP048-19 BOLD:AAH3032 MN868811
Muscidae Orchisia costata (Meigen, 1826) INV05022 IBIDP101-19 BOLD:ABX0213 MN868830
Muscidae Phaonia fuscata (Fallen, 1825) INV04952 IBIDP067-19 BOLD:ACB5198 MN868753
Muscidae Phaonia pallida (Fabricius, 1787) INV05045 IBIDP110-19 BOLD:ABW3852 MN868712
Muscidae Polietes meridionalis (Peris & Llorente, 1963) INV04964, INV05055 IBIDP072-19, IBIDP116-19 BOLD:AAY2766 MN868770, MN868865
Muscidae Pyrellia vivida Robineau-Desvoidy, 1830* INV04970 IBIDP153-19 BOLD:ADT8849 MN868828
Muscidae Schoenomyza litorella (Fallen, 1823) INV02961, INV04969 IBIDP029-19, IBIDP076-19 BOLD:ABW5574 MN868787, MN868835
Nemestrinidae Fallenia fasciata (Fabricius, 1805)'' INV07404 IBIDP390-19 BOLD:ADR9796 MN868810
Opetiidae Opetia nigra Meigen, 1830'' INV04942 IBIDP061-19 BOLD:ACD2824 MN868780
Opomyzidae Opomyza petrei Mesnil, 1934 INV04953, INV05077 IBIDP068-19, IBIDP126-19 BOLD:AAG1210 MN868887, MN868745
Pallopteridae Toxoneura muliebris (Harris, 1780)* INV05115 IBIDP139-19 BOLD:ACQ9316 MN868763
Periscelididae Periscelis fugax* INV05109 IBIDP181-19 BOLD:ADU2556 MN868715
Platystomatidae Rivellia syngenesiae (Fabricius, 1781) INV04931, INV07385 IBIDP054-19, IBIDP383-19 BOLD:AAX8866 MN868768, MN868792
Psychodidae Clogmia albipunctata (Williston, 1893) INV05093 IBIDP177-19 BOLD:ACS5395 MN868879
Ptychopteridae Ptychoptera albimana (Fabricius, 1787) INV07376 IBIDP379-19 BOLD:ACL4518 MN868771
Rhiniidae Rhyncomya columbina (Meigen, 1824)* INV04981 IBIDP156-19 BOLD:ADU6456 MN868859
Rhiniidae Rhyncomya felina (Fabricius, 1794)* INV05057 IBIDP171-19 BOLD:ADV4310 MN868896
Rhiniidae Stomorhina lunata (Fabricius, 1805)'' INV04929, INV05044 IBIDP053-19, IBIDP109-19 BOLD:ACD9536 MN868816, MN868892
Rhinophoridae Melanophora roralis (Linnaeus, 1758) INV04949 IBIDP066-19 BOLD:AAG6862 MN868885
Rhinophoridae Oplisa aterrima (Strobl, 1899)'' INV04926 IBIDP149-19 BOLD:ADU0356 MN868890
Sarcophagidae Sarcophaga crassipalpis Macquart, 1839 INV00698 IBIDP010-19 BOLD:AAC1709 MN868822
Sarcophagidae Sarcophaga longestylata Strobl, 1906* INV05116 IBIDP182-19 BOLD:ADV1383 MN868891
Scathophagidae Norellia tipularia (Fabricius, 1794)'' INV07396 IBIDP388-19 BOLD:ACE2160 MN868870
Scathophagidae Norellisoma spinimanum (Fallen, 1819) INV04924 IBIDP049-19 BOLD:ACD3336 MN868721
Scathophagidae Scathophaga stercoraria (Linnaeus, 1758) INV00527, INV02883, INV04913, INV07377 IBIDP004-19, IBIDP023-19, IBIDP041-19, IBIDP380-19 BOLD:AAD0853 MN868858, MN868799, MN868719, MN868829
Sciomyzidae Euthycera alaris Vala, 1983* INV01287 IBIDP146-19 BOLD:ADV6563 MN868813
Sciomyzidae Euthycera cribrata (Rondani, 1868)* INV05031 IBIDP168-19 BOLD:ADU4073 MN868789
Sciomyzidae Ilione trifaria (Loew, 1847)'' INV05084, INV05024 IBIDP128-19, IBIDP102-19 BOLD:ADR6909 MN868748, MN868717
Sciomyzidae Pherbellia cinerella (Fallen, 1820) INV05004 IBIDP089-19 BOLD:ACB5604 MN868757
Sciomyzidae Pherbellia dorsata (Zetterstedt, 1846)'' INV05061 IBIDP119-19 BOLD:ACD6777 MN868901
Sciomyzidae Pherbina mediterranea Mayer, 1953* INV05117 IBIDP183-19 BOLD:ADU0215 MN868714
Stratiomyidae Chloromyia formosa (Scopoli, 1763) INV04925, INV07375 IBIDP050-19, IBIDP378-19 BOLD:ABU9940 MN868798, MN868735
Stratiomyidae Hermetia illucens (Linnaeus, 1758) INV01259, INV04643, INV05003, INV05035 IBIDP012-19, IBIDP032-19, IBIDP088-19, IBIDP106-19 BOLD:AAG3698, BOLD:AAD0622 MN868718, MN868889, MN868825, MN868864
Syrphidae Chalcosyrphus nemorum (Fabricius, 1805) INV05104 IBIDP133-19 BOLD:AAG6762 MN868908
Syrphidae Chrysotoxum intermedium Meigen, 1822 INV05041 IBIDP108-19 BOLD:AAE9233 MN868747
Syrphidae Dasysyrphus albostriatus (Fallen, 1817) INV07391 IBIDP386-19 BOLD:AAL1242 MN868722
Syrphidae Episyrphus balteatus (De Geer, 1776) INV01909, INV07402 IBIDP015-19, IBIDP389-19 BOLD:AAC6833 MN868761, MN868738
Syrphidae Eristalinus aeneus (Scopoli, 1763) INV05013 IBIDP095-19 BOLD:AAF3600 MN868802
Syrphidae Eristalinus sepulchralis (Linnaeus, 1758) INV05025, INV05072 IBIDP103-19, IBIDP123-19 BOLD:AAZ5387 MN868777, MN868819
Syrphidae Eristalinus taeniops (Wiedemann, 1818)'' INV01912, INV04912 IBIDP017-19, IBIDP040-19 BOLD:ACL5309 MN868857, MN868779
Syrphidae Eristalis arbustorum (Linnaeus, 1758) INV01948, INV02915, INV04917, INV05071 IBIDP021-19, IBIDP027-19, IBIDP045-19, IBIDP122-19 BOLD:AAA8223 MN868782, MN868832, MN868878, MN868725
Syrphidae Eristalis pertinax (Scopoli, 1763) INV04965 IBIDP073-19 BOLD:AAQ3585 MN868733
Syrphidae Eristalis similis (Fallen, 1817) INV01910, INV04915 IBIDP016-19, IBIDP043-19 BOLD:AAY9892 MN868866, MN868894
Syrphidae Eristalis tenax (Linnaeus, 1758) INV01937, INV02914, INV04916 IBIDP019-19, IBIDP026-19, IBIDP044-19 BOLD:AAB0391 MN868900, MN868756, MN868909
Syrphidae Ferdinandea cuprea (Scopoli, 1763) INV05021 IBIDP100-19 BOLD:AAJ0402 MN868897
Syrphidae Helophilus pendulus (Linnaeus, 1758) INV04914 IBIDP042-19 BOLD:AAI6747 MN868765
Syrphidae Melanostoma mellinum (Linnaeus, 1758) INV04977 IBIDP078-19 BOLD:AAB2866 MN868833
Syrphidae Milesia crabroniformis (Fabricius, 1775)'' INV04153, INV05016 IBIDP031-19, IBIDP097-19 BOLD:ADS0144 MN868804, MN868904
Syrphidae Myathropa florea (Linnaeus, 1758) INV01938, INV04963 IBIDP020-19, IBIDP071-19 BOLD:AAP9713, BOLD:ADQ8445 MN868821, MN868847
Syrphidae Paragus quadrifasciatus Meigen, 1822 INV00560 IBIDP008-19 BOLD:ACG5063 MN868744
Syrphidae Platycheirus rosarum (Fabricius, 1787) INV04911, INV05074 IBIDP039-19, IBIDP124-19 BOLD:AAG4683 MN868812, MN868740
Syrphidae Scaeva pyrastri (Linnaeus, 1758) INV05070 IBIDP121-19 BOLD:AAF2374 MN868785
Syrphidae Sphaerophoria rueppelli (Wiedemann, 1830)* INV05058 IBIDP117-19 BOLD:AAA7374 MN868820
Syrphidae Sphaerophoria scripta (Linnaeus, 1758) INV02901, INV04900 IBIDP025-19, IBIDP033-19 BOLD:AAA7374 MN868774, MN868784
Syrphidae Syritta flaviventris Macquart, 1842 INV04973 IBIDP077-19 BOLD:AAG4663 MN868803
Syrphidae Syritta pipiens (Linnaeus, 1758) INV04937, INV05042, INV05097 IBIDP057-19, IBIDP170-19, IBIDP132-19 BOLD:AAC6291 MN868778, MN868754, MN868869
Syrphidae Syrphus vitripennis Meigen, 1822 INV07372 IBIDP377-19 BOLD:AAB5577 MN868776
Syrphidae Volucella zonaria (Poda, 1761) INV04979 IBIDP080-19 BOLD:AAH7785 MN868837
Tabanidae Chrysops caecutiens (Linnaeus, 1758) INV07371 IBIDP376-19 BOLD:ADZ0489 MN868849
Tabanidae Chrysops viduatus (Fabricius, 1794)'' INV04978 IBIDP079-19 BOLD:ACB5910 MN868728
Tabanidae Haematopota ocelligera (Krober, 1922)* INV05023 IBIDP166-19 BOLD:ADU0467 MN868772
Tachinidae Besseria dimidiata (Zetterstedt, 1844)* INV04998 IBIDP163-19 BOLD:ADT0060 MN868755
Tachinidae Compsilura concinnata (Meigen, 1824) INV05119 IBIDP141-19 BOLD:ADK6725 MN868913
Tachinidae Cylindromyia bicolor (Olivier, 1811) INV02245, INV04921 IBIDP022-19, IBIDP047-19 BOLD:AAN3295 MN868867, MN868808
Tachinidae Cylindromyia rufipes (Meigen, 1824)'' INV05014 IBIDP165-19 BOLD:AAU6684 MN868795
Tachinidae Dexia rustica (Fabricius, 1775)'' INV04945 IBIDP064-19 BOLD:ACD9618 MN868750
Tachinidae Ectophasia crassipennis (Fabricius, 1794)'' INV05026 IBIDP104-19 BOLD:ADJ6473 MN868852
Tachinidae Eloceria delecta (Meigen, 1824)'' INV04905 IBIDP035-19 BOLD:ACA9834 MN868895
Tachinidae Frontina laeta (Meigen, 1824)'' INV05027 IBIDP105-19 BOLD:ABW4362 MN868874
Tachinidae Leskia aurea (Fallen, 1820)'' INV05011 IBIDP094-19 BOLD:AAV7830 MN868759
Tachinidae Microphthalma europaea Egger, 1860 INV05111 IBIDP137-19 BOLD:AAU6726 MN868814
Tachinidae Mintho rufiventris (Fallen, 1817) INV05053 IBIDP114-19 BOLD:AAX3938 MN868730
Tachinidae Nemoraea pellucida (Meigen, 1824)'' INV05108 IBIDP180-19 BOLD:ACD9580 MN868848
Tachinidae Peleteria rubescens (Robineau-Desvoidy, 1830)'' INV05113 IBIDP138-19 BOLD:AAZ5252 MN868713
Tachinidae Peribaea tibialis (Robineau-Desvoidy, 1851) INV07382 IBIDP382-19 BOLD:ACB1892 MN868907
Tachinidae Periscepsia carbonaria (Panzer, 1798) INV05046, INV05085 IBIDP111-19, IBIDP129-19 BOLD:ACD9481 MN868815, MN868767
Tachinidae Phasia pusilla Meigen, 1824 INV07360 IBIDP371-19 BOLD:AAY2270 MN868790
Tachinidae Tachina lurida (Fabricius, 1781)'' INV07369 IBIDP375-19 BOLD:ACA9827 MN868845
Tachinidae Tachina magnicornis (Zetterstedt, 1844) INV04967, INV05052 IBIDP074-19, IBIDP113-19 BOLD:AAN9512 MN868752, MN868741
Tachinidae Triarthria setipennis (Fallen, 1810) INV00529 IBIDP005-19 BOLD:ADK0727 MN868911
Tachinidae Zophomyia temula (Scopoli, 1763)'' INV04927 IBIDP051-19 BOLD:ACD1492 MN868886
Tephritidae Ceratitis capitata (Wiedemann, 1824) INV05118 IBIDP140-19 BOLD:AAA3297 MN868742
Trichoceridae Trichocera saltator (Harris, 1776) INV06188 IBIDP143-19 BOLD:ACQ9998 MN868805
Ulidiidae Ceroxys urticae (Linnaeus, 1758)'' INV05059 IBIDP118-19 BOLD:AAI7007 MN868893
Ulidiidae Myennis octopunctata (Coquebert, 1798)'' INV00518 IBIDP003-19 BOLD:AAG7348 MN868824
Ulidiidae Physiphora alceae (Preyssler, 1791) INV03580 IBIDP030-19 BOLD:ABA5170 MN868875
Ulidiidae Ulidia apicalis Meigen, 1826'' INV02952, INV05037, INV07366 IBIDP028-19, IBIDP169-19, IBIDP373-19 BOLD:ABX4821 MN868743, MN868836, MN868860
Figure 1.

Examples of the diversity of species that are part of the dataset of distribution data and DNA barcodes of Portuguese Diptera 01. All photos by Rui Andrade.

aLucilia caesar, Lordelo do Ouro - Porto, BOLD:IBIDP083-19, GenBank: MN868752  
bHydrotaea dentipes, Campo - Valongo, BOLD: IBIDP136-19, GenBank: MN868754   
cTrigonometopus frontalis, Canelas - Estarreja, BOLD: IBIDP099-19, GenBank: MN868863   
dEpisyrphus balteatus, Vale de Algoso - Vimioso, BOLD: IBIDP015-19, GenBank: MN868781  
eCeratitis capitata, Gilmonde - Barcelos, BOLD: IBIDP140-19, GenBank: MN868854   

Project description

Title: 

The name “DNA barcodes of Portuguese Diptera 01” refers to the first data release of DNA barcodes and distribution data of dipterans within the InBIO Barcoding Initiative.

Personnel: 

Pedro Beja (project coordinator), Nuno Fonseca (project chair), Sónia Ferreira (taxonomist and IBI manager), Joana Paupério (IBI manager), Pedro Sousa (project technician), all affiliated to CIBIO-InBIO, University of Porto; Rui Andrade (taxonomist) independent researcher and Ana Rita Gonçalves (taxonomist) cE3c, Faculty of Science, University of Lisbon.

Study area description: 

North of the Tagus river in Portugal (Fig. 2).

Figure 2.  

Map of the localities where Diptera samples were collected in northern Portugal.

Design description: 

Dipteran specimens were collected in the field, morphologically identified and DNA barcoded.

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).

Sampling methods

Study extent: 

North of the Tagus river in Portugal

Sampling description: 

The studied material was collected in 59 different localities from the northern half of continental Portugal (Fig. 2, Table 1). Sampling was conducted between 2014 and 2018 on a wide range of habitats, using mainly hand-held sweep-nets or direct search for 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).

DNA extraction and sequencing followed the general pipeline used in the InBIO Barcoding Initiative. Briefly, genomic DNA was extracted from leg tissue using EasySpin Genomic DNA Tissue Kit (Citomed) following manufacturer’s protocol. The cytochrome c oxidase I (COI) barcoding fragment was amplified as two overlapping fragments (LC and BH), using two sets of primers: LCO1490 (Folmer et al. 1994) + Ill_C_R (Shokralla et al. 2015) and Ill_B_F Shokralla et al. 2015) + HCO2198 (Folmer et al. 1994), respectively. The COI mitochondrial gene (Folmer region), was then sequenced in a MiSeq benchtop system. OBITools (https://git.metabarcoding.org/obitools/obitools) was used to process the initial sequences which were then assembled into a single 658 bp fragment using Geneious 9.1.8. (https://www.geneious.com).

Quality control: 

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

Step description: 

Specimens were collected in 59 different localities of continental Portugal. Sampling was conducted from 2014 to 2018, and consisted of direct search of specimens (e.g. Hecamede albicans, Eutropha fulvifrons, Canace nasica), the use of entomological nets to intercept specimens flight (e.g. Hemipenthes morio, Sphaerophoria scripta) or to sweep the vegetation (e.g. Opetia nigra, Trigonometopus frontalis). Specimens collected were stored in 96% ethanol. A tissue sample was removed, from which DNA was extracted and the COI DNA barcode fragment was sequenced. Data generated were submitted to BOLD, GenBank and GBIF.

Geographic coverage

Description: 

Continental Portugal

Coordinates: 

40.054 and 42.002 Latitude; 6.274 and -8.774 Longitude.

Taxonomic coverage

Description: 

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 (Fig. 3). These five families account for 54% of the total species represented (Fig. 3). Nineteen families are represented by a single species.

Figure 3.  

Distribution of specimens (A) and species (B), in percentage, per Diptera family present in the dataset. Families representing less than 2% of specimens/species were lumped together.

Temporal coverage

Data range: 
2014-5-27 - 2018-7-07.
Notes: 

The sampled material was collected in the period from 27 May 2014 to 07 July 2018

Collection data

Collection name: 
InBIO Barcoding Initiative
Collection identifier: 
4ec2b246-f5fa-4b90-9a8d-ddafc2a3f970
Specimen preservation method: 
“Alcohol”
Curatorial unit: 
Voucher tube - 1 to 203, DNA extractions - 1 to 203

Usage rights

Use license: 
Creative Commons Public Domain Waiver (CC-Zero)

Data resources

Data package title: 
The InBIO Barcoding Initiative Database: Diptera 01
Number of data sets: 
1
Data set name: 
DS-IBIDP01 IBI Diptera 01
Data format: 
dwc, xml, tsv, fasta
Description: 

The InBIO Barcoding Initiative Database: Diptera 01 dataset can be downloaded from the Public Data Portal of BOLD (dx.doi.org/10.5883/DS-IBIDP01) in different formats (data as dwc, xml or tsv, and sequences as fasta files). Alternatively, BOLD users can log-in and access the dataset via the Workbench platform of BOLD. All records are also searchable within BOLD, using the search function of the database.

The InBIO Barcoding Initiative will continue sequencing Diptera for the BOLD database, with the ultimate goal of comprehensive coverage. The version of the dataset, at the time of writing the manuscript, is included as Suppl. materials 2, 3, 4 in the form of two text files for record information as downloaded from BOLD, one text file with the collecting and identification data in Darwin Core Standard format (downloaded from GBIF) and of a fasta file containing all sequences as downloaded from BOLD.

It should be noted that, as the BOLD database is not compliant with the Darwin Core Standard format, the Darwin Core formatted file (dwc) that can be downloaded from BOLD is not strictly Darwin Core formatted. For a proper Darwin Core formatted file, see http://ipt.gbif.pt/ipt/resource?r=ibi_diptera_i&v=1.0 (Suppl. material 3).

Column labels below follow the labels downloaded in the tsv format. Columns with no content in our dataset are left out in the list below.

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
sex The sex of the specimen
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
elev Elevation of sampling site (in metres above sea level)
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

Acknowledgements

We would like to thank the many contributors to InBIO Barcoding Initiative that assisted the project along its design and implementation, and to our lab technicians Cátia Chaves, Filipa Martins, Catarina Pinho, Joana Pinto, Pamela Puppo and Joana Veríssimo. This project has received funding from 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 the 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).

References

Supplementary materials

Suppl. material 1: References used for morphological identification 
Authors:  Rui Andrade
Data type:  References
Brief description: 

References used for morphological identification

Suppl. material 2: IBI- Diptera 01 library - Specimen details 
Authors:  Sónia Ferreira, Rui Andrade, Ana Rita Gonçalves, Pedro Sousa, Pedro Beja
Data type:  Record information - specimen data
Brief description: 

The file includes information about all records in BOLD for the IBI- Diptera 01 library. It contains collecting and identification data. The data are as downloaded from BOLD, without further processing.

Suppl. material 3: IBI- Diptera 01 library - Specimen details - Darwin Core Standard 
Authors:  Sónia Ferreira, Rui Andrade, Ana Rita Gonçalves, Pedro Sousa, Pedro Beja
Data type:  Record information - specimen data in Darwin Core Standard format
Brief description: 

The file includes information about all records in BOLD for the IBI- Diptera 01 library. It contains collecting and identification data. The data are downloaded from GBIF, without further processing.

Suppl. material 4: IBI- Diptera 01 library - DNA sequences 
Authors:  Sónia Ferreira, Rui Andrade, Ana Rita Gonçalves, Pedro Sousa, Pedro Beja
Data type:  Genomic data, DNA sequences
Brief description: 

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.