Biodiversity Data Journal : Data Paper (Biosciences)
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Data Paper (Biosciences)
The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Hemiptera 01
expand article infoPedro Sousa, José Manuel Grosso-Silva§, Rui Andrade|, Cátia Chaves, Joana Pinto, Joana Paupério, Pedro Beja‡,, Sónia Ferreira
‡ CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Vila do Conde, Portugal
§ Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal
| Rua Calouste Gulbenkian 237 4H3 4050-145, Porto, 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) Hemiptera 01 dataset contains records of 131 specimens of Hemiptera. Most specimens have been morphologically identified to species or subspecies level and represent 88 species in total. The species of this dataset correspond to about 7.3% of continental Portuguese hemipteran species diversity. All specimens were collected in continental Portugal. Sampling took place from 2015 to 2019 and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

New information

This dataset increases the knowledge on the DNA barcodes and distribution of 88 species of Hemiptera from Portugal. Six species, from five different families, were new additions to the Barcode of Life Data System (BOLD), with another twenty five species barcodes' added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF). Eutettix variabilis and Fieberiella florii are recorded for the first time for Portugal and Siphanta acuta, an invasive species, previously reported from the Portuguese Azores archipelago, is recorded for the first time for continental Portugal.

Keywords

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

Introduction

Hemiptera is the most diverse order of non-holometabolan insects, with more than 107,000 described species (Henry 2017, Bartlett et al. 2018, Hardy 2018), being second only to the four so-called “megadiverse” holometabolan orders (Coleoptera, Lepidoptera, Diptera, and Hymenoptera), which include over 150,000 described species each (Zhang 2013). Hemipterans are among the most abundant and widespread insects on land and in freshwater habitats (Andersen 1999). The Hemiptera, or true bugs, have piercing‐sucking mouthparts that constrain them to feed on liquid food (Schuh and Slater 1995, Scudder 2017, Panfilio and Angelini 2018). The primary feeding habit of Hemiptera is herbivory but the order also includes numerous carnivores, scavengers, hematophages and some necrophages (Forero 2008, Gullan and Cranston 2014). As a result their ecological role is strongly linked to their trophic interaction with plants, several species are among the most important crop pests (Schuh and Slater 1995, Schaefer and Panizzi 2000, Dietrich 2009, Gullan and Martin 2009, Scudder 2017). A few hematophagous hemipterans in the subfamily Triatominae (Reduviidae) have a direct impact on human health as vectors of Chagas disease (Balczun et al. 2012).

In continental Portugal, the knowledge about the order Hemiptera is fragmentary and heterogeneous. The latest diversity estimate was close to 1,100 species (Grosso-Silva 2003), but the description of new species (e.g., Emeljanov and Drosopoulos 2004, Ribes and Baena 2006, Sanchez et al. 2006), as well as the detection of previously unrecorded ones (e.g. Grosso-Silva 2004, Hollier 2005, Goula and Mata 2011, Baena and Zuzarte 2012, Foster 2019, Grosso-Silva and Ferreira 2020) lead to an estimated number of more than 1,200 species to date. However, additional studies are needed to validate the distribution of the species in general. Furthermore, the introduction or expansion of alien species from nearby areas has also occurred regularly (e.g. Valente et al. 2004, Franco et al. 2011, Sánchez 2011, Borges et al. 2013, Garcia et al. 2013, Bella 2014, Grosso-Silva et al. 2020).

DNA barcoding is a standard molecular biology method for species identification based on the sequencing of a short mitochondrial DNA sequence that is then compared to a library of known sequences (Hebert et al. 2003). The construction of such libraries is an essential step in the process that requires the morphological identification of specimens to establish a baseline for comparisons (Kress et al. 2015, Ferreira et al. 2018). Open libraries of DNA barcodes exist, namely the Barcode of Life Data System (BOLD), but they are not comprehensive yet, especially in regions of high diversity or endemicity. Furthermore, regional variation in species genetic variability can confound identification results (Phillips et al. 2019). DNA barcodes can be used as a discovery step, on a two-step approach of species delimitation (e.g. Rannala 2015), but also combined with ecological traits (Kress et al. 2015), greatly contributing to the solution of the taxonomic impediment problem in Biology (e.g. Riedel et al. 2013, Kekkonen and Hebert 2014). DNA barcodes usefulness has rapidly extended beyond organism and species identification; they are increasingly used in ecological and biological conservation studies, as well as in forensic applications, such as food source identification (Pečnikar and Buzan 2013, Kress et al. 2015, DeSalle and Goldstein 2019). DNA barcoding has been successfully applied to the Hemiptera (e.g. Jung et al. 2011, Park et al. 2011, Raupach et al. 2014, Havemann et al. 2018, Govender and Willows-Munro 2019), with identification success rates of 80% to 100%. It is especially useful to identify immature and female individuals’ (e.g. Raupach et al. 2014, Havemann et al. 2018), which may not be reliably identified through morphological characters, or in areas where diversity remains poorly known (e.g. Govender and Willows-Munro 2019). DNA barcoding as also highlighted the existence of cryptic diversity and the need for taxonomic revisions of certain taxa (e.g. Jung et al. 2011, Park et al. 2011, Raupach et al. 2014, Havemann et al. 2018, Govender and Willows-Munro 2019).

In this context, Portuguese biodiversity is still underestimated and undersampled, although being part of the westernmost portion of the Mediterranean hotspot of biodiversity. The paucity of genetic data on Portuguese biodiversity led to the creation of a DNA barcoding initiative by the Research Network in Biodiversity and Evolutionary Biology - InBIO. The InBIO Barcoding Initiative (IBI) makes use of High-Throughput Sequencing technologies to construct a reference collection of morphologically identified Portuguese specimens and respective DNA barcodes. Within IBI, invertebrates, and insects in particular, are prioritied, given their large contribution to overall biodiversity and ecosystems (e.g. Weisser and Siemann 2004, Losey and Vaughan 2006, Mata et al. 2016, Silva et al. 2019) and the clear shortage of DNA barcodes available in public databases (e.g. Corley and Ferreira 2017, Corley et al. 2017, Ferreira et al. 2019, Weigand et al. 2019).

The IBI Hemiptera 01 dataset contains records of 131 specimens of Hemiptera collected in continental Portugal, all of which were identified to species level, mostly through morphological identification, for a total of 88 species and one additional subspecies. This dataset is the first IBI dataset on Hemiptera and is part of the ongoig IBI database public releases in both the Global Biodiversity Information Facility (GBIF) and the Barcode of Life Data System (BOLD) (e.g. Ferreira et al. 2020a, Ferreira et al. 2020b). We have included in this dataset the barcodes of all identified Hemiptera specimens in IBI up to December 2020. Overall, this paper contributes to the open dissemination and sharing of the distribution records and DNA barcodes of Hemiptera specimens that are part of our reference collection, to increase the available public information on a group of Portuguese Invertebrates.

General description

Purpose: 

This dataset aims to provide a first contribution to an authoritative DNA barcode sequences library for Portuguese Hemiptera. Such a library aims to enable DNA-based identification of species for both traditional molecular studies and DNA-metabarcoding studies. Furthermore, it constitutes an important resource for taxonomic research on Portuguese Hemiptera and its distribution.

Additional information: 

A total of 131 specimens of hemipterans were collected and DNA Barcodes (Suppl. materials 1, 2). Fig. 1 illustrates examples of the diversity of species that are part of the dataset of distribution data and DNA barcodes of Portuguese Hemiptera 01. All sequences of cytochrome c oxidase I (COI) DNA barcodes are 658 base pairs (bp) long, except for one with 418 bp. From the 88 species barcoded, six (7%) from five families are new to the DNA barcode database BOLD at the moment of its release (January 2021, marked with * in Species field of Table 1). Twenty-five additional taxa (28%) from 17 families were already represented in BOLD with less than 10 DNA barcode sequences (marked with " in Species field of Table 1). A few noteworthy species are included in the dataset. The record of the species Eutettix variabilis Hepner, 1942 is, to the best of our knowledge, the first record published for Portugal. European records for this north American species (Metcalf 1967) exist online (e.g. http://boldsystems.org/index.php/Taxbrowser_Taxonpage?taxon=+Eutettix+variabilis&searchTax=Search+Taxonomy; all European records in BOLD are based on genetic identifications). The species Fieberiella florii Stål, 1864, a vector for phytoplasmas, is also recorded for Portugal for the first time, with a few records known for Spain (e.g. Aguin-Pombo et al. 2007). Another important result is the record of the invasive species Siphanta acuta (Walker, 1851), recorded here for the first time for continental Portugal, although it has been previously reported from the São Miguel Island in the Azores Archipelago (Borges et al. 2013). Moreover, Stictopleurus punctatonervosus, first recorded from Murtosa (Aveiro) (Valcárcel and Prieto Piloña 2021), is recorded for the second time for Portugal.

Table 1.

List of species that were collected and DNA barcoded within this project. In column Taxa: * - indicates taxa without a DNA barcode prior to this study; '' - indicates taxa with less than 10 sequences available prior to this study; # - indicates taxa that are important Portuguese records.

Family Taxa IBI code BOLD code BOLD BIN

GenBank

Suborder Auchenorrhyncha
Aphrophoridae Aphrophora alni (Fallén, 1805) INV09012 IBIHP182-20 BOLD:AEE6925 MW535978
Aphrophoridae Aphrophora corticea Germar, 1821'' INV06714, INV07137 IBIHP128-20, IBIHP141-20 BOLD:ACT0928 MW536000, MW535990
Aphrophoridae Philaenus spumarius (Linnaeus, 1758) INV00536, INV08398, INV08399, INV08417 IBIHP100-20, IBIHP076-20, IBIHP077-20, IBIHP078-20 BOLD:AAB1850 MW535975, MW536068, MW535998, MW535976
Cercopidae Cercopis intermedia Kirschbaum, 1868'' INV02955, INV07443 IBIHP046-20, IBIHP068-20 BOLD:AEC5811 MW536014, MW536066
Cercopidae Haematoloma dorsata (Ahrens, 1812)'' INV06363 IBIHP055-20 BOLD:ABV4901 MW535969
Cicadellidae Cicadella viridis (Linnaeus, 1758) INV00537, INV02935 IBIHP010-19, IBIHP019-19 BOLD:ACB8347 MW535965, MW536088
Cicadellidae Eupelix cuspidata Fabricius, 1775'' INV08568 IBIHP179-20 BOLD:ADN9562 MW536080
Cicadellidae Eutettix variabilis Hepner, 1942# INV00888 IBIHP185-21 BOLD:AAV0162 MW536051
Cicadellidae Fieberiella florii Stål, 1864# INV06761 IBIHP191-21 BOLD:ACJ7053 MW536009
Cicadellidae Iassus lanio Linnaeus, 1761'' INV00854 IBIHP107-20 BOLD:ABW6633 MW536053
Cicadellidae Tremulicerus fulgidus (Fabricius, 1775)* INV00544 IBIHP011-19 BOLD:ABX8897 MW536072
Cicadidae Tettigettalna estrellae (Boulard, 1982) INV05324 IBIHP117-20 BOLD:ACQ4286 MW536030
Delphacidae Laodelphax striatellus (Fallén, 1826) INV07220 IBIHP193-21 BOLD:ABY1518 MW536002
Dictyopharidae Almana longipes (Dufour, 1849)* INV02255 IBIHP109-20 BOLD:AEE5516 MW535980
Dictyopharidae Dictyophara europaea (Linnaeus, 1767) INV10744 IBIHP074-20 BOLD:ADJ8496 MW535967
Flatidae Siphanta acuta (Walker, 1851)# INV00638 IBIHP183-21 BOLD:AAJ7097 MW535981
Membracidae Centrotus cornutus (Linnaeus, 1758)'' INV06292 IBIHP125-20 BOLD:ACP8681 MW536003
Suborder Heteroptera
Acanthosomatidae Cyphostethus tristriatus (Fabricius, 1787) INV08561 IBIHP081-20 BOLD:ACX9740 MW536060
Acanthosomatidae Elasmostethus interstinctus (Linnaeus, 1758) INV01286, INV03659 IBIHP186-21, IBIHP050-20 BOLD:ABZ2225 MW536008, MW535966
Alydidae Camptopus lateralis (Germar, 1817)'' INV06810 IBIHP134-20 BOLD:ACP6596 MW536041
Alydidae Micrelytra fossularum (Rossi, 1790)'' INV10738 IBIHP072-20 BOLD:AEA8911 MW536052
Aradidae Aradus flavicornis Dalman, 1823'' INV07327 IBIHP063-20 BOLD:ABW4545 MW536087
Berytidae Berytinus montivagus (Meyer, 1841)'' INV00836 IBIHP106-20 BOLD:ACA7025 MW536032
Coreidae Centrocoris spiniger (Fabricius, 1781)'' INV06382 IBIHP189-21 BOLD:AEF4063 MW536019
Coreidae Ceraleptus lividus Stein, 1858 INV00158 IBIHP040-20 BOLD:ACA7307 MW535973
Coreidae Enoplops scapha (Fabricius, 1794) INV04363, INV06334 IBIHP052-20, IBIHP053-20 BOLD:ABW9378 MW535971, MW536013
Coreidae Haploprocta sulcicornis (Fabricius, 1794)* INV06214 IBIHP120-20 BOLD:AAZ9600 MW536044
Coreidae Syromastus rhombeus (Linnaeus, 1767) INV00189, INV07148 IBIHP003-19, IBIHP033-19 BOLD:ABX4334 MW536095, MW535972
Corixidae Corixa affinis Leach, 1817 INV06766 IBIHP133-20 BOLD:ACY0615 MW535977
Corixidae Corixa punctata (Illiger, 1807) INV03620, INV06765 IBIHP187-21, IBIHP192-21 BOLD:ACB1799 MW536081, MW536011
Corixidae Hesperocorixa sahlbergi (Fieber, 1848) INV06758 IBIHP131-20 BOLD:AAN0795 MW535983
Corixidae Paracorixa concinna (Fieber, 1848) INV00874 IBIHP184-21 BOLD:ADG5371 MW536062
Corixidae Sigara nigrolineata (Fieber, 1848) INV03590 IBIHP116-20 BOLD:ACB1978 MW536074
Corixidae Sigara venusta (Douglas & Scott, 1869)'' INV00312 IBIHP005-19 BOLD:ABA5309 MW535962
Cydnidae Cydnus aterrimus (Forster, 1771)'' INV00179 IBIHP002-19 BOLD:ABX7003 MW536015
Cydnidae Macroscytus brunneus (Fabricius, 1803)'' INV07326, INV07329, INV08565 IBIHP144-20, IBIHP145-20, IBIHP082-20 BOLD:ADX9400 MW536058, MW535979, MW536077
Gerridae Aquarius najas (DeGeer, 1773) INV00319 IBIHP042-20 BOLD:AAN1521 MW536079
Gerridae Aquarius paludum (Fabricius, 1794) INV00384 IBIHP008-19 BOLD:AAI7450 MW536075
Gerridae Gerris gibbifer Schummel, 1832 INV00354, INV00399 IBIHP006-19, IBIHP009-19 BOLD:ACB1756 MW536050, MW536031
Hydrometridae Hydrometra stagnorum (Linnaeus, 1758) INV00415 IBIHP043-20 BOLD:AEC2693 MW535986
Lygaeidae Lygaeus equestris (Linnaeus, 1758) INV06335, INV07424 IBIHP054-20, IBIHP066-20 BOLD:ACB9437 MW536020, MW535992
Lygaeidae Melanocoryphus albomaculatus Goeze, 1778'' INV02909 IBIHP112-20 BOLD:AEE6008 MW536033
Lygaeidae Spilostethus pandurus Scopoli, 1763 INV03741 IBIHP025-19 BOLD:AAV0102 MW536010
Lygaeidae Spilostethus saxatilis (Scopoli, 1763) INV00147 IBIHP001-19 BOLD:ADS4825 MW536006
Miridae Capsodes flavomarginatus (Donovan, 1798)'' INV07922 IBIHP168-20 BOLD:ACR3434 MW536045
Miridae Closterotomus trivialis (A.Costa, 1853)'' INV08815 IBIHP089-20 BOLD:AEA3807 MW536038
Miridae Harpocera thoracica (Fallén, 1807) INV08427 IBIHP080-20 BOLD:ABU6305 MW536078
Miridae Heterocordylus tibialis (Hahn, 1833) INV07441, INV07442 IBIHP152-20, IBIHP195-21 BOLD:ADM8543 MW536054, MW535993
Miridae Liocoris tripustulatus (Fabricius, 1781) INV10737 IBIHP071-20 BOLD:AAY9524 MW536005
Miridae Phytocoris varipes Boheman, 1852 INV08602 IBIHP086-20 BOLD:AAH9369 MW535974
Miridae Psallus ambiguus (Fallén, 1807) INV07923 IBIHP169-20 BOLD:AAY8936 MW536057
Miridae Psallus varians (Herrich-Schäffer, 1841) INV08423 IBIHP079-20 BOLD:AAY8935 MW536027
Miridae Stenodema laevigata (Linnaeus, 1758) INV06213, INV07428 IBIHP119-20, IBIHP150-20 BOLD:AAY9089 MW535964, MW536092
Nabidae Himacerus mirmicoides (O.Costa, 1834) INV02906 IBIHP111-20 BOLD:AAY9075 MW536034
Nepidae Nepa cinerea Linnaeus, 1758 INV00165, INV00628, INV02496 IBIHP041-20, IBIHP044-20, IBIHP045-20 BOLD:AEC3215 MW536073, MW535968, MW535999
Nepidae Ranatra linearis (Linnaeus, 1758) INV00744, INV00745, INV03529, INV03530, INV03531 IBIHP016-19, IBIHP017-19, IBIHP020-19, IBIHP021-19, IBIHP022-19 BOLD:AAL1328 MW535994, MW536004, MW536067, MW535995, MW536048
Notonectidae Anisops sardeus Herrich-Schäffer, 1850'' INV03534 IBIHP114-20 BOLD:ABV0079 MW536012
Notonectidae Notonecta maculata Fabricius, 1794 INV00310, INV00378, INV00681, INV03281 IBIHP004-19, IBIHP007-19, IBIHP015-19, IBIHP048-20 BOLD:AAN1703 MW536040, MW536091, MW536069, MW536061
Pentatomidae Aelia acuminata (Linnaeus, 1758) INV06436 IBIHP056-20 BOLD:AAY9083 MW536042
Pentatomidae Aelia rostrata Boheman, 1852'' INV02960, INV03567, INV06812 IBIHP113-20, IBIHP115-20, IBIHP135-20 BOLD:AEE2078 MW536063, MW536076, MW536096
Pentatomidae Carpocoris mediterraneus atlanticus Tamanini, 1959'' INV06846, INV00523 IBIHP060-20, IBIHP099-20 BOLD:ACD7499 MW536043, MW536029
INV10749 IBIHP075-20 BOLD:ACD6303 MW536064
Pentatomidae Dolycoris baccarum (Linnaeus, 1758) INV07921 IBIHP036-19 BOLD:AAP3525 MW536086
Pentatomidae Eurydema ornata (Linnaeus, 1758) INV06849 IBIHP061-20 BOLD:AEC2842 MW536016
INV07035 IBIHP139-20 BOLD:AEE5125 MW536022
Pentatomidae Eysarcoris venustissimus (Schrank, 1776)'' INV06293, INV06337, INV07432 IBIHP030-19, IBIHP031-19, IBIHP035-19 BOLD:ADZ2301 MW536070, MW536026, MW536007
Pentatomidae Graphosoma italicum (O.F.Müller, 1766) INV03552, INV07430, INV08816 IBIHP049-20,IBIHP034-19, IBIHP090-20 BOLD:AAY9133 MW536059, MW536036, MW536094
Pentatomidae Graphosoma semipunctatum (Fabricius, 1775) INV00620 IBIHP013-19 BOLD:ADT8242 MW536018
Pentatomidae Holcogaster fibulata (Germar, 1831)'' INV07688 IBIHP069-20 BOLD:ACS3305 MW535988
Pentatomidae Nezara viridula (Linnaeus, 1758) INV00142, INV03969, INV04120 IBIHP039-20, IBIHP026-19, IBIHP028-19 BOLD:AAU3346 MW535996, MW536046, MW536001
Pentatomidae Palomena prasina (Linnaeus, 1761) INV00676, INV07422 IBIHP014-19, IBIHP065-20 BOLD:AAG8727 MW536049, MW536037
Pentatomidae Pentatoma rufipes (Linnaeus, 1758) INV04074, INV10253 IBIHP027-19, IBIHP070-20 BOLD:AAZ7767 MW536047, MW536039
Pentatomidae Piezodorus lituratus (Fabricius, 1794) INV08914 IBIHP091-20 BOLD:AAY9491 MW536093
Pentatomidae Rhaphigaster nebulosa (Poda, 1761) INV03554 IBIHP023-19 BOLD:AAY8964 MW536089
Potamocoridae Naucoris maculatus Fabricius, 1798'' INV00631 IBIHP104-20 BOLD:AEE8147 MW536056
Pyrrhocoridae Pyrrhocoris apterus (Linnaeus, 1758) INV01258, INV06470 IBIHP018-19, IBIHP032-19 BOLD:AAY8951 MW536084, MW535963
Pyrrhocoridae Scantius aegyptius (Linnaeus, 1758)'' INV04125 IBIHP051-20 BOLD:ACL0625 MW536071
Reduviidae Empicoris rubromaculatus (Blackburn, 1888) INV07642 IBIHP164-20 BOLD:ACN7256 MW536083
Reduviidae Oncocephalus gularis Reuter, 1882* INV08587 IBIHP085-20 BOLD:AEH0127 MW535991
Reduviidae Reduvius personatus (Linnaeus, 1758) INV06813 IBIHP059-20 BOLD:AEC5973 MW536035
INV08753 IBIHP088-20 BOLD:AEE8716 MW536025
Reduviidae Rhynocoris cuspidatus Ribaut, 1922* INV02959 IBIHP047-20 BOLD:ADJ4404 MW535984
Rhopalidae Brachycarenus tigrinus (Schilling, 1829) INV00545 IBIHP012-19 BOLD:AAD4531 MW536017
Rhopalidae Chorosoma schillingii (Schilling, 1829) INV02601, INV03608, INV06759 IBIHP029-19, IBIHP024-19, IBIHP057-20 BOLD:ABV9616 MW536028, MW535987, MW536082
Rhopalidae Liorhyssus hyalinus (Fabricius, 1794) INV08920 IBIHP092-20 BOLD:AAG8881 MW536021
Rhopalidae Rhopalus subrufus (Gmelin, 1790) INV07425 IBIHP067-20 BOLD:AAY9322 MW536085
Rhopalidae Stictopleurus punctatonervosus (Goeze, 1778)# INV10743 IBIHP073-20 BOLD:AAZ3560 MW535985
Rhyparochromidae Beosus maritimus (Scopoli, 1763) INV07290 IBIHP062-20 BOLD:ABW9272 MW536023
Rhyparochromidae Eremocoris fenestratus (Herrich-Schäffer, 1839)* INV06764 IBIHP058-20 BOLD:ABU6590 MW535989
Stenocephalidae Dicranocephalus agilis (Scopoli, 1763)'' INV07328 IBIHP064-20 BOLD:ADK7724 MW536090
Thaumastocoridae Thaumastocoris peregrinus Carpintero & Dellapé, 2006 INV07942, INV07943 IBIHP037-19, IBIHP038-19 BOLD:ACY9011 MW535982, MW535970
Figure 1.

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

aAphrophora corticea - BIN URI: BOLD:ACT0928  
bCicadella viridis - BIN URI: BOLD:ACB8347  
cEmpicoris rubromaculatus - BIN URI: BOLD:ACN7256  
dMicrelytra fossularum - BIN URI: BOLD:AEA8911  
eDolycoris baccarum - BIN URI: BOLD:AAP3525  
fSpilostethus pandurus - BIN URI: BOLD:AAV0102  

Project description

Personnel: 

Pedro Beja (project coordinator), Sónia Ferreira (taxonomist and IBI manager), Joana Paupério (IBI manager), Pedro Sousa (taxonomist, project technician), Cátia Chaves (project technician), Joana Pinto (project technician), all affiliated to CIBIO-InBIO, University of Porto, José Manuel Grosso-Silva (taxonomist), affiliated to the MHNC-UP, University of Porto and Rui Andrade (taxonomist), independent researcher.

Sampling methods

Study extent: 

Continental Portugal.

Sampling description: 

The studied material was collected in 60 different localities from continental Portugal, almost half of which (47%) belong to the Bragança District (Fig. 2, Table 2). Two specimens were integrated in the IBI reference collection without further sampling information available besides being collected in Portugal. Sampling was conducted between 2015 and 2019 in a wide range of habitats, by direct search of specimens or by sweeping the vegetation. Collected specimens were examined using a stereoscopic microscope and stored in 96% ethanol for downstream molecular analysis. Morphological identification was performed, based on keys and descriptions from literature (Suppl. material 3). DNA extraction and sequencing followed the general pipeline used in the InBIO Barcoding Initiative. Genomic DNA was extracted from leg tissue using EasySpin Genomic DNA Tissue Kit (Citomed) following the manufacturer’s protocol. The mitochondrial 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 and Ill_B_F (Shokralla et al. 2015) + HCO2198 (Folmer et al. 1994), respectively. The COI gene (Folmer region), was then sequenced in a MiSeq benchtop system. OBITools (Boyer et al. 2015) 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).

Table 2.

Number of specimens and species collected per Portuguese District and corresponding percentage.

District Specimens (n) Specimens (%) Taxa (n) Taxa (%)
Bragança 72 55.0% 55 62.5%
Porto 13 9.9% 13 14.8%
Guarda 10 7.6% 9 10.2%
Setúbal 7 5.3% 7 8.0%
Aveiro 5 3.8% 4 4.5%
Leiria 5 3.8% 3 3.4%
Castelo Branco 4 3.1% 3 3.4%
Faro 4 3.1% 2 2.3%
Lisboa 3 2.3% 3 3.4%
Vila Real 3 2.3% 3 3.4%
Viseu 2 1.5% 2 2.3%
Beja 1 0.8% 1 1.1%
not known 2 1.5% 2 2.3%
TOTAL 131 88
Figure 2.  

Map of the localities where Hemiptera samples were collected in continental Portugal. Portuguese Districts are also represented, with those referred in Table 2 numbered as follows: 1 - Bragança, 2 - Porto, 3 - Guarda, 4 - Setúbal, 5 - Aveiro, 6 - Leiria, 7 - Castelo Branco, 8 - Faro, 9 - Lisboa, 10 - Vila Real, 11 - Viseu, 12 - Beja.

Quality control: 

All DNA barcode sequences were compared against the BOLD database and the 99 top results were inspected in order to detect possible problems due to contaminations or misidentifications. Prior to GBIF submission, data were checked for errors and inconsistencies with OpenRefine 3.3 (http://openrefine.org).

Step description: 
  1. Specimens were collected in 60 different localities of continental Portugal. Fieldwork was carried out between 2015 and 2019.
  2. Specimens were collected during fieldwork by direct search of specimens or by sweeping the vegetation with a hand-net and preserved in 96% alcohol. Captured specimens were deposited in the IBI reference collection at CIBIO (Research Center in Biodiversity and Genetic Resources).
  3. Specimens were morphologically identified with the assistance of stereoscopic microscopes (Leica MZ12, 8x to 100x; Olympus SZX16, 7x to 115x) and using the available literature (Suppl. material 3). A subset (23%) was identified using the BOLD Identification Engine directly.
  4. DNA barcodes were sequenced from all specimens. For this, one leg was removed from each individual, DNA was then extracted and a 658 bp COI DNA barcode fragment was amplified and sequenced. For one specimen of Ceraleptus lividus, only a 418 bp fragment was sequenced. DNA extracts were deposited in the IBI collection.
  5. All obtained sequences were submitted to BOLD and GenBank databases and, to each sequenced specimen, the morphological identification, when available, was contrasted with the results of the BLAST of the newly-generated DNA barcodes in the BOLD Identification Engine.
  6. Prior to submission to GBIF, data were checked for errors and inconsistencies with OpenRefine 3.3 (http://openrefine.org/).

Geographic coverage

Description: 

Continental Portugal .

Coordinates: 

37.257 and 41.979 Latitude; -9.465 and -6.344 Longitude.

Taxonomic coverage

Description: 

This dataset is composed of data relating to 131 Hemiptera specimens. All specimens were determined to species level, with three specimens further identifed to subspecies level. Overall, 88 species are represented in the dataset. These species belong to 30 families. The Pentatomidae family accounts for 21% of the total collected specimens (Fig. 3A) and no other family accounts for more than 8%. The Pentatomidae and Miridae families combined account for 26% of the total taxa represented (Fig. 3B) and no other family accounts for more than 7%. Eleven families are represented by a single taxon and nine by two taxa.

Figure 3.  

Distribution of specimens (A) and species (B), in percentage, per Hemiptera family present in the dataset. Families representing less than 3% of the total specimens/species are represented together in the respective graph.

Taxa included:
Rank Scientific Name
kingdom Animalia
phylum Arthropoda
subphylum Hexapoda
class Insecta
order Hemiptera
superorder Auchenorrhyncha
superorder Heteroptera
family Acanthosomatidae
family Alydidae
family Aphrophoridae
family Aradidae
family Berytidae
family Cercopidae
family Cicadellidae
family Cicadidae
family Coreidae
family Corixidae
family Cydnidae
family Delphacidae
family Dictyopharidae
family Flatidae
family Gerridae
family Hydrometridae
family Lygaeidae
family Membracidae
family Miridae
family Nabidae
family Nepidae
family Notonectidae
family Pentatomidae
family Potamocoridae
family Pyrrhocoridae
family Reduviidae
family Rhopalidae
family Rhyparochromidae
family Stenocephalidae
family Thaumastocoridae

Temporal coverage

Data range: 
2015-3-16 - 2019-9-20.
Notes: 

The sampled material was collected in the period from 16 March 2015 to 20 September 2019.

Usage licence

Usage licence: 
Other
IP rights notes: 

Creative Commons Attribution 4.0 International (CC BY 4.0)

Data resources

Data package title: 
The InBIO Barcoding Initiative Database: Hemiptera 01
Number of data sets: 
1
Data set name: 
DS-IBIHP01 IBI Hemiptera 01
Data format: 
dwc, xml, tsv, fasta
Description: 

The InBIO Barcoding Initiative Database: Hemiptera 01 dataset can be downloaded from BOLD (dx.doi.org/10.5883/DS-IBIHP01) in different formats (records as dwc, xml or tsv and sequences as fasta files). All records are also searchable within BOLD, using the search function of the platform.

The InBIO Barcoding Initiative will continue to sequence Hemiptera for the BOLD database, with the ultimate goal of achieving a comprehensive coverage of the Portuguese Hemiptera fauna. The version of the dataset, at the time of the writing of the manuscript, is included as Suppl. materials 1, 2, 4 in the form of two text files with specimen data information, as downloaded from BOLD and GBIF (the latter in Darwin Core Standard format) and one fasta file containing all sequences as downloaded from BOLD.

It should be noted that the BOLD database is not strictly compliant with the Darwin Core Standard (DwC) format and, as such, the file downloadable from BOLD (Suppl. material 1) is not in the standard DwC. For a proper DwC formatted file, see http://ipt.gbif.pt/ipt/resource?r=ibi_hemiptera_01&v=1.0 (Suppl. material 2).

Column labels below follow the labels downloaded in the tsv format from BOLD. 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
subspecies_taxID Subspecies taxonomic numeric code
subspecies_name Subspecies name

Acknowledgements

We would like to thank all contributors to the InBIO Barcoding Initiative who assisted the project along its design and execution and to our lab technicians Filipa Martins, Catarina Pinho, 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).

References

Supplementary materials

Suppl. material 1: IBI - Hemiptera 01 library - Specimen details 
Authors:  Pedro Sousa, José Manuel Grosso-Silva, Rui Andrade, Pedro Beja, Sónia Ferreira
Data type:  Specimen data records
Brief description: 

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

Suppl. material 2: IBI - Hemiptera 01 library - Specimen details - Darwin Core Standard 
Authors:  Pedro Sousa, José Manuel Grosso-Silva, Rui Andrade, Pedro Beja, Sónia Ferreira
Data type:  Specimen data records in Darwin Core Standard format
Brief description: 

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

Suppl. material 3: References used for morphological identification 
Authors:  José Manuel Grosso-Silva, Pedro Sousa
Data type:  References
Brief description: 

References used for morphological identification.

Suppl. material 4: IBI- Hemiptera 01 library - DNA sequences 
Authors:  Pedro Sousa, Cátia Chaves, Joana Pinto, Joana Paupério, Pedro Beja, Sónia Ferreira
Data type:  Specimen genomic data, DNA sequences
Brief description: 

COI sequences in fasta format. Each sequence is identified by the BOLD ProcessID, species name, genetic marker name and GenBank accession number, all separated by a vertical bar. The data are as downloaded from BOLD.