Biodiversity Data Journal : Data Paper (Biosciences)
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Data Paper (Biosciences)
The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot
expand article infoJoana Pauperio‡,§,|, Luis Martin Gonzalez, Jesus Martinez, Marcos A González, Filipa MS Martins‡,§, Joana Veríssimo‡,§,#, Pamela Puppo¤, Joana Pinto‡,§, Cátia Chaves‡,§, Catarina J. Pinho‡,§,#, José Manuel Grosso-Silva«, Lorenzo Quaglietta»,§, Teresa Luísa L Silva‡,§, Pedro Sousa‡,§, Paulo Celio Alves‡,§,˄, Nuno Fonseca‡,§, Pedro Beja‡,§,», Sónia Ferreira‡,§,˄
‡ CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, Portugal
§ BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, Portugal
| European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
¶ Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, Spain
# Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
¤ Marshall University, Department of Biological Sciences, Huntington, United States of America
« Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal
» CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
˄ EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, Portugal
Corresponding author: Sónia Ferreira (hiporame@gmail.com)
Academic editor: Henrique Paprocki
Received: 12 Nov 2022 | Accepted: 28 Dec 2022 | Published: 19 Jan 2023
© 2023 Joana Pauperio, Luis Martin Gonzalez, Jesus Martinez, Marcos González, Filipa MS Martins, Joana Veríssimo, Pamela Puppo, Joana Pinto, Cátia Chaves, Catarina J. Pinho, José Manuel Grosso-Silva, Lorenzo Quaglietta, Teresa Luísa Silva, Pedro Sousa, Paulo Alves, Nuno Fonseca, Pedro Beja, Sónia Ferreira
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Pauperio J, Gonzalez LM, Martinez J, González MA, Martins FM, Veríssimo J, Puppo P, Pinto J, Chaves C, Pinho CJ, Grosso-Silva JM, Quaglietta L, Silva TLL, Sousa P, Alves PC, Fonseca N, Beja P, Ferreira S (2023) The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot. Biodiversity Data Journal 11: e97484. https://doi.org/10.3897/BDJ.11.e97484
 Open Access

Abstract

Background

The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or in the collection Marcos A. González at the University of Santiago de Compostela (Spain).

New information

Twenty-nine species, from nine different families, were new additions to the Barcode of Life Data System (BOLD). A success identification rate of over 80% was achieved when comparing morphological identifications and DNA barcodes for the species analysed. This encouraging step advances incorporation of informed Environmental DNA tools in biomonitoring schemes, given the shortcomings of morphological identifications of larvae and adult Caddisflies in such studies. DNA barcoding was not successful in identifying species in six Trichoptera genera: Hydropsyche (Hydropsychidae), Athripsodes (Leptoceridae), Wormaldia (Philopotamidae), Polycentropus (Polycentropodidae) Rhyacophila (Rhyacophilidae) and Sericostoma (Sericostomatidae). The high levels of intraspecific genetic variability found, combined with a lack of a barcode gap and a challenging morphological identification, rendered these species as needing additional studies to resolve their taxonomy.

Keywords

Trichoptera, occurrence records, species distributions, continental Portugal, continental Spain, DNA barcode, cytochrome c oxidase subunit I (COI)

Introduction

DNA barcoding is a molecular biology method for species identification that was proposed almost twenty years ago (Hebert et al. 2003). DNA barcoding relies on the comparison of a short mitochondrial DNA sequence of interest, usually a 658 bp fragment of the cytochrome c oxidase subunit I (COI) of the mitochondrial genome, known as the “Folmer region” (Folmer et al. 1994), although other regions and genes can also be used, including ones with different systematic scopes (e.g. Woese and Fox (1977)). For DNA barcoding to work, the sequence of interest must be compared to a library containing sequences with known species identification (Hebert et al. 2003, Hebert et al. 2004). As such, the construction of comprehensive reference libraries is essential and these require the morphological identification of vouchers by an expert taxonomist (Baird and Sweeney 2011, Ferreira et al. 2018, Kress et al. 2015). DNA barcoding applications have since expanded beyond single organism and species identification studies.

Development of DNA metabarcoding (Taberlet et al. 2012) was made possible with the advances in PCR technologies and high-throughput sequencing (HTS) (Liu et al. 2019). Multiple DNA barcodes are sequenced in a single sample, allowing the study of complex samples as bulk samples and environmental DNA. DNA metabarcoding has broadened the use of the two. DNA barcodes are now a ubiquitous tool in ecological and biological conservation studies, as well as, for example, in forensic applications (DeSalle and Goldstein 2019, Fišer Pečnikar and Buzan 2013, Kress et al. 2015).

Aquatic ecosystems are suffering high losses in biodiversity due to degradation and habitat destruction (Blancher et al. 2022). These ecosystems can be logistically challenging and time-consuming to monitor, as the current methodology is based on inventories and taxonomical diversity, based on morphology (Blancher et al. 2022). DNA metabarcoding has great potential for conservation and monitoring of aquatic ecosystems studies as it allows efficient, non-invasive and standardised sampling, without a priori knowledge of the existing biodiversity in an area (Thomsen and Willerslev 2015, Valentini et al. 2016). The choice of DNA markers and the biomass of the communities to monitor are important factors that can influence successful use of DNA metabarcoding (Thomsen and Willerslev 2015, Valentini et al. 2016, Casey et al. 2021).

The Trichoptera, or caddisflies, is an order of holometabolous insects that rank seventh overall amongst insect orders regarding species number, with 16,267 described species (Morse 2022) and is the most speciose of the primarily aquatic insect orders. Species of this order can be found in all continents, except Antarctica (Morse et al. 2019). While adults are mostly terrestrial and capable of flight, most species’ eggs, larvae and pupae are found in freshwater habitats (Morse et al. 2019). Adult caddisflies are moth-like insects having their bodies covered with setae or hairs (Holzenthal et al. 2007, Morse et al. 2019, Thomas et al. 2020). Their larvae are known for their ability to use silk to construct shelters and retreats, but some species can also be free-living (Casey et al. 2021, González and Cobo 2006, Holzenthal et al. 2015, Martín 2017, Martínez 2014, Morse et al. 2019, Thomas et al. 2020, Zhou et al. 2016). Caddisfly larvae provide several important ecological services, including their crucial role in the trophic dynamics and energy flow in the lakes, rivers and streams freshwater food webs (Holzenthal et al. 2015, Morse et al. 2019, Zhou et al. 2016). They show differential sensitivity to pollution and their diversity and abundance are widely used in biological freshwater monitoring (Resh and Rosenberg 1984). However, these programmes rely on larval morphological identification, which is much more challenging than adult determination and still impossible in the many species, whose larvae have not yet been described (Morse et al. 2019).

Environmental DNA has the potential to be used as a complement or as an alternative to the hurdles of current morphology-based identification in the scope of freshwater monitoring schemes (Lefrançois et al. 2020). However, successful application of eDNA in Europe will necessitate comprehensive reference collections of DNA sequences, representing existing European aquatic biodiversity (Baird and Sweeney 2011, Ferreira et al. 2018, Kress et al. 2015). Several studies have used barcodes to advance the knowledge on Trichoptera, either expanding the knowledge on their phylogeny or improving the DNA barcodes of Trichoptera species (e.g. Morinière et al. (2017), Zhou et al. (2016)).

In the Iberian Peninsula, approximately 380 Trichoptera taxa, from 23 families are known (Coppa et al. 2022, González et al. 1992, González and Martínez 2011, Malicky 2005, Martín 2017, Martínez 2014, Oláh et al. 2019a, Oláh et al. 2019b, Oláh et al. 2020, Valladolid et al. 2018, Titos et al. 2018). Of these, 374 are known in Spain and 190 in Portugal. The rate of endemicity of Iberian caddisflies is very high, with around one third of the taxa known to occur in the region being endemic (González et al. 1987, Martínez 2014, Martín 2017).

In this work, we present a contribution to the DNA barcode library of the Iberian Peninsula species of Trichoptera representing 37% (n = 142) of the Caddisflies known in the region and 38% (n = 57) of the known endemic Iberian taxa. This work was conducted within the framework of the InBIO Barcoding Initiative.

General description

Purpose: 

This dataset aims to provide a first contribution to an authoritative DNA barcode sequences library for Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot. Such a library aims to enable DNA-based identification of species for both traditional molecular studies and DNA-metabarcoding studies. Furthermore, it constitutes a relevant resource for taxonomic research on Iberian Trichoptera and its distribution.

Additional information: 

A total of 438 Trichoptera specimens were sequenced (Suppl. material 1). A full-length barcode of 658 bp was obtained for 400 specimens (91.3%) (Table 1, Suppl. material 2). These specimens represent 142 (37%) of the approximately 380 Caddisflies species known to occur in the Iberian Peninsula (González and Martínez 2011, Martínez 2014, Martín 2017). Furthermore, 57 taxa are Iberian endemics, representing 38% of the total endemic Iberian taxa (González and Martínez 2011, Martínez 2014, Martín 2017). The dataset includes 22 of the 23 families known to occur in the Iberian Peninsula (Table 1). These data contribute with 29 new taxa, 26 new species and three new subspecies of Trichoptera to the BOLD database (Table 1). For five additional species, the dataset contributes for the first time a full-length barcode.

Table 1.
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List of species that were collected and DNA barcoded within this project.

Family Taxa IBI code BOLD code BOLD BIN
Apataniidae Apatania theischingerorum Malicky, 1981 INV05962 IBITR421-20 BOLD:ADL7734
Beraeidae Beraea alva Malicky, 1975 INV05488 IBITR348-20 BOLD:AAJ8091
Beraea malatebrera Schmid, 1952 INV04753 IBITR267-20 BOLD:AAO2491
INV04267 IBITR173-20
Brachycentridae Micrasema cenerentola Schmid, 1952 INV05952 IBITR414-20 BOLD:AAO3157
Micrasema longulum McLachlan, 1876 INV06484 IBITR435-20 BOLD:AAK7456
Micrasema minimum McLachlan, 1876 INV05973 IBITR430-20 BOLD:AAH6898
INV05974 IBITR431-20
Micrasema moestum (Hagen, 1868) INV00475 IBITR054-20 BOLD:AAO1660
INV00476 IBITR055-20
INV00477 IBITR056-20
Micrasema servatum (Navás, 1918) INV04731 IBITR252-20 BOLD:AAH3018
INV04732 IBITR253-20
Calamoceratidae Calamoceras marsupus Brauer, 1865 INV02470 IBITR101-20 BOLD:AAO2482
INV05476 IBITR336-20
Ecnomidae Ecnomus deceptor McLachlan, 1884 INV03539 IBITR140-20 BOLD:ABU6618
INV03546 IBITR141-20
INV03605 IBITR146-20
INV05502 IBITR360-20
Glossosomatidae Agapetus delicatulus McLachlan, 1884 INV05812 IBITR388-20 BOLD:AAE6313
INV05813 IBITR389-20
INV05814 IBITR390-20 BOLD:AAE6313
Agapetus fuscipes Curtis, 1834 INV05815 IBITR391-20 BOLD:AAJ7120
INV05816 IBITR392-20
INV02468 IBITR099-20 BOLD:AEC9758
INV05817 IBITR393-20 BOLD:AAJ7120
Agapetus incertulus McLachlan, 1884 INV04759 IBITR273-20 BOLD:AEC9946
Agapetus nimbulus McLachlan, 1879 INV04762 IBITR274-20 BOLD:AEM2297
Agapetus ochripes Curtis, 1834 INV04763 IBITR275-20 BOLD:AAB3823
Agapetus segovicus Schmid, 1952 INV05818 IBITR394-20 BOLD:AEC7102
INV05819 IBITR395-20
INV01163 IBITR075-20 BOLD:AEC7102
INV04819 IBITR317-20
Agapetus theischingeri Malicky, 1980 INV05823 IBITR396-20 BOLD:AEL9298
Catagapetus maclachlani Malicky, 1975 INV05826 IBITR399-20 BOLD:ABA7173
INV02477 IBITR108-20
INV02929 IBITR127-20
INV03936 IBITR169-20
INV05824 IBITR397-20
INV05825 IBITR398-20
Glossosoma privatum McLachlan, 1884 INV05831 IBITR401-20 BOLD:AAM0930
INV00461 IBITR050-20
INV00468 IBITR052-20
INV04688 IBITR219-20
INV04689 IBITR220-20
INV05830 IBITR400-20
Synagapetus diversus (McLachlan, 1884) INV05491 IBITR351-20 BOLD:ABX9025
Synagapetus lusitanicus Malicky, 1980 INV05833 IBITR402-20 BOLD:AAO4326
Goeridae Larcasia partita Navás, 1917 INV00320 IBITR027-20 BOLD:AEC6981
INV00327 IBITR029-20
INV00329 IBITR030-20
INV00341 IBITR034-20
INV00451 IBITR047-20
INV02473 IBITR104-20
INV02474 IBITR105-20
INV04733 IBITR254-20
Silo graellsii Pictet, 1865 INV05951 IBITR413-20 BOLD:AEC7954
Helicopsychidae Helicopsyche lusitanica McLachlan, 1884 INV00005 IBITR012-20 BOLD:AEC8414
INV04823 IBITR321-20 BOLD:AED0915
Helicopsyche sp. INV04824 IBITR322-20 BOLD:AEC8747
INV04825 IBITR323-20
Hydropsychidae Cheumatopsyche lepida (Pictet, 1834) INV04778 IBITR283-20 BOLD:AAD1893
INV04779 IBITR284-20
INV06149 IBITR432-20
INV06590 IBITR436-20
Diplectrona felix McLachlan, 1878 INV04718 IBITR243-20 BOLD:AAO2443
INV04719 IBITR244-20
INV05479 IBITR339-20
INV05957 IBITR418-20
Hydropsyche ambigua Schmid, 1973 INV03635 IBITR151-20 BOLD:AAB5092
INV05480 IBITR340-20 BOLD:AAB9587
INV05960 IBITR420-20
INV04720 IBITR245-20
INV04721 IBITR246-20
INV05493 IBITR353-20
Hydropsyche brevis Mosely, 1930 INV04780 IBITR285-20 BOLD:AEC9027
INV04781 IBITR286-20
Hydropsyche bulbifera McLachlan, 1878 INV04783 IBITR288-20 BOLD:AAO1831
INV00809 IBITR071-20
INV04503 IBITR190-20
INV04782 IBITR287-20
Hydropsyche dinarica Marinkovic-Gospodnetic, 1979 INV05956 IBITR417-20 BOLD:AAE5138
Hydropsyche exocellata Dufour, 1841 INV02678 IBITR111-20 BOLD:AAF0933
INV04785 IBITR289-20
INV00433 IBITR045-20
INV00434 IBITR046-20
INV02920 IBITR121-20
INV02922 IBITR123-20
INV02979 IBITR135-20
Hydropsyche iberomaroccana González & Malicky, 1999 INV04788 IBITR292-20 BOLD:AED0538
Hydropsyche infernalis Schmid, 1952 INV04789 IBITR293-20 BOLD:AAB5092
Hydropsyche instabilis (Curtis, 1834) INV04722 IBITR247-20 BOLD:AAB1966
INV04723 IBITR248-20 BOLD:ABZ1867
INV05959 IBITR419-20 BOLD:AAB1966
Hydropsyche lobata McLachlan, 1884 INV04501 IBITR189-20 BOLD:AEC7586
INV04787 IBITR291-20
INV00561 IBITR069-20
INV02669 IBITR110-20
INV03591 IBITR144-20
INV03592 IBITR145-20
INV04786 IBITR290-20
Hydropsyche pictetorum Botosaneanu & Schmid, 1973 INV00421 IBITR037-20 BOLD:AAO2260
INV02962 IBITR132-20 BOLD:AAB5092
INV04790 IBITR294-20 BOLD:AAO2260
INV05505 IBITR363-20
Hydropsyche siltalai Doehler, 1963 INV04269 IBITR175-20 BOLD:AAB5092
INV00186 IBITR025-20
INV00460 IBITR049-20
INV04724 IBITR249-20 BOLD:AAB9587
INV03680 IBITR160-20 BOLD:AAB5092
INV05481 IBITR341-20
INV05482 IBITR342-20
INV05494 IBITR354-20
Hydropsyche tenuis Navás, 1932 INV00318 IBITR026-20 BOLD:AAB9587
Hydropsyche tibialis McLachlan, 1884 INV04725 IBITR250-20 BOLD:AED0962
INV04726 IBITR251-20
INV06211 IBITR433-20
Hydroptilidae Agraylea sexmaculata Curtis, 1834 INV04524 IBITR192-20 BOLD:AAE7232
INV02924 IBITR124-20
INV02927 IBITR125-20
INV02928 IBITR126-20
INV03549 IBITR142-20
Hydroptila fuentaldeala Schmid, 1952 INV05477 IBITR337-20 BOLD:AEC8395
Ithytrichia clavata Morton, 1905 INV00520 IBITR066-20 BOLD:AEC8346
INV00839 IBITR073-20
Oxyethira frici Klapalek, 1891 INV05503 IBITR361-20 BOLD:ABY2898
Lepidostomatidae Lepidostoma hirtum (Fabricius, 1775) INV00009 IBITR002-16 BOLD:AAB4052
INV00010 IBITR003-16
INV00011 IBITR004-16
INV04579 IBITR202-20
INV04584 IBITR204-20
Leptoceridae Adicella meridionalis Morton, 1906 INV05510 IBITR367-20 BOLD:AEM0162
Adicella reducta (McLachlan, 1865) INV00422 IBITR038-20 BOLD:AAJ1835
INV00426 IBITR041-20
INV00012 IBITR005-16
INV00013 IBITR006-16
INV00014 IBITR007-16
INV00470 IBITR053-20
INV00482 IBITR058-20
INV02475 IBITR106-20
INV04856 IBITR325-20
Athripsodes alentexanus Martín, González & Martínez, 2016 INV06592 IBITR437-20 BOLD:AAI7978
INV06593 IBITR438-20
Athripsodes braueri (Pictet, 1865) INV04268 IBITR174-20
INV05485 IBITR345-20
Athripsodes inaequalis (McLachlan, 1884) INV02463 IBITR094-20 BOLD:AED0841
INV02919 IBITR120-20
INV03273 IBITR137-20
Athripsodes tavaresi (Navás, 1916) INV02764 IBITR116-20 BOLD:AEC8026
INV03612 IBITR147-20
INV04754 IBITR268-20
Ceraclea albimacula (Rambur, 1842) INV00184 IBITR024-20 BOLD:AAN2950
INV02233 IBITR084-20
INV04556 IBITR197-20 BOLD:AAD8966
Ceraclea sobradieli (Navás, 1917) INV02950 IBITR001-16 BOLD:AAD8965
INV02948 IBITR128-20
INV04554 IBITR196-20
INV04510 IBITR191-20
INV05474 IBITR334-20
INV05484 IBITR344-20
Leptocerus tineiformis Curtis, 1834 INV00812 IBITR072-20 BOLD:AAJ1160
INV00846 IBITR074-20
INV04287 IBITR177-20
Mystacides azureus (Linnaeus, 1761) INV02239 IBITR085-20 BOLD:AAB1494
INV03563 IBITR143-20
INV04818 IBITR316-20
Oecetis testacea (Curtis, 1834) INV05473 IBITR333-20 BOLD:AAD7208
Setodes argentipunctellus McLachlan, 1877 INV05352 IBITR327-20 BOLD:ACB2223
INV05353 IBITR328-20
INV00549 IBITR068-20
INV04817 IBITR315-20
Triaenodes ochreellus McLachlan, 1877 INV02467 IBITR098-20 BOLD:AAJ8708
Limnephilidae Allogamus laureatus (Navás, 1918) INV02246 IBITR086-20 BOLD:AEC7060
Allogamus ligonifer (McLachlan, 1876) INV00321 IBITR028-20 BOLD:AAO2353
INV02462 IBITR093-20
INV02466 IBITR097-20
INV04748 IBITR264-20
INV03724 IBITR164-20
INV03727 IBITR167-20
Allogamus mortoni (Navás, 1907) INV04793 IBITR297-20 BOLD:AAM3837
INV04794 IBITR298-20
INV04795 IBITR299-20
Annitella esparraguera (Schmid, 1952) INV05963 IBITR422-20 BOLD:AAM4103
Chaetopteryx atlantica Malicky, 1975 INV05965 IBITR424-20 BOLD:AEC7901
Drusus berthelemyi Sipahiler, 1992 INV05964 IBITR423-20 BOLD:ACO5446
Drusus bolivari (McLachlan, 1880) INV04791 IBITR295-20 BOLD:ACO5618
INV04792 IBITR296-20
Enoicyla pusilla (Burmeister, 1839) INV04796 IBITR300-20 BOLD:AAO2902
Grammotaulius submaculatus (Rambur, 1842) INV02799 IBITR117-20 BOLD:AEC8384
INV04740 IBITR257-20
Halesus radiatus (Curtis, 1834) INV01836 IBITR083-20 BOLD:AAF7718
INV02469 IBITR100-20
INV04743 IBITR260-20
INV03722 IBITR162-20
Limnephilus bipunctatus Curtis, 1834 INV02609 IBITR109-20 BOLD:AAA4844
Limnephilus guadarramicus Schmid, 1955 INV03661 IBITR156-20 BOLD:AEC8200
INV03664 IBITR159-20
INV03946 IBITR170-20
Limnephilus hirsutus (Pictet, 1834) INV03655 IBITR155-20 BOLD:AAE6322
INV03685 IBITR161-20
INV01281 IBITR078-20
Limnephilus sparsus Curtis, 1834 INV04258 IBITR171-20 BOLD:AAB6375
INV01284 IBITR079-20
INV03651 IBITR153-20
INV03653 IBITR154-20
INV04738 IBITR255-20
Limnephilus vittatus (Fabricius, 1798) INV02256 IBITR089-20 BOLD:AAK8602
INV04739 IBITR256-20
INV05478 IBITR338-20
Mesophylax aspersus (Rambur, 1842) INV04573 IBITR199-20 BOLD:AAG5761
INV04662 IBITR207-20
INV04672 IBITR208-20
INV04530 IBITR193-20
Potamophylax cingulatus (Stephens, 1837) INV01300 IBITR081-20 BOLD:AAC4985
INV04746 IBITR263-20
INV03662 IBITR157-20
INV05388 IBITR329-20
INV01299 IBITR080-20 BOLD:ABU7930
INV02247 IBITR087-20
INV02253 IBITR088-20
Potamophylax latipennis (Curtis, 1834) INV02257 IBITR090-20
INV02472 IBITR103-20
INV02800 IBITR118-20
INV04741 IBITR258-20
Stenophylax fissus (McLachlan, 1875) INV03616 IBITR148-20 BOLD:AEC6836
Stenophylax mucronatus McLachlan, 1880 INV03624 IBITR149-20
INV03642 IBITR152-20
INV04742 IBITR259-20
INV04744 IBITR261-20 BOLD:ABY2452
INV02900 IBITR119-20 BOLD:AED0879
Stenophylax permistus McLachlan, 1895 INV02951 IBITR130-20
Stenophylax sequax (McLachlan, 1875) INV02964 IBITR133-20
INV04655 IBITR205-20
INV04656 IBITR206-20
INV04745 IBITR262-20 BOLD:AAI0072
Stenophylax vibex (Curtis, 1834) INV02957 IBITR131-20 BOLD:AAE8973
Odontoceridae Odontocerum albicorne (Scopoli, 1763) INV00020 IBITR013-20 BOLD:AAB5626
INV00021 IBITR008-16
INV05968 IBITR426-20
INV05970 IBITR427-20
INV05971 IBITR428-20
INV05972 IBITR429-20
Odontocerum lusitanicum Malicky, 1975 INV05508 IBITR365-20 BOLD:AEC9755
INV05501 IBITR359-20
Philopotamidae Chimarra marginata (Linnaeus, 1767) INV02459 IBITR091-20 BOLD:AAO1593
INV00417 IBITR035-20
INV00419 IBITR036-20
INV00424 IBITR039-20
INV00425 IBITR040-20
INV00431 IBITR043-20
INV00432 IBITR044-20
INV00486 IBITR060-20
INV00506 IBITR064-20
INV02461 IBITR092-20
INV03259 IBITR136-20
INV05457 IBITR331-20
Philopotamus amphilectus McLachlan, 1884 INV04696 IBITR225-20 BOLD:AED0394
Philopotamus montanus caurelensis González & Terra, 1979 INV02471 IBITR102-20 BOLD:AAO1570
INV00334 IBITR032-20
INV00336 IBITR033-20
INV02465 IBITR096-20
INV02476 IBITR107-20
INV04694 IBITR223-20 BOLD:AEC7824
INV04695 IBITR224-20
Philopotamus perversus McLachlan, 1884 INV00022 IBITR014-20 BOLD:AAO1569
INV00023 IBITR015-20
INV00024 IBITR016-20
INV00025 IBITR017-20
INV05487 IBITR347-20
INV05835 IBITR403-20
Philopotamus variegatus (Scopoli, 1763) INV00458 IBITR048-20 BOLD:AEC7364
INV00465 IBITR051-20
Wormaldia beaumonti Schmid, 1952 INV01598 IBITR082-20 BOLD:AAO2217
INV03725 IBITR165-20 BOLD:AAO2216
Wormaldia corvina (McLachlan, 1884) INV04698 IBITR226-20 BOLD:ABU5927
INV04699 IBITR227-20
INV05840 IBITR408-20
INV05841 IBITR409-20
Wormaldia lusitanica González & Botosaneanu, 1983 INV05836 IBITR404-20 BOLD:AAO2217
Wormaldia occipitalis (Pictet, 1834) INV05838 IBITR406-20 BOLD:AED0699
INV05837 IBITR405-20
INV05839 IBITR407-20
Wormaldia triangulifera McLachlan, 1878 INV04765 IBITR276-20 BOLD:AAH9306
Wormaldia variegata mattheyi Schmid, 1952 INV04703 IBITR229-20 BOLD:AED0151
INV04702 IBITR228-20
INV03723 IBITR163-20
INV03726 IBITR166-20
Phryganeidae Agrypnia varia (Fabricius, 1793) INV03663 IBITR158-20 BOLD:AAE4334
INV05340 IBITR326-20
Polycentropodidae Cyrnus cintranus McLachlan, 1884 INV05500 IBITR358-20
Plectrocnemia geniculata McLachlan, 1871 INV05953 IBITR415-20
Plectrocnemia laetabilis McLachlan, 1880 INV04295 IBITR184-20 BOLD:AAL4393
INV02464 IBITR095-20
INV04704 IBITR230-20
INV04705 IBITR231-20
INV05389 IBITR330-20
Polycentropus corniger McLachlan, 1884 INV04773 IBITR278-20 BOLD:AAL0051
INV04772 IBITR277-20
INV05475 IBITR335-20
INV05483 IBITR343-20
Polycentropus flavomaculatus (Pictet, 1834) INV00503 IBITR062-20 BOLD:AAC0971
INV00504 IBITR063-20 BOLD:ACR2507
Polycentropus intricatus Morton, 1910 INV04706 IBITR232-20 BOLD:AAL0054
INV04707 IBITR233-20
INV05489 IBITR349-20
Polycentropus kingi McLachlan, 1881 INV04709 IBITR235-20 BOLD:AAL0060
INV05498 IBITR357-20
INV00478 IBITR057-20
INV04708 IBITR234-20
Polycentropus telifer McLachlan, 1884 INV04417 IBITR185-20 BOLD:AAM0001
Psychomyiidae Lype auripilis McLachlan, 1884 INV04713 IBITR238-20 BOLD:AAO2229
Lype phaeopa (Stephens, 1836) INV00485 IBITR059-20 BOLD:AAC4581
Paduniella vandeli Decamps, 1965 INV04774 IBITR279-20 BOLD:AAK7667
Psychomyia fragilis (Pictet, 1834) INV04775 IBITR280-20
INV02695 IBITR112-20 BOLD:AEC7914
Psychomyia pusilla (Fabricius, 1781) INV04710 IBITR236-20 BOLD:AAO1607
INV00427 IBITR042-20 BOLD:AEC8086
INV00806 IBITR070-20
INV02749 IBITR115-20 BOLD:AAO1607
INV04711 IBITR237-20
INV05490 IBITR350-20
INV05495 IBITR355-20 BOLD:AEC8086
Tinodes assimilis McLachlan, 1865 INV00521 IBITR067-20 BOLD:AAF7459
INV01260 IBITR076-20
INV02921 IBITR122-20
INV04716 IBITR241-20
INV04717 IBITR242-20
Tinodes foedellus McLachlan, 1884 INV04714 IBITR239-20 BOLD:AAL9978
INV04715 IBITR240-20
Tinodes maculicornis (Pictet, 1834) INV05954 IBITR416-20 BOLD:AAF7446
Tinodes waeneri (Linnaeus, 1758) INV04777 IBITR282-20 BOLD:AAB9068
INV00491 IBITR061-20
INV01280 IBITR077-20
INV04576 IBITR200-20
INV04581 IBITR203-20
INV04423 IBITR187-20
INV04500 IBITR188-20
INV04776 IBITR281-20
Ptilocolepidae Ptilocolepus extensus McLachlan, 1884 INV04266 IBITR172-20
INV04690 IBITR221-20 BOLD:AAL2306
INV04691 IBITR222-20
Ptilocolepus granulatus (Pictet, 1834) INV05967 IBITR425-20
Rhyacophilidae Rhyacophila adjuncta McLachlan, 1884 INV00035 IBITR018-20 BOLD:AAD5575
INV00330 IBITR031-20
INV04677 IBITR209-20
INV04678 IBITR210-20
Rhyacophila dorsalis (Curtis, 1834) INV04811 IBITR314-20 BOLD:AAC4103
INV05793 IBITR371-20
INV05794 IBITR372-20
INV05795 IBITR373-20
Rhyacophila dorsalis albarracina Malicky, 2002 INV05790 IBITR368-20
INV05791 IBITR369-20
Rhyacophila evoluta McLachlan, 1879 INV04807 IBITR310-20 BOLD:AAX8713
Rhyacophila intermedia McLachlan, 1868 INV04680 IBITR211-20
INV05507 IBITR364-20
INV04810 IBITR313-20 BOLD:AAF7929
Rhyacophila laevis Pictet, 1834 INV04809 IBITR312-20 BOLD:AAF8011
Rhyacophila laufferi Navás, 1918 INV05800 IBITR378-20
Rhyacophila lusitanica McLachlan, 1884 INV02967 IBITR134-20 BOLD:AEC8059
INV00039 IBITR019-20
INV03379 IBITR138-20
INV03633 IBITR150-20
INV05504 IBITR362-20
Rhyacophila martynovi Mosely, 1930 INV05799 IBITR377-20
INV04808 IBITR311-20 BOLD:AEC7148
Rhyacophila melpomene Malicky, 1976 INV04681 IBITR212-20 BOLD:AEM0544
INV04682 IBITR213-20
Rhyacophila meridionalis Pictet, 1865 INV04683 IBITR214-20 BOLD:AEC9268
INV04684 IBITR215-20
Rhyacophila mocsaryi tredosensis Schmid, 1952 INV05796 IBITR374-20 BOLD:AEC7310
Rhyacophila munda McLachlan, 1862 INV05803 IBITR379-20 BOLD:AAM4449
INV05804 IBITR380-20
INV05805 IBITR381-20
INV02949 IBITR129-20 BOLD:AEC7678
INV03535 IBITR139-20
INV04572 IBITR198-20 BOLD:AAM4448
INV04577 IBITR201-20 BOLD:AEC7678
INV03900 IBITR168-20
INV04420 IBITR186-20
Rhyacophila nevada Schmid, 1952 INV05792 IBITR370-20
Rhyacophila obelix Malicky, 1979 INV00044 IBITR020-20 BOLD:AEC8711
INV00045 IBITR021-20 BOLD:AEC8521
INV05947 IBITR410-20 BOLD:AEC8711
INV05949 IBITR411-20
Rhyacophila obliterata McLachlan, 1863 INV05797 IBITR375-20
INV05798 IBITR376-20
Rhyacophila occidentalis McLachlan, 1879 INV04685 IBITR216-20 BOLD:AAJ3548
INV04686 IBITR217-20
Rhyacophila pascoei McLachlan, 1879 INV04755 IBITR269-20 BOLD:AEC7530
Rhyacophila pulchra Schmid, 1952 INV04687 IBITR218-20 BOLD:AEC8544
Rhyacophila relicta McLachlan, 1879 INV05806 IBITR382-20 BOLD:AAI0887
INV04532 IBITR195-20
INV04531 IBITR194-20
INV05807 IBITR383-20
INV06215 IBITR434-20
Rhyacophila sociata Navás 1916 INV05808 IBITR384-20 BOLD:AAD5575
INV05809 IBITR385-20
Rhyacophila terpsichore Malicky, 1976 INV04756 IBITR270-20 BOLD:AEC8427
Rhyacophila terrai González & Martínez, 2010 INV04757 IBITR271-20 BOLD:AEM3903
INV04758 IBITR272-20
Rhyacophila tristis Pictet, 1834 INV05810 IBITR386-20 BOLD:ABA2486
INV05811 IBITR387-20
Sericostomatidae Schizopelex festiva (Rambur, 1842) INV00053 IBITR022-20 BOLD:AAI0810
INV00054 IBITR023-20
INV00513 IBITR065-20
Sericostoma pyrenaicum Pictet, 1865 INV02747 IBITR113-20 BOLD:AAJ7690
INV02748 IBITR114-20
INV04292 IBITR182-20
INV04749 IBITR265-20
INV04803 IBITR306-20
INV05509 IBITR366-20 BOLD:AEC8551
INV04288 IBITR178-20
INV04289 IBITR179-20 BOLD:AAJ7690
INV04290 IBITR180-20 BOLD:AEC8551
INV04291 IBITR181-20
INV04293 IBITR183-20 BOLD:ABZ0751
INV04804 IBITR307-20 BOLD:AAJ7690
INV04805 IBITR308-20
INV04806 IBITR309-20
INV05472 IBITR332-20 BOLD:AEC8551
Sericostoma vittatum Rambur, 1842 INV04270 IBITR176-20 BOLD:ABZ0751
INV04797 IBITR301-20 BOLD:AAM4952
INV04822 IBITR320-20 BOLD:AAJ7690
INV05486 IBITR346-20 BOLD:ABZ0751
INV05492 IBITR352-20 BOLD:AAJ7690
INV04752 IBITR266-20
INV04798 IBITR302-20 BOLD:AAM4952
INV04799 IBITR303-20
INV04800 IBITR304-20 BOLD:AEC9666
INV04801 IBITR305-20 BOLD:AAJ7690
INV04820 IBITR318-20
INV04821 IBITR319-20
Thremmatidae Thremma gallicum McLachlan, 1880 INV05950 IBITR412-20 BOLD:AAF7946
INV00056 IBITR009-16
INV00057 IBITR010-16
INV00058 IBITR011-16
Thremma tellae González, 1978 INV04833 IBITR324-20 BOLD:AAL9956
INV05497 IBITR356-20

Average nucleotide composition of the Trichoptera sequences is 37.7% thymine (T), 17.9% cytosine (C), 30.5% adenine (A) and 13.9% guanine (G), for a total GC content of 31.8% for the COI barcode fragment analysed. Genetic p-distances ranged from 0.00% between Athripsodes alentexanus Martín, González and Martínez, 2016 (n = 2) and A. braueri (Pictet, 1865) to 33.97% between Ptilocolepus granulatus (Pictet, 1834) (n = 1) and Potamophylax latipennis (Curtis, 1834) (n = 4) (Suppl. material 3). Intraspecifc genetic p-distances ranged from 0.00% in 12 species, including several species of Athripsodes, Hydropsyche and Rhyacophila (average n = 3.16 specimens per species), to 6.16% in Hydropsyche pictetorum Botosaneanu and Schmid, 1973 (n = 4), 6.22% in Psychomyia pusilla (Fabricius, 1781) (n = 7), 6.65% in Rhyacophila munda McLachlan, 1862 (n = 9) and 7.45% in Helicopsyche lusitanica McLachlan, 1884 (n = 2). Forty-seven species were represented by a single specimen in the dataset and, for this reason, no intraspecifc distance is calculated.

The BOLD BIN system uses algorithms to cluster sequences into operational taxonomic units (OTUs) that closely correspond to species (Ratnasingham and Hebert 2013). A total of 146 BINs were retrieved by BOLD (Ratnasingham and Hebert 2007). Seven specimens have not been BIN attributed as their sequence is only 418 bp and no other specimens have been sequenced (Suppl. material 1). Two specimens, identified to the genus level only as Helicopsyche sp., clustered together in a separate BIN, “BOLD:AEC8747”. Of the 146 BINs, 45 BINs are unique to our dataset (Table 1, Suppl. material 1). Using the criteria followed by Ratnasingham and Hebert (2013), there were 83.6% of matches, 3.7% of merges, 6.7% of splits and 6.0% of mixtures when comparing BINs to the morphological identifications (Fig. 1). The BINs generated by BOLD clustered together sequences that closely agree with the morphological identifications of the specimens, with only a few exceptions in nine of the 22 Trichoptera families analysed.

Figure 1.  

Comparison in OTU assignment performance between BOLD’s BIN and RESL stand-alone algorithms. The BIN dataset comprised 135 taxa (134 species) and the RESL stand-alone run comprised the entire 142 taxa (141 species) dataset. The four categories: MATCH, MERGE, SPLIT and MIXTURE into which the OTUs were divided, follow the criteria used by Ratnasingham and Hebert (2013).

The independent RESL run (Ratnasingham and Hebert 2013, Ratnasingham and Hebert 2007) retrieved 153 OTUs, plus one OTU for the Helicopsyche sp. specimens (Suppl. material 4). The differences found between the RESL OTUs and the morphological identifications were similar to those found between the latter and BOLD’s BINs, with 81.7% of matches, 4.2% of merges, 7.7% of splits and 6.3% of mixtures when comparing OTUs to the morphological identifications (Fig. 1).

Nevertheless, some differences existed between the RESL OTU clustering and the BINs created by BOLD (Suppl. materials 1, 4). In the family Hydropsychidae, sequences identified as Hydropsyche instabilis (Curtis, 1834) clustered into a single OTU, but were split into two BINs. In the family Leptoceridae, sequences of specimens identified as Athripsodes alentexanus and A. braueri clustered in a single BIN. In the family Philopotamidae, sequences identified as Philopotamus perversus McLachlan, 1884 clustered into two OTUs, but were represented by a single BIN. In the family Polycentropodidae, sequences identified as Polycentropus flavomaculatus clustered into a single OTU, but were split into two BINs. In the family Rhyacophilidae, sequences identified as R. dorsalis (Curtis, 1834) and its subspecies, R. d. albarracina Malicky, 2002 clustered into a single OTU, but other sequences identified as R. dorsalis clustered into a different OTU. All R. dorsalis sequences share a single BIN, but the subspecies’ sequences have not been BIN attributed as their sequences are only 418 bp. Sequences identified as R. intermedia McLachlan, 1868 clustered into three OTUs, but were represented by a single BIN. Additionally, sequences identified as R. martynovi Mosely, 1930 clustered into two OTUs, but were represented by a single BIN. Furthermore, sequences identified as Rhyacophila munda clustered into two OTUs, but were split into three BINs. In the family Sericostomatidae, there was no separation of the species Sericostoma pyrenaicum and S. vittatum. These species clustered together into two different BINs, but sequences of S. pyrenaicum and S. vittatum also clustered in additional BINs (Suppl. materials 1, 4).

This work provided new DNA barcode sequences and distributional data for 436 specimens of Iberian Trichoptera, plus two French specimens. The dataset represents 37% of the Caddisflies known to occur in Iberia and the work added 29 taxa previously not represented in the BOLD database. To our knowledge, this is the first study to focus on DNA barcoding of the Trichoptera order for the Iberian Peninsula.

This study showed that DNA barcode sequences, based on the COI mitochondrial gene fragment, can be useful in identifying Iberian Trichoptera samples to species level. We achieved more than 80% success in matching the sequences generated to the morphological identification of the specimens. This is similar to the success rate achieved in 2017 (Morinière et al. 2017) for German Caddisflies (79.8%). A DNA barcode library is an essential tool for incorporating Environmental DNA techniques in monitoring schemes of aquatic ecosystems that use Iberian Caddisflies (Lefrançois et al. 2020). Our results constitute a first step in the construction of a DNA barcode database of a curated reference collection of Iberian Trichoptera species, which could be used to overcome the difficulties in identifying many of the Trichoptera larval specimens of traditional biological freshwater monitoring studies.

Incongruences were found in nine families. In six of them, Glossosomatidae, Helicopsychidae, Polycentropodidae, Limnephilidae, Rhyacophilidae and Psychomyiidae, the barcode analysis identified no species boundaries, with high levels of intraspecific genetic diversity (Suppl. material 3). It is possible that such levels of genetic diversity point to undescribed, distinct species. This hypothesis requires further morphological studies to search for diagnostic morphological traits that might separate these species.

In the family Hydropsychidae, nine species of the genus Hydropsyche could be identified through their barcodes and their genetic distances ranged between 13.4% and 23%. However, five other species could not be identified through DNA barcodes. These species, H. ambigua, H. infernalis, H. pictetorum, H. siltalai and H. tenuis were spliced between different BINs and OTUs, shared by some, but not all of the same species, further complicating their relationships. For the species with enough sequenced specimens, all were found to have moderate to high levels of intraspecific genetic diversity (Suppl. material 3). These species are difficult to identify morphologically and this study emphasises the need for further work towards a better understanding of the taxonomy of the genus in the Iberian Peninsula (Zamora-Muñoz et al. 2017).

In the family Leptoceridae, sequences identified as Athripsodes alentexanus and A. braueri clustered in a single BIN. All four sequences were identical. As such, DNA barcodes, based on COI, might not differentiate between these two species. This can be the result of an introgression event, if they had split very recently or alternatively, if their taxonomic identity needs revision.

In the family Philopotamidae, two Wormaldia beaumonti and one W. lusitanica sequences were in the dataset. Two BINs are present in BOLD with both species represented in each (from previous data, but also with the new data). This genus is very difficult to identify morphologically and is likely that the morphological characters used are not able to separate both taxa.

In the family Sericostomatidae, there were problems separating two species of the genus Sericostoma, S. pyrenaicum and S. vittatum. These species clustered together into two different BINs, but sequences of S. pyrenaicum and S. vittatum also clustered in additional BINs. Intraspecific genetic diversity is relatively high in both species (2.49% and 2.89%, respectively). González et al. (1992) and Martínez (2014) already pointed out that, under these two names, a complex of species is actually hidden, some of them quite variable morphologically. A detailed morphological-molecular study may help to solve one of the most difficult taxonomic problems of our fauna. These findings suggest that both species need a taxonomic revision.

Our results did not corroborate the findings of Valladolid et al. (2018) and suggest further work is necessary regarding the identity of Rhyacophila adjuncta and R. sociata. These authors restored the species R. sociata, previously considered a junior synonym of R. denticulata McLachlan, 1879. However, both BOLD clustering algorithms merged our samples, identified as R. adjuncta (2 specimens) and R. sociata (2 specimens), into a single BIN “BOLD:AAD5575”. Furthermore, this BIN includes all publicly available sequences in BOLD identified as R. adjuncta and R. sociata, including all sequences generated by Valladolid et al. (2018). In their paper, the authors did not investigate a possible relationship between these two species, nor was that relationship assessed in a subsequent study on the European species of the R. fasciata group (Valladolid et al. 2021). Finally, the BIN mentioned above also includes other sequences identified as R. tristis Pictet, 1834. and R. fasciata Hagen, 1859, although these are probably misidentifications.

We also identified several cases that require further study by taxonomists. Other possibilities for the incongruence found amongst the results include the existence of hybridisation, introgression or incomplete lineage sorting in these species, especially if they result from recent speciation events (e.g. Behrens-Chapuis et al. (2021), Morinière et al. (2017), Zhou et al. (2016)). These hypotheses require the combination of nuclear and mitochondrial markers to be resolved, preferably in an integrative taxonomic approach.

Project description

Title: 

The InBIO Barcoding Initiative Database: DNA Barcodes of Iberian Trichoptera 01

Personnel: 

Luis Martín (taxonomist), Jesús Martínez (taxonomist), Marcos A. González (taxonomist), affiliated to Universidad de Santiago de Compostela; Pedro Beja (project coordinator), Joana Paupério (IBI manager), Sónia Ferreira (taxonomist and IBI manager), Filipa M.S. Martins (molecular biologist), Joana Veríssimo (molecular biologist), Pamela Puppo (molecular biologist), Joana C. Pinto (project technician), Cátia Chaves (project technician), Catarina J. Pinho (project technician), Pedro Sousa (project technician), Lorenzo Quaglietta (ecologist), Teresa Silva (molecular biologist), Paulo Célio Alves,(molecular biologist), Nuno Fonseca (bioinformatician), all affiliated to CIBIO-InBIO, University of Porto and José Manuel Grosso-Silva (taxonomist), affiliated to the MHNC-UP, University of Porto.

Study area description: 

Iberian Peninsula (Fig. 2).

Figure 2.  

Sampling localities of the Trichoptera specimens analysed in this study. Nine localities could not be mapped because geographic coordinates were not available.

Design description: 

Specimens were collected during field expeditions in the Iberian Peninsula, from 1975 to 2018 (n = 434 Fig. 2, Suppl. material 1), with more than 60% of specimens collected in the period between 2015 and 2017 (274 out of 434). Two additional specimens were collected in the French Pyrenees. Specimens kept at the InBIO Barcoding Initiative (IBI) reference collection (Vairão, Portugal), 230 in total, were stored in 96% ethanol. Specimens kept at the Colección Marcos A. González (Universidad de Santiago de Compostela, Spain), 206 in total, were stored in either 70% or 96% ethanol.

For each species, we selected, on average, three specimens for DNA sequencing, based on their location of capture, attempting to maximise the geographical coverage of the study.

DNA was extracted using two different kits: EasySpin Genomic DNA Microplate Tissue Kit (Citomed, Odivelas, Portugal) or QIAmp DNA Micro Kit (Qiagen, Hilden, Germany). QIAmp DNA Micro Kit is designed to extract higher concentrations of genetic material from samples with small amounts of DNA.

DNA amplification was performed using three different primer pairs, that amplify three overlapping fragments of the same 658 bp region of the COI mitochondrial gene. In the beginning of the project (2015), we used two primer pairs, 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) (henceforth referred to as LC and BH, respectively) to amplify two overlapping fragments of 325 bp and 418 bp, respectively. After the publication of the third primer pair, BF2 + BR2 (422 bp fragment), by (Elbrecht and Leese 2017), this started to be used instead of the second primer pair (Ill_B_F + HCO2198) due to higher amplification efficiency. PCRs were performed in 10 µl reactions, containing 5 µl of Multiplex PCR Master Mix (Qiagen, Germany), 0.3 (BF2-BR2) – 0.4 mM of each primer, and 1-2 µl of DNA, with the remaining volume in water. The thermocycling for PCR reactions was performed in T100 Thermal Cycler (Bio-Rad, California, USA) and carried out with an initial denaturation at 95ºC for 15 min, followed by 5 cycles at 95ºC for 30 sec, 47ºC for 45 sec, 72ºC for 45 sec (only for LC and BH); then 40 cycles at 95ºC for 30 sec, 51ºC for 45 sec (48ºC for 60 sec for BF2 + BR2), 72ºC for 45 sec; and a final elongation step at 60ºC for 10 min.

All PCR products were analysed by agarose gel electrophoresis and samples selected for sequencing were then organised for assignment of sequencing ‘indexes’. One of two types of index was used for each run. For Illumina indexes, samples were pooled into one plate, as described in Shokralla et al. (2015). When using custom indexes, designed, based on Meyer and Kircher (2010), no pooling was required. The latter allow for a maximum of 1920 unique index combinations. A second PCR was then performed where the ‘indexes’ and Illumina sequencing adapters were attached to the PCR product. The index PCR was performed in a volume of 10 µl, including 5 µl of Phusion® High-Fidelity PCR Kit (New England Biolabs, U.S.A.) or KAPA HiFi PCR Kit (KAPA Biosystems, U.S.A.), 0.5 µl of each ‘index’ and 2 µl of diluted PCR product (usually 1:4). This PCR reaction runs for 10 cycles at an annealing temperature of 55ºC. The amplicons were purified using AMPure XP beads (Beckman Coulter Genomics, Massachusetts, United States) before quantification using NanoDrop 1000 (Thermo Fisher Scientific, Massachusetts, USA). Concentrations between samples were then normalised and samples were pooled, based on used primer sets. Quantification of final pools was assessed through qPCR using the KAPA Library Quantification Kit Illumina® Platforms (Kapa Biosystems) and the 2200 Tapestation System (Agilent Technologies, California, USA) was used for fragment length analysis as described by Paupério et al. (2018).

Sequencing was conducted in an Illumina MiSeq benchtop system, using a V2 MiSeq sequencing kit (2x 250 bp) to perform sequencing at CIBIO facilities.

Sequences were filtered and processed with OBITools (Boyer et al. 2015) and the fragments were assembled into their consensus 658 bp-long sequences using Geneious 6.1.8 (https://www.geneious.com). The obtained DNA sequences were then compared against the Barcode of Life Data Systems (BOLD) database (Ratnasingham and Hebert 2007) using the built-in identification engine, based on the BLAST algorithm. Sequences were submitted to the BOLD database and the Barcode Index Numbers (BIN) for every sequence were retrieved and analysed (Suppl. materials 1, 2). As not all our sequences matched the criteria used in BOLD (sequence length) to be clustered in a BIN, we ran the Refined Single Linkage algorithm (RESL, Ratnasingham and Hebert (2013)) on our dataset in the BOLD system (Ratnasingham and Hebert 2007) in an independent run (Suppl. material 4). This process clusters sequences independent of their BIN registry, generating OTUs that can be analysed independently.

All DNA barcode sequences were aligned in Geneious 6.1.8 with MUSCLE (Edgar 2004) plug-in. Nucleotide composition of all sequences, as well as intra and interspecific p-distances,were calculated in MEGA11 (Tamura et al. 2021).

Funding: 

InBIO Barcoding Initiative 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). The fieldwork benefited from EDP Biodiversity Chair, including research conducted at the Long Term Research Site of Baixo Sabor (LTER_EU_PT_002), the project “Promoção dos serviços de ecossistemas no Parque Natural Regional do Vale do Tua: Controlo de Pragas Agrícolas e Florestais por Morcegos” funded by the Agência de Desenvolvimento Regional do Vale do Tua. SF was supported by individual research contract (2020.03526.CEECIND) and CJP, JV and FMSM by a PhD grant (SFRH/BD/145851/2019; SFRH/BD/133159/2017; SFRH/BD/104703/2014) funded by FCT.

Sampling methods

Description: 

Iberian Peninsula.

Sampling description: 

Specimens were captured during direct searches of the environment, using mainly hand-held sweep-nets or lured by light trapping, the latter with UV (black-light) LEDs. Morphological identification was done, based on Malicky (2004) using a stereoscopic microscope for the study of genitalia. In some cases, genitalia were cleared in 10% potassium hydroxide (KOH) at room temperature for 4–8 hours, rinsed in water and placed in a drop of glycerine or resin (DMHF) on a clean slide for further study. From each specimen, one tissue sample (a leg) was removed and stored in 96% ethanol for DNA extraction at the IBI collection.

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: 

Specimens were collected in 66 different localities in Portugal and 74 localities in Spain. Collections were carried out between 1975 and 2018. Specimens were collected during fieldwork by direct search of specimens, by sweeping the vegetation with a hand-net and by using light traps and were preserved in 96% alcohol. Captured specimens were deposited in the IBI reference collection at CIBIO (Research Center in Biodiversity and Genetic Resources) or in the collection Marcos A. González at the University of Santiago de Compostela (Spain). Specimens were morphologically identified with the assistance of stereoscopic microscopes (Leica MZ12, 8x to 100x; Olympus SZX16, 7x to 115x). 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. 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. Prior to submission to GBIF, data were checked for errors and inconsistencies with OpenRefine 3.3 (http://openrefine.org/).

Geographic coverage

Description: 

Specimens were collected in the Iberian Peninsula, 229 from 66 localities in Portugal and 207 from 74 localities in Spain (Fig. 2, Suppl. material 5 for further details). Two additional specimens were collected in two French localities. The Rhyacophila laevis Pictet, 1834 specimen represented in the dataset was collected in the French Pyrenees.

Coordinates: 

-8.94 and -0.22 Latitude; 42.89 and 37.50 Longitude.

Taxonomic coverage

Description: 

This dataset is composed of data relating to 438 Trichoptera specimens. All specimens were determined to species level, with 14 specimens further identifed to subspecies level. Overall, 141 species are represented in the dataset. These species belong to 22 families.

Taxa included:
Rank Scientific Name Common Name
kingdom Animalia Animals
subkingdom Eumetazoa
phylum Arthropoda
class Insecta
family Apataniidae
family Beraeidae
family Brachycentridae
family Calamoceratidae
family Ecnomidae
family Glossosomatidae
family Goeridae
family Helicopsychidae
family Hydropsychidae
family Hydroptilidae
family Lepidostomatidae
family Leptoceridae
family Limnephilidae
family Odontoceridae
family Philopotamidae
family Phryganeidae
family Polycentropodidae
family Psychomyiidae
family Ptilocolepidae
family Rhyacophilidae
family Sericostomatidae
family Uenoidae

Temporal coverage

Data range: 
1975-5-03 - 2018-5-16.

Collection data

Collection name: 
InBIO Barcoding Initiative
Collection identifier: 
4ec2b246-f5fa-4b90-9a8d-ddafc2a3f970
Specimen preservation method: 
“Alcohol”
Curatorial unit: 
DNA extractions - 1 to 438

Usage licence

Usage licence: 
Creative Commons Public Domain Waiver (CC-Zero)

Data resources

Data package title: 
The InBIO Barcoding Initiative Database: DNA Barcodes of Iberian Trichoptera
Resource link: 
http://dx.doi.org/10.5883/DS-IBITR01
Number of data sets: 
1
Data set name: 
DS-IBITR01 IBI-Trichoptera 01
Download URL: 
http://www.boldsystems.org/index.php/Public_SearchTerms?query=DS-IBITR01
Data format: 
dwc, xml, tsv, fasta
Description: 

The InBIO Barcoding Initiative Database: DNA Barcodes of Iberian Trichoptera dataset can be downloaded from the PublicData Portal of BOLD (http://www.boldsystems.org/index.php/Public_SearchTerms?query=DS-IBITR01) 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 research function of the database. The InBIO Barcoding Initiative will continue sequencing Iberian Trichoptera 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 in the form of one text file for record information as downloaded from BOLD, one text file with the collection and identification data in Darwin Core Standard format (downloaded from GBIF, Martín et al. (2022)) 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_trichoptera_01& v = 1.1 (Suppl. material 5). All data are available in the BioStudies database (http://www.ebi.ac.uk/biostudies) under accession number S-BSST920.

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

The InBIO Barcoding Initiative was 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). The fieldwork benefited from EDP Biodiversity Chair, the project “Promoção dos serviços de ecossistemas no Parque Natural Regional do Vale do Tua: Controlo de Pragas Agrícolas e Florestais por Morcegos” funded by the Agência de Desenvolvimento Regional do Vale do Tua and includes research conducted at the Long Term Research Site of Baixo Sabor (LTER_EU_PT_002). SF was supported by an individual research contract (2020.03526.CEECIND) and CJP, JV and FMSM by a PhD grant (SFRH/BD/145851/2019; SFRH/BD/133159/2017; SFRH/BD/104703/2014) funded by FCT. Work co-funded by the project NORTE-01-0246-FEDER-000063, supported by Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).

References

Supplementary materials

Suppl. material 1: IBI-Trichoptera 01 library - Specimen details 
Authors:  Joana Paupério, Luis Martín, Sónia Ferreira, Jesús Martínez, Marcus A. González, Martin Corley, José Manuel Grosso-Silva, Lorenzo Quaglietta, Pedro Sousa, Pedro Beja
Data type:  Record information - specimen data
Brief description: 

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

Download file (180.30 kb)
Suppl. material 2: IBI-Trichoptera 01 library - DNA sequences 
Authors:  Joana Paupério, Luis Martín, Sónia Ferreira, Jesús Martínez, Marcus A. González, Filipa M.S. Martins, Joana Veríssimo, Pamela Puppo, Joana C. Pinto, Cátia Chaves, Catarina Pinho, 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.

Download file (298.19 kb)
Suppl. material 3: Genetic Distances 
Authors:  Joana Paupério, Luis Martín, Sónia Ferreira, Jesús Martínez, Marcus A. González, Filipa M.S. Martins, Joana Veríssimo, Pamela Puppo, Joana C. Pinto, Cátia Chaves, Catarina Pinho, José Manuel Grosso-Silva, Lorenzo Quaglietta, Pedro Sousa, Paulo Célio Alves, Nuno Fonseca, Pedro Beja
Data type:  Genetic distances between analysed specimens
Brief description: 

Brief description: Estimates of average genetic divergence (uncorrected p- distances) for species of Trichoptera. Values under the diagonal refer to interspecifc divergence, while values in the diagonal represent intraspecifc divergence.

Download file (127.58 kb)
Suppl. material 4: OTUs generated by the Refined Single Linkage algorithm (RESL,) 
Authors:  Joana Paupério, Luis Martín, Sónia Ferreira, Jesús Martínez, Marcus A. González, Filipa M.S. Martins, Joana Veríssimo, Pamela Puppo, Joana C. Pinto, Cátia Chaves, Catarina Pinho, José Manuel Grosso-Silva, Lorenzo Quaglietta, Pedro Sousa, Paulo Célio Alves, Nuno Fonseca, Pedro Beja
Data type:  OTUs generated by the RESL algorithm and respective sequence composition
Brief description: 

OTUs generated by the RESL algorithm (Ratnasingham and Hebert, 2013) in the BOLD system (Ratnasingham and Hebert, 2007), respective sequence composition and Nearest Neighbour genetic distance. The data are downloaded from BOLD, without further processing.

Download file (43.36 kb)
Suppl. material 5: IBI-Trichoptera 01 library - Specimen details - Darwin Core Standard 
Authors:  Luis Martín, Sónia Ferreira, Jesús Martínez, Marcus A. González, Martin Corley, José Manuel Grosso-Silva, Lorenzo Quaglietta, 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-Trichoptera 01 library. It contains collection and identification data. The data are downloaded from GBIF, without further processing.

Download file (442.98 kb)
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