Frontiers in DNA Barcoding and Implications for Entomology

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Conservation".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 8030

Special Issue Editors


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Guest Editor
Division of Molecular Biology, Ruđer Bošković Institute,10000 Zagreb, Croatia
Interests: molecular phylogenetics; evolutionary biology; DNA-barcoding; integrative taxonomy; non-coding DNA sequences

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Guest Editor
Croatian Natural History Museum, 10000 Zagreb, Croatia
Interests: molecular evolution; phylogeography and phylogeny; DNA-barcoding; conservation biology; integrative taxonomy

Special Issue Information

Dear Colleagues,

Insects (Insecta, Arthropoda) are undoubtedly the most evolutionarily successful group of organisms. The origin of insects dates back to 400-500 mya, and many insect groups have been preserved in a very similar form to the present day. With over 1.3 million described species, they account for more than ¾ of all known species on Earth, and it is estimated that at least 4-5 million insect species still remain undiscovered and undescribed. Insects are adapted to a wide variety of habitats, biotopes, and living conditions. They occupy all ecological niches except marine habitats and account for the largest part of the world's biodiversity.

People's interest in insects dates far into human history. Many insect groups and species are recognized for their medical, agricultural, or economic importance, whether beneficial or as pests, parasites, and vectors of pathogens that globally impact human communities. The focus of scientific research has therefore traditionally been on numerous insect groups, requiring accurate and reliable identification of taxa. At the same time, in a large number of insect and arthropod groups, morphological identification is extremely difficult due to the lack of reliable diagnostic characters or the existence of cryptic species and species complexes. Furthermore, as the number of trained professional taxonomists, particularly those specialized in less-studied insect groups, is declining, alternative methods of species identification are required.

In the last two decades, DNA barcoding, a rapid and reliable method for species identification, has given new impetus to taxonomic research. The establishment of a public BOLD database allows the scientific community to access public data and provides a starting point for a number of additional studies. Currently, nearly ¾ of all public records in the BOLD database are related to insects and their arthropod relatives, representing ~250,000 species in ~500,000 BINs. Entomology as a science has therefore also benefited greatly from the advent of the DNA barcoding method. Applied in the numerous studies of insects (and arthropods in general), this approach has often revealed new and hitherto undiscovered or cryptic species and flagged the existence of species complexes and evolutionarily important units, thus laying the foundation for further comprehensive integrative taxonomic research. Through DNA barcoding, the monitoring of invasive species, vectors, and economically important arthropod species is greatly facilitated, as well as monitoring the status of populations of endangered and endemic species and research on the biodiversity of specific geographic areas. In addition, DNA metabarcoding of various environmental samples is increasingly being used in ecological and surveillance projects, allowing rapid biodiversity assessment of otherwise unattainable arthropod biosystems and communities.

This Special Issue welcomes all contributions describing the advantages and application of the method of DNA barcoding and metabarcoding in most various aspects of entomological research. Descriptions of new species based on DNA barcoding will only be considered within the broader integrative taxonomic framework. In light of the current rapid loss of biodiversity, contributions that have an impact on the broadening of our knowledge of insect species richness and that aim at establishing further biodiversity screening and conservation projects, especially in understudied geographic areas, will be highly appreciated.

Dr. Branka Bruvo Mađarić
Dr. Martina Podnar Lešić
Guest Editors

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Keywords

  • Insecta
  • Arthropoda
  • DNA barcoding
  • eDNA metabarcoding
  • cryptic diversity
  • species complex
  • biodiversity conservation
  • monitoring
  • integrative taxonomy

Published Papers (5 papers)

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Research

17 pages, 4113 KiB  
Article
Elmis syriaca (Kuwert, 1890) and E. zoufali (Reitter, 1910) (Coleoptera: Elmidae) confirmed as distinct species based on molecular data, morphology and geographical distribution
by Manfred A. Jäch, Michaela Brojer, Vlatka Mičetić Stanković, Marija Bošnjak, Dafna Luz, Netta Dorchin, Yaron Hershkovitz, Boris Novaković, Ivana Živić, Wolfgang Dorfer and Branka Bruvo Mađarić
Diversity 2023, 15(9), 994; https://doi.org/10.3390/d15090994 - 05 Sep 2023
Viewed by 1091
Abstract
Molecular data for 19 specimens of Elmis syriaca syriaca and E. s. zoufali from eight countries have been analysed in order to investigate the taxonomic status and the geographical distribution of these two subspecies. The nominative subspecies was previously thought to be endemic [...] Read more.
Molecular data for 19 specimens of Elmis syriaca syriaca and E. s. zoufali from eight countries have been analysed in order to investigate the taxonomic status and the geographical distribution of these two subspecies. The nominative subspecies was previously thought to be endemic to the Levant (Israel, Lebanon, Syria), while E. s. zoufali was regarded as being widespread from the Balkans to eastern Anatolia and Afghanistan. The results of our molecular studies using DNA barcoding and nuclear DNA data reveal that the two taxa are in fact distinct species, which separated around 2 Mya. A distinction based on the external morphological characters of 354 specimens was found to be impossible due to the pronounced variability, especially of the pronotal microsculpture, which had hitherto been used as the main distinguishing feature. The two species can only be distinguished by the aedeagal parameres and by the geographical distribution, which deviates considerably from the concept of previous authors. Elmis zoufali is distributed in Romania, the Balkan Peninsula, some Aegean Islands and in western Anatolia, while E. syriaca occurs from the Caucasus region southwards to eastern Turkey, Iran (probably also Afghanistan) and the Levant. Geographically, both species are widely separated by the so-called Anatolian Diagonal. Elmis zoufali resp. E. syriaca are recorded for the first time from Croatia, Romania, Azerbaijan, Georgia, Iran and Turkey. In addition, we examined 13 specimens tentatively identified as Elmis quadricollis (Reitter, 1887), a closely related species from Central Asia; we sequenced one specimen from China, which was revealed to be a sister to E. zoufali and E. syriaca. Full article
(This article belongs to the Special Issue Frontiers in DNA Barcoding and Implications for Entomology)
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14 pages, 1295 KiB  
Article
Insight into Trophic Interactions of Spiders in Olive Groves with Integrated and Ecological Pest Management Using DNA Metabarcoding
by Barbara Anđelić Dmitrović, Domagoj Gajski, Tomislav Kos, Mišel Jelić and Lucija Šerić Jelaska
Diversity 2023, 15(9), 976; https://doi.org/10.3390/d15090976 - 29 Aug 2023
Viewed by 1023
Abstract
Spiders act as one of the major predators among arthropods in agroecosystems and are crucial to the control of pest densities. As they are almost exclusively predators, they have developed a number of hunting strategies, which have consequently impacted their complex trophic interactions. [...] Read more.
Spiders act as one of the major predators among arthropods in agroecosystems and are crucial to the control of pest densities. As they are almost exclusively predators, they have developed a number of hunting strategies, which have consequently impacted their complex trophic interactions. The development of molecular biology methods for environmental DNA analysis has made it easier to analyze such complex trophic networks. In order to ascertain the trophic interactions of spiders, a sampling of spider species was carried out in two olive groves in Zadar County, Croatia, under integrated and ecological pest management. To construct the trophic networks of spiders, we performed DNA metabarcoding. The combined general and spider-excluding primers were able to recognize prey from 12 distinct orders in the guts of the 57 spiders. According to our results, spiders have a complex trophic network that exhibits seasonal and site-specific variations. The results obtained from both sites having different pest management also confirmed that spiders consumed phytophagous insects in the highest ratio, including some important pests, in comparison to other prey and that management and guild type had an impact on the predation of phytophagous insects. Full article
(This article belongs to the Special Issue Frontiers in DNA Barcoding and Implications for Entomology)
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13 pages, 1761 KiB  
Article
The Case for a Nuclear Barcode: Using the CAD CPS Region for Species and Genus Level Discrimination in Beetles
by Patrick S. Gorring and Anthony I. Cognato
Diversity 2023, 15(7), 847; https://doi.org/10.3390/d15070847 - 11 Jul 2023
Cited by 1 | Viewed by 1071
Abstract
DNA barcoding has revolutionized how we discover, identify, and detect species. A substantial foundation has been established with millions of mitochondrial cytochrome c oxidase I sequences freely available for eukaryotes. However, issues with COI ranging from uniparental inheritance and small genetic population sizes [...] Read more.
DNA barcoding has revolutionized how we discover, identify, and detect species. A substantial foundation has been established with millions of mitochondrial cytochrome c oxidase I sequences freely available for eukaryotes. However, issues with COI ranging from uniparental inheritance and small genetic population sizes to nuclear and asymmetric introgression can impede its use. We propose using CAD as the “nuclear barcode” to complement the COI barcode and ameliorate these concerns. We focused on beetles from taxonomically diverse species-level studies that used COI and CAD. An ambiguous barcode gap was present between intra- and interspecific genetic distances in CAD and COI; this led to difficulty with automated gap detection methods. We found pseudogenes, problematic population structure, introgression, and incomplete lineage sorting represented in the COI data. A CAD gene tree illuminated these cryptic problems. Placement tests of species and outgroups using distance-based tree building were largely successful for CAD, demonstrating its phylogenetic signal at the species and genus levels. Species placement issues were typically unique to one locus, allowing for recognition of misdiagnosis. We conclude that a CAD barcode is a valuable tool for beetle diagnostics, metabarcoding, and faunistic surveys. Full article
(This article belongs to the Special Issue Frontiers in DNA Barcoding and Implications for Entomology)
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17 pages, 8118 KiB  
Article
DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification
by Niko Kasalo, Josip Skejo and Martin Husemann
Diversity 2023, 15(6), 696; https://doi.org/10.3390/d15060696 - 23 May 2023
Cited by 2 | Viewed by 1538
Abstract
The COI gene is widely used as a DNA barcode in animals that can assist in the identification of species. One of the widely used aggregators of DNA barcodes is the Barcode of Life Data System (BOLD Systems), which contains around 2500 sequences [...] Read more.
The COI gene is widely used as a DNA barcode in animals that can assist in the identification of species. One of the widely used aggregators of DNA barcodes is the Barcode of Life Data System (BOLD Systems), which contains around 2500 sequences of Tetrigidae, an understudied orthopteran family with unresolved taxonomy and species that are difficult to identify. In this paper, we provide a summary of the metadata provided with the COI sequences and present a phylogenetic analysis of photographically vouchered sequences using Maximum Likelihood and Bayesian analysis. We found that (1) the subfamily Tetriginae is disproportionately represented in the dataset, (2) most of the records are not identified beyond the family level, (3) most regions, except for Costa Rica, are undersampled, (4) most of the sequences do not have photographic vouchers, and (5) the taxonomic backbone of BOLD is out of date. The phylogenetic analysis showed that the clusters of COI barcodes mostly correspond to species, but some clusters remain ambiguous. The deeper nodes in the phylogenetic trees are not well-supported, indicating that this gene has a very weak phylogenetic signal beyond the specific level. Full article
(This article belongs to the Special Issue Frontiers in DNA Barcoding and Implications for Entomology)
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12 pages, 1137 KiB  
Article
DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity
by Peter Huemer and Christian Wieser
Diversity 2023, 15(2), 214; https://doi.org/10.3390/d15020214 - 02 Feb 2023
Cited by 3 | Viewed by 2311
Abstract
Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete [...] Read more.
Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete inventory of the megadiverse insect order Lepidoptera in a protected area in the Alps (Cottian Alps, Italy) was intended to test the possibilities and reliability of DNA-based identifications. From voucher material collected between 2019 and 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas DNA barcoding failed for another 18 species. A total of 35 species shared a BIN with one or more taxa, but a majority of 19 species could still be discriminated by divergent sequences. A total of 12 morphospecies split into two BINs. These species and a further 22 taxa with unique BINs and barcode divergences >2% to the nearest neighbor require taxonomic re-assessment. Two additional cryptic species from the study area were described recently. Finally, 16 species are newly recorded for Italy. Our study, therefore, demonstrates the importance of DNA barcoding for both faunistics and the discovery of cryptic diversity, even in apparently well-studied protected areas. Full article
(This article belongs to the Special Issue Frontiers in DNA Barcoding and Implications for Entomology)
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