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DNA Barcodes for Evolution and Biodiversity—2nd Edition

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 15940

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Dr. Stephan Koblmüller

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Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
Interests: conservation biology; biodiversity; genomics; ecology and evolution; DNA sequencing; DNA
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Dear Colleagues,

The world is currently facing an unprecedented loss of biodiversity. As highlighted in the latest IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) global assessment report on biodiversity and ecosystem services, about 1 million animal and plant species are currently threatened with extinction. Biodiversity, however, is not something static, but rather dynamic and sensitive to changing environmental conditions. For documenting, maintaining, and monitoring changes in biodiversity and its numerous functions, it is necessary to be able to identify which entities contribute to biodiversity. For many taxa, a reliable species identification, the prerequisite for studying biodiversity, is, if at all, only able to be made possible by taxonomic experts, whose numbers have been drastically declining over the last few decades.

DNA barcoding is a method for identifying specimens (ideally to a species level) via employing an expert-based reference system (open access database) that drastically increases the number of people able to identify organisms down to species level and reduces the rate of misidentifications among morphologically similar taxa. Specifically, DNA barcoding is a standardized approach for identifying organisms based on specific sections of their DNA. Depending on the taxonomic group, different genes have been established as standard DNA barcoding markers, even though for certain applications or taxa other genes might be used. Consequently, DNA barcodes should allow for (in most cases) unambiguous specimen identification (also of morphologically unidentifiable life stages/sexes or parts of organisms) once a reliable DNA barcode reference database is available, and thus are an important tool in basic and applied biodiversity, as well as evolutionary biology research.

This Special Issue shall provide a platform with which to highlight new research and significant advances in DNA barcoding (incl. metabarcoding, eDNA, etc.) and its relevance for biodiversity and evolutionary biology research. In addition to empirical studies, submissions that focus on new methods, technologies, and analyses that aid in the generation and application of DNA barcoding data are also highly welcome.

Dr. Stephan Koblmüller
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

DNA barcoding
biodiversity
evolution
species delimitation
conservation
monitoring

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Related Special Issue

DNA Barcodes for Evolution and Biodiversity in Diversity (15 articles)

Published Papers (11 papers)

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Research

22 pages, 4602 KiB

Open AccessArticle

Dynamics of Phyto- and Bacterioplankton in Southern Baikal and Irkutsk Reservoir During the Open Water Period of 2023 According to Metabarcoding Data

by Yuri Galachyants, Darya Petrova, Artem Marchenkov, Maria Nalimova and Yelena Likhoshway

Diversity 2025, 17(6), 369; https://doi.org/10.3390/d17060369 - 22 May 2025

Viewed by 232

Abstract

Artificial reservoirs formed by hydroelectric dams are young ecosystems requiring water quality monitoring, as they often serve local populations. Traditionally, this is performed through hydrochemical and sanitary assessments, alongside phytoplankton composition analysis. This study aimed to assess the seasonal dynamics of microbial communities—both bacterioplankton and microeukaryotes including phytoplankton—in the Irkutsk Reservoir (IR), which is fed by the cold oligotrophic waters of Southern Baikal (SB). Using parallel metabarcoding of 16S and 18S rRNA gene fragments, we analyzed community composition during the open-water season and evaluated the ecological connectivity between these two freshwater systems. We demonstrated that seasonal changes in microeukaryotic communities were closely linked between SB and IR, with the greatest divergence observed in early summer and progressive convergence by autumn. Metabarcoding confirmed microscopy-based observations while providing higher taxonomic resolution and detecting otherwise overlooked groups. Bacterioplankton communities also exhibited seasonal variation and were shaped by environmental gradients and reservoir characteristics. Cyanobacteria peaked in SB in late summer but did not dominate communities, unlike in mesotrophic lowland reservoirs. These findings demonstrate the value of metabarcoding for freshwater monitoring and provide new insights into microbial community dynamics in river–reservoir systems influenced by oligotrophic lake inflow. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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26 pages, 16973 KiB

Open AccessArticle

DNA Barcoding Southwestern Atlantic Skates: A 20-Year Effort in Building a Species Identification Library

by Ezequiel Mabragaña, Valeria Gabbanelli, Florencia Matusevich, Diego Martín Vazquez, Sergio Matías Delpiani, Victoria Malvina Lenain, Juan José Rosso, Mariano González-Castro, Robert Hanner and Juan Martín Díaz de Astarloa

Diversity 2025, 17(5), 311; https://doi.org/10.3390/d17050311 - 25 Apr 2025

Viewed by 597

Abstract

The skate fauna in the Southwest Atlantic Ocean (SWA; 34–55° S) is represented by ~32 species, many of which share external features that have led to misidentifications and deficient fishery statistics. The use of DNA barcoding to discriminate SWA skate species was explored after 20 years of surveys. COI sequences were subjected to distance-based neighbor-joining (NJ), maximum likelihood (ML), barcode index number (BIN), automatic barcode gap discovery (ABGD), and nucleotide diagnostic character (NDC) analyses. For widely distributed species, a haplotype network was built. Overall, 187 specimens and 31 egg cases from 26 skate species were barcoded. NJ and ML analyses showed that nearly all species exhibited unique barcodes or clusters of closely related haplotypes, except for Psammobatis normani/P. rudis and Dipturus trachyderma/D. argentinensis. The first pair was discriminated by NCD. BIN analysis recovered 17 groups, whereas ABGD recovered 23, better reflecting taxonomic diversity. In summary, 24 species were resolved by COI. Phylogeographic signals were observed for Amblyraja doellojuradoi and Zearaja brevicaudata. Compiling our results with data from BOLD, almost all the species occurring in the area possess barcodes, contributing to completing and curating the BOLD reference library, which constitutes an important tool for resolving taxonomic issues, tracing fishery products, and performing eDNA biomonitoring. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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22 pages, 2255 KiB

Open AccessArticle

Where Meiofauna? An Assessment of Interstitial Fauna at a Belgian Beach

by Jill Monnissen, Sofie Thijs, Tom Artois, Philippe Jouk, Emma Van de Reydt, Thomas Van Dijck and Marlies Monnens

Diversity 2025, 17(4), 287; https://doi.org/10.3390/d17040287 - 18 Apr 2025

Viewed by 389

Abstract

Meiofauna are frequently overlooked in biodiversity assessments, resulting in a lack of understanding regarding their current status, the potential impact of anthropogenic activities, and climate change. This study on the intertidal zone of the Small Beach of Ostend marks a new effort to characterize meiofaunal communities along the Belgian coast. Sampling was carried out on five separate occasions throughout the year, with abiotic data collected during each event. Collected specimens were sorted according to their taxonomic group, resulting in a retrieval of 1742 organisms. Among these, Platyhelminthes and Nematoda were most abundant. Through metabarcoding of the 18S ribosomal region, a biodiversity assessment was conducted, yielding a total of 106 Amplicon Sequence Variants (ASVs). After filtering out rare reads, 65 metazoan ASVs were retained: 18 representing Platyhelminthes, 16 Nematoda, 15 Copepoda, 12 Polychaeta, and 4 Acoela. Identification of the ASVs through blasting generated 23 unique species-level identifications. The highest species richness was observed among Proseriata and Nematoda, each comprising six different species. Additionally, four different species of Polychaeta and Copepoda, two species of Acoela, and one species of Rhabdocoela were identified. Compared to findings on similar beaches along the Belgian coast from about 40 years ago, the meiofaunal communities on this beach exhibit an overall low species richness. Finding fewer and other species might be linked to the potential impact of beach nourishments, human trampling, and climate change. However, confirming this hypothesis requires future research. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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38 pages, 6948 KiB

Open AccessArticle

DNA Barcoding of Red Algae from Bocas del Toro, Panamá, with a Description of Gracilaria bocatorensis sp. nov. and G. dreckmannii sp. nov. (Gracilariales, Gracilariaceae)

by Maycol Ezequiel Madrid Concepcion, Rachel Collin, Kenneth S. Macdonald III, Amy C. Driskell, Suzanne Fredericq, Brian Wysor and D. Wilson Freshwater

Diversity 2025, 17(4), 222; https://doi.org/10.3390/d17040222 - 23 Mar 2025

Viewed by 643

Abstract

Bocas del Toro is an archipelago on the Caribbean coast of Panamá, recognized as a biodiversity hotspot. While marine red macroalgae in the Western Atlantic are well studied, the marine flora of Panamá, particularly Bocas del Toro, remains underexplored using DNA barcoding. This study documents the diversity of marine red macroalgae in the region using COI-5P barcoding to identify species, detect cryptic diversity, and assess the presence of invasive and amphi-isthmian species. Specimens collected in 2008 and 2009 yielded 179 COI-5P sequences. Barcode Index Numbers (BINs) were assigned to 82 genetic clusters, many lacking GenBank matches, suggesting potential new species. Morphology and phylogenetic analyses of rbcL, UPA, and cox1 confirmed two new species of Gracilaria (G. bocatorensis sp. nov. and G. dreckmannii sp. nov.). Despite advances in DNA barcoding, red macroalgal diversity in Panamá remains understudied, particularly Corallinales, where rbcL sequences are lacking. No introduced or amphi-isthmian species were detected. This study adds 16 new species records for the Caribbean coast of Panamá, emphasizing the importance of DNA barcoding in biodiversity research. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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36 pages, 18552 KiB

Open AccessArticle

Integrative Taxonomy of Costa Rican Tetrigidae (Orthoptera) Reveals Eight New Species

by Niko Kasalo, Daniel H. Janzen, Winnie Hallwachs, Allison Brown, Martin Husemann, Mathias Vielsäcker, Tomislav Domazet-Lošo, Damjan Franjević, Madan Subedi, Domagoj Bogić and Josip Skejo

Diversity 2025, 17(3), 190; https://doi.org/10.3390/d17030190 - 6 Mar 2025

Viewed by 1484

Abstract

Tetrigidae is one of the largest orthopteran families, but very few studies so far have integrated molecular and morphological data. Unsurprisingly, few species have been DNA barcoded, and the unresolved taxonomy makes Tetrigidae a difficult group to work with. Here, we examined a sample of 90 specimens collected as a part of the Costa Rican DNA barcoding project and identified 20 species assigned to 24 BINs, among which are 8 newly described species: Scaria bimaculata sp. nov., Lophotettix semicristatus sp. nov., Otumba auricarinata sp. nov., Otumba tenuis sp. nov., Otumba ignicula sp. nov., Metrodora mollilobata sp. nov., Metrodora ala sp. nov., and Platythorus inabsolutus sp. nov. We found that coloration and lateral lobe shape are species-specific among the examined species of Batrachideinae and Metrodorinae and that Lophotettiginae and Metrodora might be more closely related than previously assumed. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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16 pages, 3301 KiB

Open AccessArticle

Catfishes from the North-Western Part of Lake Tanganyika: Contribution to a Reference Library of DNA Barcodes

by Archimède Mushagalusa Mulega, Arthur F. Boom, Imane Rahmouni, Hocein Bazairi, Abdelaziz Benhoussa, Maarten P. M. Vanhove and Maarten Van Steenberge

Diversity 2025, 17(1), 8; https://doi.org/10.3390/d17010008 - 25 Dec 2024

Viewed by 1639

Abstract

In spite of the global barcoding effort, there is still a lack of genetic data on African freshwater fishes. We aimed to contribute to bridging this gap by providing molecular data on commercially important catfish species from the north-western part of Lake Tanganyika. We collected 215 catfish specimens and sequenced the standard vertebrate barcoding gene (COI) for 41 specimens. Additionally, we sequenced 20 specimens for the mitochondrial Cyt-b gene to make the link to previously published datasets. We identified 11 species using morphology, compared DNA sequences with those available on GenBank, and employed Automatic Barcode Gap Discovery (ABGD) and phylogenetic approaches. The dataset includes the first molecular data (COI and Cyt-b) for Chrysichthys acsiorum, as well as the first-ever COI sequences for Dinotopterus cunningtoni and Malapterurus tanganyikaensis. Our findings extend the known distribution of C. acsiorum by approximately 100 km. Additionally, we demonstrated the difficulty in delineating species of Chrysichthys and Synodontis from Lake Tanganyika with molecular tools. For Chrysichthys, automated methods, such as ABGD, failed to delineate species. However, barcoding does seem promising as all the individual species are resolved as clades. Within Synodontis, the study found a strong similarity between S. grandiops and S. multipunctatus, highlighting a need for revision. Our findings emphasize the necessity for integrative taxonomy in the study of catfishes from Lake Tanganyika. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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14 pages, 7720 KiB

Open AccessEditor’s ChoiceArticle

First Attempts at DNA Barcoding Lepidoptera in North Cyprus Reveal Unexpected Complexities in Taxonomic and Faunistic Issues

by Peter Huemer and Özge Özden

Diversity 2024, 16(11), 671; https://doi.org/10.3390/d16110671 - 31 Oct 2024

Viewed by 1311

Abstract

The fauna of Lepidoptera in the Mediterranean is still inadequately documented. As a result, even remotely complete DNA barcode libraries (mt. COI (cytochrome c oxidase 1) gene) are lacking in most areas. This proposed gap is being analyzed for the first time for the fauna of North Cyprus. In the initial phase, 248 morphospecies from 29 families (exclusive Heterocera) were sampled, sequenced and compared with existing DNA reference sequences in the global BOLD database (Barcode of Life Data Systems) via BINs (Barcode Index Numbers). A total of 194 species could be unequivocally assigned to a Linnaean taxon. Additionally, six species previously unidentified in BOLD, as well as fourteen species without reference barcodes, were identified at the species level. Twenty-four of these species were new records for Cyprus. In addition, 25 taxa with new BINs could not be assigned to a valid species due to potential cryptic diversity or the lack of relevant revisions. Furthermore, a few species could not be identified due to barcode sharing and/or potential misidentifications in BOLD. Overall, approximately 20% of the samples could not be identified using the existing DNA barcode libraries, a significant deficit for European standards, which should be addressed as a priority issue in future studies. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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42 pages, 47060 KiB

Open AccessEditor’s ChoiceArticle

A Molecular-Informed Species Inventory of the Order Ceramiales (Rhodophyta) in the Narragansett Bay Area (Rhode Island and Massachusetts), USA

by Thomas Irvine, Brian Wysor and Alicia Beauvais

Diversity 2024, 16(9), 554; https://doi.org/10.3390/d16090554 - 5 Sep 2024

Viewed by 2174

Abstract

Narragansett Bay is an estuarine system in the western North Atlantic Ocean that harbors a diverse marine flora, providing structure, habitat, and food for native biodiversity. This area has been the center of numerous environmental, biological, ecological, and oceanographic studies; however, marine macroalgae have not been extensively examined using modern molecular methods. Here, we document the biodiversity of the red algal order Ceramiales based on DNA sequence comparisons of the 3′ end of the RuBisCo large subunit (rbcL-3P) and the universal plastid amplicon (UPA). Thirty-seven distinct species of this order were identified and validated with molecular data, including five new species reports and at least one new report of an introduced species, Antithamnionella spirographidis, in the vicinity of Narraganset Bay. Novel sequence data were generated for numerous species, and it was discovered that the UPA marker, which has been less frequently used in red algal floristics, revealed an identical inventory of ceramialean algae as the rbcL-3P marker. Thus, the shorter length of the UPA marker holds promise for DNA metabarcoding studies that seek to elucidate biodiversity across algal phyla. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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12 pages, 1888 KiB

Open AccessArticle

Environmental DNA as Early Warning for Alien Species in Mediterranean Coastal Lagoons: Implications for Conservation and Management

by Francesco Zangaro, Maurizio Pinna and Valeria Specchia

Diversity 2024, 16(9), 525; https://doi.org/10.3390/d16090525 - 1 Sep 2024

Cited by 2 | Viewed by 1510

Abstract

Non-indigenous species (NIS) introduction notoriously threatens the Mediterranean Sea. In addition, Mediterranean coastal lagoons play a crucial role as nurseries for marine species, which new NIS arrivals can threaten. Therefore, monitoring and early warning of NIS presence is essential in preserving biodiversity. An innovative technique for rapid and accurate species identification and biodiversity screening is the application of environmental DNA (eDNA) metabarcoding. In this research, different Penaeidae (Arthropoda, Crustacea, Decapoda) NIS specimens were collected from a Mediterranean coastal lagoon after an early warning about a potentially invasive NIS arising from next-generation sequencing data. DNA barcoding of the DNA extracted from tissue samples and amplified with specifically designed primer pairs led to the recognition of Penaeus aztecus in this NATURA 2000 protected ecosystem for the first time. DNA barcoding from DNA isolated from the water where the living specimens were stored further validated the possibility of identifying P. aztecus starting from eDNA. This approach demonstrated the validity of environmental DNA analysis in the early screening of potentially invasive NIS presence in Mediterranean protected areas and ecosystems. This work describes an applicative example of the efficacy in improving the biomonitoring of lagoon ecosystems using molecular tools and it represents a guideline for the validation of eDNA metabarcoding data for the presence of potentially invasive species. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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22 pages, 6248 KiB

Open AccessEditor’s ChoiceArticle

DNA Metabarcoding Analysis of Arthropod Diversity in Dust from the Natural History Museum, Vienna

by Pascal Querner, Nikola Szucsich, Bill Landsberger and Peter Brimblecombe

Diversity 2024, 16(8), 476; https://doi.org/10.3390/d16080476 - 6 Aug 2024

Cited by 1 | Viewed by 2297

Abstract

This paper introduces a new method for identifying museum pests through the analysis of DNA present in settled dust. Traditionally, the identification of pests in cultural institutions such as museums and depositories has relied on insect trapping (monitoring). They give good results but need time (minimum spring until summer of one year for a complete survey) and face challenges related to the identification of small, rare, or damaged species. Our study presents a non-invasive approach that utilizes metabarcoding analysis of dust samples to identify pests and other arthropods at the species level. We collected dust samples with a handheld vacuum cleaner in summer 2023 from the six different floors of the Natural History Museum in Vienna and compared the results with the insect monitoring. We found over 359 different species of arthropods in the museum and could show how the diversity increases with the elevation of the building floor. This method could be used for rapid and cost-effective screening of pests before monitoring. But the interpretation of results is sometimes difficult (for Lepismatidae, for example), and it cannot replace a continuous monitoring of pests with traps. This investigation might present the highest indoor animal biodiversity ever found in a single building. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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13 pages, 985 KiB

Open AccessArticle

DNA Barcoding for Species Identification of Moss-Dwelling Invertebrates: Performance of Nanopore Sequencing and Coverage in Reference Database

by Stephan Koblmüller, Philipp Resl, Nadine Klar, Hanna Bauer, Lukas Zangl and Christoph Hahn

Diversity 2024, 16(4), 196; https://doi.org/10.3390/d16040196 - 25 Mar 2024

Cited by 2 | Viewed by 2471

Abstract

In view of the current biodiversity crisis and our need to preserve and improve ecosystem functioning, efficient means for characterizing and monitoring biodiversity are required. DNA barcoding, especially when coupled with new sequencing technologies, is a promising method that can, in principle, also be employed by taxonomic lay people. In this study we compare the performance of DNA barcoding by means of a third-generation sequencing technology, nanopore sequencing with classical Sanger sequencing, based on a sample of invertebrates collected from moss pads in a bog in Austria. We find that our nanopore sequencing pipeline generates DNA barcodes that are at least as good as barcodes generated with Sanger sequencing, with the MinION producing better results than the Flongle flowcell. We further find that while many arthropod taxa are well covered in the international reference DNA barcode database BOLD, this clearly is not the case for important taxa like mites and springtails, which hampers large-scale biodiversity assessments. Based on examples from our study we further highlight which factors might be responsible for ambiguous species identification based on BOLD and how this can, at least partly, be solved. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity—2nd Edition)

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