Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
3.4
2.1
Journals
Diversity
Special Issues
DNA Barcodes for Evolution and Biodiversity—2nd Edition
share announcement

DNA Barcodes for Evolution and Biodiversity—2nd Edition

A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: 25 February 2025 | Viewed by 7539

Special Issue Editor

Dr. Stephan Koblmüller

E-Mail Website
Guest Editor
Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
Interests: conservation biology; biodiversity; genomics; ecology and evolution; DNA sequencing; DNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

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

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Related Special Issue

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

14 pages, 7720 KiB  
Article
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 868
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

42 pages, 47060 KiB  
Article
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 1606
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

12 pages, 1888 KiB  
Article
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 887
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

22 pages, 6248 KiB  
Article
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
Viewed by 1544
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

13 pages, 985 KiB  
Article
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
Viewed by 1871
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop