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Diversity
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DNA Barcoding for Biodiversity Conservation and Restoration
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DNA Barcoding for Biodiversity Conservation and Restoration

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (15 August 2024) | Viewed by 90856

Special Issue Editors

Dr. Jessica Frigerio

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Guest Editor
1. FEM2-Ambiente, Piazza Della Scienza 2, I-20126 Milano, Italy
2. Biotechnology and Bioscience Department, University of Milano-Bicocca, Piazza Della Scienza 2, 20126 Milano, Italy
Interests: DNA barcoding; DNA metabarcoding; biodiversity conservation; plant biodiversity; herbal authenticity; food authenticity and traceability
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Manuel Elias-Gutierrez

E-Mail Website
Guest Editor
Department of Aquatic Ecology and Systematics, ECOSUR Chetumal, Chetumal, Quintana Roo, Mexico
Interests: freshwater zooplankton; systematics; DNA barcoding; zoogeography; eDNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I am pleased to announce an upcoming Special Issue of Diversity entitled “DNA barcoding for Biodiversity Conservation and Restoration”.

Biodiversity is under threat. Intensive human activities, such as land use, and the introduction and outbreaks of invasive species, are contributing to the degradation of ecosystems and climate change. The loss of biodiversity is an issue not only in terms of biodiversity preservation—about one million species of animal and plants are at risk of extinction—but also affects human society as a whole and its economy. Interventions for biodiversity conservation and restorations must mitigate this phenomenon. For example, the European Commission has presented the 2030 Biodiversity Strategy to address the main drivers of biodiversity loss and set legally binding targets.

To help biodiversity conservation and restoration, universal, standardized, and effective species identification systems can be used.

DNA barcoding is a method first proposed in 2003 that relies on the analysis of a specific region of organisms’ genome for a fast and reliable identification of the species. Over the past two decades, nearly ten million DNA barcodes have been collected in the international database BOLD to represent the diversity of species on Earth by international consortia which have contributed to expanding biological collections. DNA barcoding has been used to address fundamental questions in ecology, evolution, and conservational biology such as the evolution and interaction of species, identification of regulated and invasive species and the definition of methods to slow down biodiversity loss.

This Special Issue is dedicated to highlighting new research and advances in DNA barcoding and metabarcoding that are significant for the monitoring, conservation and restoration of biodiversity. In addition to empirical studies, contributions showing new methods and the application of DNA barcoding and metabarcoding in biodiversity studies are welcome.

Dr. Jessica Frigerio
Prof. Dr. Manuel Elias-Gutierrez
Guest Editors

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
  • DNA metabarcoding
  • biodiversity
  • biodiversity conservation
  • biodiversity restoration
  • ecology
  • biodiversity loss
  • climate change
  • evolution

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Published Papers (6 papers)

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Research

12 pages, 2745 KiB  
Article
Early Molecular Detection of Invasive Alien Plants in Urban and Peri-Urban Areas
by Jessica Frigerio, Malika Ouled Larbi, Werther Guidi Nissim, Fabrizio Grassi, Pierluigi Cortis and Massimo Labra
Diversity 2024, 16(10), 647; https://doi.org/10.3390/d16100647 - 19 Oct 2024
Viewed by 894
Abstract
Invasive alien plants represent one of the five major threats to biodiversity and the disruption of ecosystems. They are introduced through various routes, starting with commercial trade. Preventing their introduction is essential to avoid the spread of new invasive plants. In this paper, [...] Read more.
Invasive alien plants represent one of the five major threats to biodiversity and the disruption of ecosystems. They are introduced through various routes, starting with commercial trade. Preventing their introduction is essential to avoid the spread of new invasive plants. In this paper, we propose a new early warning DNA barcoding tool for invasive plant detection. Eight invasive alien species of European Union concern (i.e., Ludwigia grandiflora, Elodea nuttallii, Myriophyllum aquaticum, Pontederia crassipes, Ailanthus altissima, Heracleum mantegazzianum, Impatiens glandulifera, Pueraria montana) were selected and analysed. A unique DNA marker for each species was identified and amplified using species-specific primers capable of identifying the presence of alien species. To verify whether the approach could detect the presence of alien plants in urban areas from lawn clippings, mixes with typical urban spontaneous plants and invasive species were tested. In all mixes, only the invasive species was identified. This rapid detection capability will enable environmental operators to intervene promptly to contain the spread of invasive plants before they can cause significant damage to the local ecosystem. This tool could have a significant impact on the protection of local biodiversity and the integrity of urban habitats. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity Conservation and Restoration)
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22 pages, 4309 KiB  
Article
Description of the Northern Green Anaconda (Eunectes akayima sp. nov. Serpentes; Boidae): What Is in a Name?
by Jesús A. Rivas, Juliana S. Terra, Marijn Roosen, Patrick S. Champagne, Renata Leite-Pitman, Paola De La Quintana, Marco Mancuso, Luis F. Pacheco, Gordon M. Burghardt, Freek J. Vonk, Juán Elías García-Pérez, Bryan G. Fry and Sarah Corey-Rivas
Diversity 2024, 16(7), 418; https://doi.org/10.3390/d16070418 - 18 Jul 2024
Cited by 1 | Viewed by 3807
Abstract
While elucidating the evolutionary trajectory of green anacondas, we previously documented the existence of two distinct species, Eunectes akayima sp. nov. and Eunectes murinus (Linnaeus, 1758), that separated approximately 10 million years ago. Our research integrates a novel molecular clock approach, focuses on tectonic plate [...] Read more.
While elucidating the evolutionary trajectory of green anacondas, we previously documented the existence of two distinct species, Eunectes akayima sp. nov. and Eunectes murinus (Linnaeus, 1758), that separated approximately 10 million years ago. Our research integrates a novel molecular clock approach, focuses on tectonic plate movements with fossil records as minimal chronological markers, and offers a refined understanding of speciation events in relation to major biogeographical occurrences in South America. Mitochondrial DNA analysis demonstrates a significant genetic divergence between the species, which is supported by a notable difference in sexual size dimorphism (SSD) intensity between the two species, along with other morphological differences. This paper also rectifies earlier oversights in the description of the new species and clarifies taxonomic ambiguities in compliance with the International Code of Zoological Nomenclature (henceforth ICZN). In addition, we designate a neotype for E. murinus to stabilize the group. In an effort to honor Indigenous nations, E. akayima sp. nov. derives its name from the Carib language, advocating for the inclusion of traditional names in scientific discourse. Our paper not only contributes to the taxonomic stability of anacondas but also advocates for the usage of Indigenous names in zoological nomenclature by adopting a more inclusive and flexible approach to the ICZN and eliminating unintended exclusionary practices that we have inherited in science as in other disciplines. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity Conservation and Restoration)
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28 pages, 3114 KiB  
Article
Disentangling the Anacondas: Revealing a New Green Species and Rethinking Yellows
by Jesús A. Rivas, Paola De La Quintana, Marco Mancuso, Luis F. Pacheco, Gilson A. Rivas, Sandra Mariotto, David Salazar-Valenzuela, Marcelo Tepeña Baihua, Penti Baihua, Gordon M. Burghardt, Freek J. Vonk, Emil Hernandez, Juán Elías García-Pérez, Bryan G. Fry and Sarah Corey-Rivas
Diversity 2024, 16(2), 127; https://doi.org/10.3390/d16020127 - 16 Feb 2024
Cited by 5 | Viewed by 79073
Abstract
Anacondas, genus Eunectes, are a group of aquatic snakes with a wide distribution in South America. The taxonomic status of several species has been uncertain and/or controversial. Using genetic data from four recognized anaconda species across nine countries, this study investigates the [...] Read more.
Anacondas, genus Eunectes, are a group of aquatic snakes with a wide distribution in South America. The taxonomic status of several species has been uncertain and/or controversial. Using genetic data from four recognized anaconda species across nine countries, this study investigates the phylogenetic relationships within the genus Eunectes. A key finding was the identification of two distinct clades within Eunectes murinus, revealing two species as cryptic yet genetically deeply divergent. This has led to the recognition of the Northern Green Anaconda as a separate species (Eunectes akayima sp. nov), distinct from its southern counterpart (E. murinus), the Southern Green Anaconda. Additionally, our data challenge the current understanding of Yellow Anaconda species by proposing the unification of Eunectes deschauenseei and Eunectes beniensis into a single species with Eunectes notaeus. This reclassification is based on comprehensive genetic and phylogeographic analyses, suggesting closer relationships than previously recognized and the realization that our understanding of their geographic ranges is insufficient to justify its use as a separation criterion. We also present a phylogeographic hypothesis that traces the Miocene diversification of anacondas in western South America. Beyond its academic significance, this study has vital implications for the conservation of these iconic reptile species, highlighting our lack of knowledge about the diversity of the South American fauna and the need for revised strategies to conserve the newly identified and reclassified species. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity Conservation and Restoration)
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10 pages, 259 KiB  
Article
Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species
by Dana Șuteu, Mihai Pușcaș, Ioan Băcilă, Zoltán Robert Balázs and Philippe Choler
Diversity 2024, 16(2), 73; https://doi.org/10.3390/d16020073 - 23 Jan 2024
Cited by 1 | Viewed by 1624
Abstract
Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, the process of developing these markers is both costly and time-consuming. As a result, the cross-species [...] Read more.
Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, the process of developing these markers is both costly and time-consuming. As a result, the cross-species amplification has become a more rapid and more affordable alternative in biological studies. The objective of this study was to assess the applicability of 13 SSR markers, originally designed for Carex curvula, in other 14 species belonging to different sections of the genus. All the markers were successfully transferred with a mean of 90.76%, and 100% transferability was reached in two species (C. baldensis and C. rupestris). The lowest transferability was registered in the G165 marker, which did not produce amplification in six species. Together, the microsatellites amplified a total of 183 alleles, ranging from 10 to 19 alleles per locus, with an average of 14.07. The mean number of different alleles ranged from 0.846 to a maximum of 2.077 per locus. No significant departures from the Hardy–Weinberg equilibrium were detected in polymorphic loci. The transferability of the 13 SSR markers proved highly successful in various Carex species, across different clades and sections of the genus. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity Conservation and Restoration)
16 pages, 3207 KiB  
Article
Environmental DNA in a Biofilm Can Be Used to Assess Diatom Ecological Health in Stream Water Ecology
by Keonhee Kim, Hyeonjin Cho, Jeong-Hui Kim, Yun-Mo Yang, Hyunji Ju, Min-Ho Jang and Hyun-Gi Jeong
Diversity 2024, 16(1), 8; https://doi.org/10.3390/d16010008 - 22 Dec 2023
Viewed by 1727
Abstract
In urban and agricultural streams, assessing aquatic ecosystem health is critical due to widespread pollution. Traditional methods for evaluating attached diatoms crucial for ecosystem monitoring face limitations such as species misidentification and sample damage. This study was conducted in the Miho River within [...] Read more.
In urban and agricultural streams, assessing aquatic ecosystem health is critical due to widespread pollution. Traditional methods for evaluating attached diatoms crucial for ecosystem monitoring face limitations such as species misidentification and sample damage. This study was conducted in the Miho River within the Geum River system and highlights the effectiveness of environmental DNA (eDNA) techniques for more accurate and efficient genetic-based analysis than conventional microscopic analysis methods. When eDNA-based assessments were compared with traditional microscopic methods, this study found that eDNA analysis often revealed poorer ecosystem health. Notably, eDNA assessments showed a stronger correlation with phosphorus concentrations, underlining their precision and importance in ecological studies. These findings suggest that eDNA has potential as a valuable tool for comprehensive biomonitoring. However, the use of international genetic barcode databases in eDNA analysis could lead to the identification of unrecorded species in Korea. Therefore, this study recommends developing a localized genetic barcode database and constructing eDNA information through meta-barcoding, focusing on native species. This approach is crucial for enhancing the accuracy and applicability of eDNA-based health assessments in national biomonitoring efforts. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity Conservation and Restoration)
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15 pages, 2156 KiB  
Article
The Influence of Macroclimatic Drivers on the Macrophyte Phylogenetic Diversity in South African Estuaries
by Dimitri Allastair Veldkornet
Diversity 2023, 15(9), 986; https://doi.org/10.3390/d15090986 - 1 Sep 2023
Cited by 1 | Viewed by 1893
Abstract
The geographical distribution of plants is influenced by macroclimate and dispersal limitations, which have led to lineage isolation and subsequent diversification within and across various environmental gradients. Macroclimatic variables in coastal wetlands influence plant species and lineages across biogeographical boundaries. This study aimed [...] Read more.
The geographical distribution of plants is influenced by macroclimate and dispersal limitations, which have led to lineage isolation and subsequent diversification within and across various environmental gradients. Macroclimatic variables in coastal wetlands influence plant species and lineages across biogeographical boundaries. This study aimed to determine the influence of macroclimatic variables on species and phylogenetic richness in South African estuaries. Open-source chloroplast DNA barcoding sequences, species distribution and climatic data layers were used to determine the relationship between species richness, MPD, MNTD and each bioclimatic variable individually. Temperate species richness and phylogenetic diversity were positively correlated with temperature bioclimatic variables whereas subtropical and tropical species were associated with increases in precipitation. Phylogenetic niche conservatism is evident in malvids and rosids which are restricted to tropical and subtropical regions due to their physiological adaptations to tropical climates. Caryophylales was mostly associated with temperate regions. Poales and Alismatales showed wide distributions that is likely attributed to traits related to wind pollination and hydrochory, rapid, clonal, and high reproductive output, tolerance to stressful conditions, and intraspecific genetic diversity. The findings highlight the importance of considering macroclimate and phylogenetic factors in understanding the distribution and diversity of coastal wetland plants. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity Conservation and Restoration)
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