Diversity

Editorial

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5 pages, 212 KiB

Open AccessEditorial

DNA Barcodes for Evolution and Biodiversity

by Stephan Koblmüller

Diversity 2023, 15(9), 1003; https://doi.org/10.3390/d15091003 - 08 Sep 2023

Cited by 1 | Viewed by 1249

Abstract

Questions centered around how biological diversity is being generated and maintained, as well as how this biodiversity can be conserved/protected, are being frequently asked in basic and applied evolutionary biological and biodiversity research [...] Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

Research

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26 pages, 8492 KiB

Open AccessArticle

DNA Barcoding Data Reveal Important Overlooked Diversity of Cortinarius sensu lato (Agaricales, Basidiomycota) in the Romanian Carpathians

by Emerencia Szabó, Bálint Dima, Avar L. Dénes, Viktor Papp and Lujza Keresztes

Diversity 2023, 15(4), 553; https://doi.org/10.3390/d15040553 - 13 Apr 2023

Cited by 1 | Viewed by 1667

Abstract

Cortinarius s.l. is a globally distributed agaricoid genus that has been well studied in Europe with over 1000 described species. However, the information about their taxonomy and diversity in eastern Central Europe is still limited. Only 124 species have been reported so far [...] Read more.

Cortinarius s.l. is a globally distributed agaricoid genus that has been well studied in Europe with over 1000 described species. However, the information about their taxonomy and diversity in eastern Central Europe is still limited. Only 124 species have been reported so far from Romania, based solely on morphological observations. The aim of this study was to re-examine the diversity of the genus Cortinarius s.l. in the Romanian Carpathian area, employing molecular phylogenetic and morphological methods. During intensive field work in the period 2017–2020, a total of 234 Cortinarius s.l. specimens were collected and studied with integrative taxonomic methods. For all the samples, we amplified and sequenced the nrDNA ITS region, which is the widely used official barcode marker of fungi. These sequences were compared to the data found in public databases (GenBank, UNITE, BOLD). Based on phylogenetic analyses, we identified 109 Cortinarius s.l. species, which represent 40 sections and 3 clades. Out of these species, 43 have previously been documented from Romania based on morphological identification methods, while 66 species are reported as new to the country. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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15 pages, 2037 KiB

Open AccessArticle

Phylogeographic and Morphological Analysis of Botrylloides niger Herdman, 1886 from the Northeastern Mediterranean Sea

by Berivan Temiz, Esra Öztürk, Simon Blanchoud and Arzu Karahan

Diversity 2023, 15(3), 367; https://doi.org/10.3390/d15030367 - 03 Mar 2023

Cited by 5 | Viewed by 1756

Abstract

Botrylloides niger (class Ascidiacea) is an invasive marine filter-feeding invertebrate that is believed to originate from the West Atlantic region. This species of colonial tunicate has been observed in several locations along the coasts of Israel and around the Suez Canal, but it [...] Read more.

Botrylloides niger (class Ascidiacea) is an invasive marine filter-feeding invertebrate that is believed to originate from the West Atlantic region. This species of colonial tunicate has been observed in several locations along the coasts of Israel and around the Suez Canal, but it has not yet been reported on the coasts of the Northeastern Mediterranean Sea (NEMS), suggesting an ongoing Lessepsian migration. However, the extent of this invasion might be concealed by reports of other potentially misidentified species of Botrylloides, given that the strong morphological similarities within this genus renders taxonomical identification particularly challenging. In this study, we performed a phylogeographic and morphological analysis of B. niger in the NEMS. We collected 238 samples from 8 sampling stations covering 824 km of the coastlines of NEMS. We reported 14 different morphotypes, of which the orange-brown, orange, and brown-striped morphs were the most abundant. Using the mitochondrial cytochrome C oxidase I (COI) as a DNA barcode marker, we identified 4 haplotypes. The COI haplotypes clustered with the reference B. niger sequences from GenBank and differed significantly from the sister Botrylloides species. We confirmed our identification using three additional barcoding markers (Histone 3, 18S rRNA, and 28S rRNA), which all matched with over 99% similarity to reference sequences. In addition, we monitored a station for a year and conducted a temporal analysis of the collected colonies. The colonies were absent during the winter and spring, while new colonies were established in the summer and expanded during autumn. We performed demographic population analysis on our spatial data that identified a possible population subdivision at a sampling site, which might have been caused by local freshwater input. Herein, we present the first report on the presence of Botrylloides niger in the NEMS. This study represents a key step toward understanding the diversity and the propagation of this highly invasive species of colonial ascidians, both within the Mediterranean basin as well as globally. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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11 pages, 2469 KiB

Open AccessArticle

Molecular Species Delimitation Using COI Barcodes of Mealybugs (Hemiptera: Pseudococcidae) from Coffee Plants in Espírito Santo, Brazil

by Pablo Viana Oliveira, Alexandre Rosa dos Santos, Emily Lopes Olive, Karolinni Bianchi Britto, Francine Alves Nogueira de Almeida, Vitor Cezar Pacheco da Silva, Carolina Barros Machado, Maurício José Fornazier, José Aires Ventura, Mark Paul Culik and Greiciane Gaburro Paneto

Diversity 2023, 15(2), 305; https://doi.org/10.3390/d15020305 - 20 Feb 2023

Cited by 3 | Viewed by 2173

Abstract

Mealybugs are insects belonging to the family Pseudococcidae. This family includes many plant-pest species with similar morphologies, which may lead to errors in mealybug identification and delimitation. In the present study, we employed molecular-species-delimitation approaches based on distance (ASAP) and coalescence (GMYC and [...] Read more.

Mealybugs are insects belonging to the family Pseudococcidae. This family includes many plant-pest species with similar morphologies, which may lead to errors in mealybug identification and delimitation. In the present study, we employed molecular-species-delimitation approaches based on distance (ASAP) and coalescence (GMYC and mPTP) methods to identify mealybugs collected from coffee and other plant hosts in the states of Espírito Santo, Bahia, Minas Gerais, and Pernambuco, Brazil. We obtained 171 new COI sequences, and 565 from the BOLD Systems database, representing 26 candidate species of Pseudococcidae. The MOTUs estimated were not congruent across different methods (ASAP-25; GMYC-30; mPTP-22). Misidentifications were revealed in the sequences from the BOLD Systems database involving Phenacoccus solani × Ph. solenopsis, Ph. tucumanus × Ph. baccharidis, and Planacoccus citri × Pl. minor species. Ten mealybug species were collected from coffee plants in Espírito Santo. Due to the incorrect labeling of the species sequences, the COI barcode library of the dataset from the database needs to be carefully analyzed to avoid the misidentification of species. The systematics and taxonomy of mealybugs may be improved by integrative taxonomy which may facilitate the integrated pest management of these pests. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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18 pages, 654 KiB

Open AccessArticle

DNA Barcoding of Trichobilharzia (Trematoda: Schistosomatidae) Species and Their Detection in eDNA Water Samples

by Nikolaus Helmer, Christoph Hörweg, Helmut Sattmann, Susanne Reier, Nikolaus U. Szucsich, Jana Bulantová and Elisabeth Haring

Diversity 2023, 15(1), 104; https://doi.org/10.3390/d15010104 - 12 Jan 2023

Cited by 4 | Viewed by 1907

Abstract

We designed and tested species-specific PCR primers to detect Trichobilharzia species via environmental DNA (eDNA) barcoding in selected Austrian water bodies. Tests were performed with eDNA samples from the field as well as with artificial samples from the lab, where snails releasing cercariae [...] Read more.

We designed and tested species-specific PCR primers to detect Trichobilharzia species via environmental DNA (eDNA) barcoding in selected Austrian water bodies. Tests were performed with eDNA samples from the field as well as with artificial samples from the lab, where snails releasing cercariae were kept in aquariums. From two localities, Trichobilharzia was documented based on the release of cercariae from snails, enabling morphological species identification. In both cases, the corresponding species were detected via eDNA: Trichobilharzia szidati and Trichobilharzia physellae. Nonetheless, the stochasticity was high in the replicates. PCR tests with aquarium water into which the cercariae had been released allowed eDNA detection even after 44 days. As in the PCRs with eDNA samples from the field, positive results of these experiments were not obtained for all samples and replicates. PCR sensitivity tests with dilution series of T. szidati genomic DNA as well as of PCR amplification products yielded successful amplification down to concentrations of 0.83 pg/µL and 0.008 pg/µL, respectively. Our results indicate that the presumed species specificity of PCR primers may not be guaranteed, even if primers were designed for specific species. This entails misidentification risks, particularly in areas with incomplete species inventories. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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12 pages, 2440 KiB

Open AccessArticle

High-Throughput DNA Metabarcoding as an Approach for Ichthyoplankton Survey in Oujiang River Estuary, China

by Rijin Jiang, James Leonard Lusana and Yongjiu Chen

Diversity 2022, 14(12), 1111; https://doi.org/10.3390/d14121111 - 14 Dec 2022

Cited by 4 | Viewed by 1382

Abstract

High-throughput DNA metabarcoding of mitochondrial 12S rRNA and Cyt b gene sequences was coupled with a morphology-based identification tool to assess ichthyoplankton community structure in Oujiang River Estuary, China. The performances of 12S and Cyt b barcoding markers were compared in terms of [...] Read more.

High-throughput DNA metabarcoding of mitochondrial 12S rRNA and Cyt b gene sequences was coupled with a morphology-based identification tool to assess ichthyoplankton community structure in Oujiang River Estuary, China. The performances of 12S and Cyt b barcoding markers were compared in terms of taxonomic resolution, detection and coverage, and their suitability was established for use as a quick and powerful ichthyoplankton assessment tool. A total of 30,138 ichthyoplankton (2462 eggs and 27,676 larvae) samples were collected from April to August 2015 and identified to 145 taxa belonging to 57 families and 105 genera. June and July were the main spawning months. Ichthyoplankton were more abundant around Lingkun and Qidu Islands and the upper parts of Oujiang River Estuary. The 12S gene marker presented higher species coverage and detection rate than Cyt b. DNA metabarcoding exhibited more representative species identification power than morphology. The findings reported in this study provided a key attempt towards the development of time-efficient and cost-effective ichthyoplankton identification and assessment tool. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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13 pages, 1733 KiB

Open AccessCommunication

First Eastern Mediterranean Record of Xenoligophoroides cobitis, the Only Dactylogyrid Monogenean Infecting Mediterranean Gobies: Just Arrived or Missed the Boat?

by Maarten P. M. Vanhove, Sofia Giakoumi, Dimitris Zogaris, Marcelo Kovačić and Tine Huyse

Diversity 2022, 14(8), 580; https://doi.org/10.3390/d14080580 - 22 Jul 2022

Cited by 2 | Viewed by 1737

Abstract

Gobies and their ectoparasitic monogenean flatworms are promising models for species diversification because of their species richness. Recent decades have seen the discovery of several new species of Gyrodactylus (Monogenea: Gyrodactylidae) on European gobies, mostly in the sand goby lineage and especially in [...] Read more.

Gobies and their ectoparasitic monogenean flatworms are promising models for species diversification because of their species richness. Recent decades have seen the discovery of several new species of Gyrodactylus (Monogenea: Gyrodactylidae) on European gobies, mostly in the sand goby lineage and especially in the eastern Mediterranean. However, the monogenean fauna of other gobies is much less understood. Therefore, we inspected five gobiid species (34 specimens, vouchered, with some representatives sequenced), sampled in Greece, for monogenean ectoparasites. Only specimens of the giant goby, Gobius cobitis, were infected; they harbored Xenoligophoroides cobitis (Monogenea: Dactylogyridae) on their gills. Here, we provide the first record from Greece, and the first ITS rDNA and COI sequences of the representative of this monotypic genus. Additionally, 28S rDNA was sequenced and compared with published data from across its known distribution, suggesting clinal variation. No sister-group for Xenoligophoroides could be proposed, nor could we explain the presence of a single known member of this genus on gobies, due to a lack of sequence data of closely related dactylogyrid monogeneans in public databases. Possible hypotheses include either the ancestral long-term presence on gobiids but “missing the boat” of the diversification events in the “Gobius-lineage”, or a recent host switch from a non-gobiid host. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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13 pages, 879 KiB

Open AccessArticle

Population Genetic Differentiation and Structure of Maruca vitrata (Lepidoptera: Crambidae) in India

by Rashmi Manohar Mahalle, Snehel Chakravarty and Chandra Prakash Srivastava

Diversity 2022, 14(7), 546; https://doi.org/10.3390/d14070546 - 07 Jul 2022

Cited by 4 | Viewed by 1870

Abstract

Maruca vitrata is one of the primary biotic constraints for pigeon pea production in India. The present study assessed the genetic variation and population structure of M. vitrata from diverse agro-ecologies in India using the mitochondrial cytochrome c oxidase I gene. A low [...] Read more.

Maruca vitrata is one of the primary biotic constraints for pigeon pea production in India. The present study assessed the genetic variation and population structure of M. vitrata from diverse agro-ecologies in India using the mitochondrial cytochrome c oxidase I gene. A low number of segregating sites (10), haplotypes (13), nucleotide diversity (0.00136), and overall mean genetic distance (0.0013) were observed among the populations. The negative values of the neutrality tests and unimodal mismatch distribution supported its demographic expansion in the country. The analysis of molecular variance (AMOVA) revealed that the variation among populations or groups was only 13.91%, and the geographical distance did not significantly contribute to the genetic differentiation (R² = 0.0024, p = 0.280). The clustering of haplotypes was also independent of the geographical location. Overall, our results suggest the existence of low genetic variation and high gene flow among populations of M. vitrata in India. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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13 pages, 1026 KiB

Open AccessArticle

DNA Barcoding and Species Delimitation for Dogfish Sharks Belonging to the Squalus Genus (Squaliformes: Squalidae)

by Ailton A. Ariza, Aisni M. C. L. Adachi, Pollyana Roque, Fabio H. V. Hazin, Marcelo Vianna, Matheus M. Rotundo, Sergio M. Delpiani, Juan M. Díaz de Astarloa, Gabriela Delpiani, Claudio Oliveira, Fausto Foresti and Vanessa P. Cruz

Diversity 2022, 14(7), 544; https://doi.org/10.3390/d14070544 - 06 Jul 2022

Cited by 5 | Viewed by 2337

Abstract

The Squalus genus comprises a group of small demersal sharks occurring circumglobally, popularly known as dogfish sharks. This genus exhibits a conserved morphology, thus making correct morphological identification difficult. Considering these taxonomic problems and the scarcity of molecular data, the present study aimed [...] Read more.

The Squalus genus comprises a group of small demersal sharks occurring circumglobally, popularly known as dogfish sharks. This genus exhibits a conserved morphology, thus making correct morphological identification difficult. Considering these taxonomic problems and the scarcity of molecular data, the present study aimed to identify Squalus genus MOTUs, using DNA barcoding for species delimitation via ABGD (automatic barcode gap discovery), PTP (Poisson tree process), and GMYC (general mixed Yule coalescent) employing the mitochondrial COI gene. A total of 69 sequences were generated from samples obtained from the American coast in both the Atlantic and Pacific Oceans. The ABGD analysis was the most conservative among the three applied delimitations, indicating three taxonomic units, while the PTP analysis revealed nine MOTUs, with two conflicting units noted between S. clarkae + S. mitsukurii and S. albicaudus + S. cubensis. The GMYC analysis indicated an excessive division, with S. acanthias and S. mitsukurii subdivided into six MOTUs each and S. blainville, into four. These findings demonstrated that Squalus presents a complex of previously defined species, with misidentified samples deposited in databases leading to difficulties in analyzing the real distribution and diversity of species belonging to this genus. Thus, further efforts to highlight possible new species are recommended. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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12 pages, 2130 KiB

Open AccessArticle

DNA Barcoding of the Market Samples of Single-Drug Herbal Powders Reveals Adulteration with Taxonomically Unrelated Plant Species

by Raju Balaji and Madasamy Parani

Diversity 2022, 14(6), 495; https://doi.org/10.3390/d14060495 - 17 Jun 2022

Cited by 10 | Viewed by 2952

Abstract

Herbal drugs are increasingly becoming a viable alternative to allopathic medicine. Since powdered herbal drugs are more prone to adulteration than intact plant parts, their authentication becomes essential to ensure the safety and efficacy of herbal drugs. This study authenticated 107 single-drug herbal [...] Read more.

Herbal drugs are increasingly becoming a viable alternative to allopathic medicine. Since powdered herbal drugs are more prone to adulteration than intact plant parts, their authentication becomes essential to ensure the safety and efficacy of herbal drugs. This study authenticated 107 single-drug herbal powders, representing 65 species from 60 genera and 35 families, collected from the markets in Tamil Nadu, India. DNA barcoding using the rbcL marker revealed that 58 samples (54%) were authentic, and 49 (46%) were adulterant. About 41% of the adulterant samples were a mixture of more than one species, possibly due to unintentional cross-contamination during processing. In 59% of the adulterant samples, the authentic species was entirely substituted with taxonomically and medicinally unrelated species, 72% of which belonged to different orders and families, while 28% were from other genera. Despite the taxonomic diversity, 20% of adulterant spe, cies had a morphological resemblance to the authentic species. It is not known whether their use as adulterants is intentional. In a detailed study on DNA barcoding of 17 powder samples from Ocimum tenuiflorum, 88% of the samples were authentic. These results indicate that the extent of adulteration is not high in all the species. Approximately, 95% of the samples collected for this study were produced by companies with limited resources and expertise in the unorganized sector. Hence, training them on species identification and providing simple and cost-effective authentication tools will likely reduce adulteration in the market samples. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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17 pages, 3286 KiB

Open AccessArticle

DNA Barcoding of Invertebrates Inhabiting Olive Orchards and Vineyards Accelerates Understudied Mediterranean Biodiversity Assessment

by Barbara Anđelić Dmitrović, Mišel Jelić, Emilia Rota and Lucija Šerić Jelaska

Diversity 2022, 14(3), 182; https://doi.org/10.3390/d14030182 - 28 Feb 2022

Cited by 5 | Viewed by 3056

Abstract

The Mediterranean region has a high but unevenly studied level of invertebrate diversity. Genetic-based methods, such as DNA barcoding and metabarcoding, are proposed for biodiversity assessment; however, their application is not always straightforward. The current state of data available in genetic databases limits [...] Read more.

The Mediterranean region has a high but unevenly studied level of invertebrate diversity. Genetic-based methods, such as DNA barcoding and metabarcoding, are proposed for biodiversity assessment; however, their application is not always straightforward. The current state of data available in genetic databases limits species identification, especially in the case of certain invertebrate groups. The aim of the study was (1) to assess the diversity of seven invertebrate groups, which are potential prey for predatory arthropods, in order to facilitate the analysis of the metabarcoding of trophic interactions and, thus, expand our knowledge on biocontrol potential, and (2) to estimate the representation of local species in BOLD and NCBI GenBank databases. The DNA barcoding results consisting of sequences for 269 specimens, collected in Zadar County, within Mediterranean part of Croatia, were used for species identification and species richness assessment through the comparison of our data with the data available in BOLD and NCBI databases, and by applying species delimitation methods. Previous barcode records enabled Lepidopteran, Hemipteran, Dipteran, and Hymenopteran species identification, while Collembolan and Oligochaetes species numbers were assessed using species delimitation. Our results showed that a high number of species were unique to the study area, especially in the case of Collembolans and Oligochaetes. We confirmed that the studied area is under-researched, which was particularly evident in taxonomically demanding groups, such as Collembolans and Oligochaetes, which are rich in rare endemic species. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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8 pages, 347 KiB

Open AccessArticle

An Incomplete European Barcode Library Has a Strong Impact on the Identification Success of Lepidoptera from Greece

by Peter Huemer and Marko Mutanen

Diversity 2022, 14(2), 118; https://doi.org/10.3390/d14020118 - 07 Feb 2022

Cited by 4 | Viewed by 1841

Abstract

Species identification by means of DNA barcodes depends essentially on the scope and quality of a relevant reference library. The first analysis of a large number (about 600 morphospecies) of southern European Lepidoptera (Greece: Peloponnese) shows both the advantages and disadvantages with regard [...] Read more.

Species identification by means of DNA barcodes depends essentially on the scope and quality of a relevant reference library. The first analysis of a large number (about 600 morphospecies) of southern European Lepidoptera (Greece: Peloponnese) shows both the advantages and disadvantages with regard to a reliable identification of Mediterranean species. We determined 946 DNA barcode sequences from 47 families, of which 929 sequences from 46 families were successfully assigned to a Barcode Index Number (BIN) in the global Barcode of Life Data Systems (BOLD) database. A species level identification for 485 BINs representing 477 Linnaean names was successful. These taxa include 34 new records for Greece. However, 128 BINs (c. 20% of the inventory) could not be attached to a Linnaean name from referenced sequences available in BOLD. Of these BINs, 99 are new and hence represent unique records for BOLD. Intra- and inter-BIN divergences are presented and discussed. An initial and preliminary in-depth analysis of randomly selected species indicates an incomplete DNA barcode library in terms of Linnean taxa, in addition to a considerable number of probably undescribed species. It is therefore strongly recommended that the already advanced European barcode library of Lepidoptera should be supplemented with not-yet-sequenced taxa from the Mediterranean. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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10 pages, 2179 KiB

Open AccessArticle

Molecular Identification of an Invasive Sarotherodon Species from the Atchakpa Freshwater Reservoir (Ouémé River Basin, Benin) and Comparison within S. melanotheron Using COI Markers

by Rodrigue Orobiyi Edéya Pèlèbè, Ibrahim Imorou Toko, Erik Verheyen and Maarten Van Steenberge

Diversity 2021, 13(7), 297; https://doi.org/10.3390/d13070297 - 30 Jun 2021

Cited by 3 | Viewed by 2611

Abstract

The Atchakpa freshwater reservoir (Ouémé Basin, Benin) was found to harbour an unexpected population of a cichlid species that was presumed to be Sarotherodon melanotheron. This species became dominant in the reservoir and became the main fisheries target species. We applied DNA [...] Read more.

The Atchakpa freshwater reservoir (Ouémé Basin, Benin) was found to harbour an unexpected population of a cichlid species that was presumed to be Sarotherodon melanotheron. This species became dominant in the reservoir and became the main fisheries target species. We applied DNA barcoding to identify this population. Besides specimens from the reservoir, we also sequenced S. melanotheron from its native range in Benin at the lower Ouémé and Sô Rivers, and from Lake Nokoué, and Porto-Novo Lagoon. High sequence similarity indicated that all specimens were conspecific. Hence, we cannot exclude that a natural range extension led to the presence of the species in the reservoir. A comparison with sequences from NCBI GenBank confirmed that all samples belonged to the subspecies S. m. melanotheron, which is native to Benin. This comparison also showed that this subspecies was previously introduced in the Philippines. We call for further studies to investigate the socioeconomic, ecological and environmental impacts of the species in the Atchakpa reservoir. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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15 pages, 316 KiB

Open AccessPerspective

Environmental DNA-Based Methods in Biodiversity Monitoring of Protected Areas: Application Range, Limitations, and Needs

by Kathrin Pascher, Vid Švara and Michael Jungmeier

Diversity 2022, 14(6), 463; https://doi.org/10.3390/d14060463 - 09 Jun 2022

Cited by 13 | Viewed by 5180

Abstract

Novel methods for species detection based on collection of environmental DNA (eDNA) are not only important in biodiversity assessment in a scientific context, but are also increasingly being applied in conservation practice. The eDNA-based biodiversity detection methods have significant potential for regular use [...] Read more.

Novel methods for species detection based on collection of environmental DNA (eDNA) are not only important in biodiversity assessment in a scientific context, but are also increasingly being applied in conservation practice. The eDNA-based biodiversity detection methods have significant potential for regular use in biodiversity status assessments and conservation actions in protected areas (PAs) and other effective area-based conservation measures (OECMs) worldwide. Species detection based on DNA from environmental samples, such as water, sediment, soil, air, or organic material, has a broad application scope with precise, comprehensive, and rapid species identification. Here, we provide an overview of the application range of eDNA-based methods for biodiversity monitoring in PAs, evaluate environmental assessments in which this technology has already been implemented for nature conservation, and examine the challenges that can hamper further application in real world practice. Based on the outcomes of two projects, practical experience, and current scientific literature focusing on their application, we conclude that eDNA-based species detection methods provide promising novel approaches that have strong potential as supplement methods, or in some cases even as substitutes for the conventional monitoring methods used for PAs. This advancement is expected to affect decision-making in biodiversity conservation efforts in PAs and OECMs. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

11 pages, 1537 KiB

Open AccessEditor’s ChoiceOpinion

The Future of DNA Barcoding: Reflections from Early Career Researchers

by Danielle M. Grant, Ole Bjørn Brodnicke, Ann M. Evankow, André O. Ferreira, João T. Fontes, Aslak Kappel Hansen, Mads Reinholdt Jensen, Tuğba Ergül Kalaycı, Alexandra Leeper, Shalaka Kiran Patil, Sebastian Prati, Anna Reunamo, Aradhana J. Roberts, Rajesh Shigdel, Valentina Tyukosova, Mika Bendiksby, Rakel Blaalid, Filipe O. Costa, Peter M. Hollingsworth, Elisabeth Stur and Torbjørn Ekrem Show full author list Hide full author list

Diversity 2021, 13(7), 313; https://doi.org/10.3390/d13070313 - 09 Jul 2021

Cited by 27 | Viewed by 9890

Abstract

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, [...] Read more.

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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