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Diversity
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DNA Barcoding for Biodiversity
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DNA Barcoding for Biodiversity

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

Deadline for manuscript submissions: closed (30 September 2018) | Viewed by 27616

Special Issue Editor

Dr. Andrea Galimberti

E-Mail Website
Guest Editor
ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126-I Milano, Italy
Interests: integrative taxonomy; DNA barcoding; DNA metabarcoding; metazoans; diet analysis; food authenticity; high-throughput sequencing; ecosystem services
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The reliability of DNA barcoding relies on three main pillars which are i) a strict standardization of analytical procedures, ii) an efficient computerization of sequence data through accurate bioinformatics approaches and iii) an integration of different disciplines to provide solid reference publicly available databases for species assignation.

This special issue is devoted to the advances in DNA barcoding to address all the aspects related to biodiversity with the main goals of i) elucidating the analytical and bioinformatics advances currently available for this molecular approach; ii) defining the new frontiers of application in the context of biodiversity and biomonitoring and iii) encouraging the population of public genetic archives to also include those neglected groups of animal and plant biodiversity.

I cordially invite researchers working actively in these fields to submit their original research manuscripts to this special issue.

Dr. Andrea Galimberti
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

  • Biodiversity
  • Biomonitoring
  • Ecosystem services
  • High Throughput Sequencing
  • Environmental matrices
  • Diet analysis
  • Integrative taxonomy

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Published Papers (5 papers)

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Research

10 pages, 6901 KiB  
Article
Effectiveness of DNA Barcoding in Speyeria Butterflies at Small Geographic Scales
by Ryan I. Hill, Maya Ganeshan, Lindsay Wourms, Marcus R. Kronforst, Sean P. Mullen and Wesley K. Savage
Diversity 2018, 10(4), 130; https://doi.org/10.3390/d10040130 - 14 Dec 2018
Cited by 11 | Viewed by 4442
Abstract
North American Speyeria butterflies are a group of conservation concern and a challenge to butterfly systematists. Establishing species delimitation and evolutionary relationships among Speyeria has proven difficult due to the polytypic nature of many species, coupled with the similarity of wing patterns of [...] Read more.
North American Speyeria butterflies are a group of conservation concern and a challenge to butterfly systematists. Establishing species delimitation and evolutionary relationships among Speyeria has proven difficult due to the polytypic nature of many species, coupled with the similarity of wing patterns of sympatric species. Recent molecular work has found not all Speyeria species to be monophyletic, which could be explained by improper species definitions, incomplete lineage sorting, or ongoing hybridization and introgression. However, these studies involved broad geographic sampling where molecular markers such as the DNA barcode may be especially subject to incomplete lineage sorting. Here we focus on a more local scale, analyzing the mitochondrial gene cytochrome oxidase subunit I (CoI) to test whether this marker recovers four sympatric Speyeria species: adiaste (W. H. Edwards, 1864), callippe (Boisduval, 1852), coronis (Behr, 1864), and zerene (Boisduval, 1852), in the greater San Francisco Bay Area. We found that CoI works well to separate all four species. Subspecies were less well-defined, with the S. adiaste subspecies clustering separately, but more mixed for the S. zerene and S. callippe subspecies. Overall, our analyses illustrate the utility of the DNA barcode for separating the Speyeria species and suggest further studies to investigate different geographic scales in order to elucidate genetic diversity patterns in this genus in North America. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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14 pages, 2956 KiB  
Article
DNA Barcoding and Taxonomic Challenges in Describing New Putative Species: Examples from Sootywing and Cloudywing Butterflies (Lepidoptera: Hesperiidae)
by Edward Pfeiler
Diversity 2018, 10(4), 111; https://doi.org/10.3390/d10040111 - 15 Oct 2018
Cited by 7 | Viewed by 5302
Abstract
DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on [...] Read more.
DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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13 pages, 1855 KiB  
Article
cpDNA Barcoding by Combined End-Point and Real-Time PCR Analyses to Identify and Quantify the Main Contaminants of Oregano (Origanum vulgare L.) in Commercial Batches
by Alessandro Vannozzi, Margherita Lucchin and Gianni Barcaccia
Diversity 2018, 10(3), 98; https://doi.org/10.3390/d10030098 - 4 Sep 2018
Cited by 8 | Viewed by 4763
Abstract
Oregano (Origanum vulgare L.) is a flowering plant that belongs to the mint family (Lamiaceae). It is used as a culinary herb and is often commercialized as a fine powder or a mixture of small fragments of dried leaves, which makes morphological [...] Read more.
Oregano (Origanum vulgare L.) is a flowering plant that belongs to the mint family (Lamiaceae). It is used as a culinary herb and is often commercialized as a fine powder or a mixture of small fragments of dried leaves, which makes morphological recognition difficult. Like other commercial preparations of drugs and spices, the contamination of oregano mixtures with vegetable matter of lower quality, or the use of generic misleading names, are frequent and stress the need to develop a molecular traceability system to easily, quickly, and cheaply unveil these scams. The DNA-based analytical approach known as cpDNA barcoding is particularly suited for fraud identification in crop plant species (fresh products and food derivatives), and it represents a promising traceability tool as an alternative or complement to traditional detection methods. In the present study, we used a combined approach based on both qualitative and quantitative cpDNA barcoding with end-point and real-time polymerase chain reaction (PCR) analyses to assess the type and degree of contamination in commercial batches of common oregano. In a preliminary qualitative screening, we amplified, cloned, and sequenced a number of universal trnH-psbA- and trnL-barcoded regions, to identify the main contaminants in the samples under investigation. On the basis of these findings, we then developed and validated a species-specific and sequence-targeted method of testing for the quantitative assessment of contaminants, using trnL gene intron assays. Surprisingly, the results obtained in our case study indicated an almost total absence of O. vulgare in the commercial batches analyzed, but a high presence of group I contaminants (Satureja pilosa Velen.), and a moderate presence of group II contaminants (Cistus lanidifer L./Cistus albidus). Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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18 pages, 1496 KiB  
Article
DNA Barcoding Highlights Cryptic Diversity in the New Zealand Psylloidea (Hemiptera: Sternorrhyncha)
by Francesco Martoni, Simon Bulman, Andrew Pitman, Gary Taylor and Karen Armstrong
Diversity 2018, 10(3), 50; https://doi.org/10.3390/d10030050 - 22 Jun 2018
Cited by 31 | Viewed by 5844
Abstract
The insect superfamily Psylloidea (Hemiptera) includes economically important biocontrol agents, pests and plant pathogen vectors, for which a rapid and accurate identification is fundamental for international biosecurity. Australasia is a hot spot for psyllid diversity, but previous species assessments in the region were [...] Read more.
The insect superfamily Psylloidea (Hemiptera) includes economically important biocontrol agents, pests and plant pathogen vectors, for which a rapid and accurate identification is fundamental for international biosecurity. Australasia is a hot spot for psyllid diversity, but previous species assessments in the region were largely based on morphology and host plant association. Morphological identification of psyllids remains challenging for a wide number of species and for juvenile insects, while a robust molecular framework for identification is not available. Consequently, knowledge of psyllid biology is compromised. Here, incorporating morphological evidence and host plant associations, insects collected from almost 600 primarily New Zealand locations were linked to 67 previously described species. By applying species delimitation methods including GYMC (General Mixed Yule–Coalescent method), PTP (Poisson Tree Processes), mPTP (multi–rate Poisson Tree Processes) and ABGD (Automatic Barcode Gap Discovery) to a dataset composed of 425 cytochrome oxidase I (COI) DNA barcode sequences, further cryptic diversity was revealed among the psyllid collection; more than 20 undescribed taxa are reported here for the first time, resulting in a total of 90 taxa across 21 genera and six families included in this study. Our improved understanding of psyllid diversity in New Zealand revealed new plant host-psyllid associations and geographical variation. The DNA barcode resource will enable future studies of psyllid ecology and more accurate, rapid identifications of psyllids that pose biosecurity threats to Australasia. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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23 pages, 37686 KiB  
Article
Ants in Australia’s Monsoonal Tropics: CO1 Barcoding Reveals Extensive Unrecognised Diversity
by Stefanie K. Oberprieler, Alan N. Andersen and Craig C. Moritz
Diversity 2018, 10(2), 36; https://doi.org/10.3390/d10020036 - 14 May 2018
Cited by 13 | Viewed by 6438
Abstract
The Australian monsoonal tropics (AMT) is a significant biodiversity hotspot, and recent genetic studies of several vertebrate groups have revealed its level of diversity is far higher than previously thought. However, the extent to which this applies to the AMT’s insect fauna, which [...] Read more.
The Australian monsoonal tropics (AMT) is a significant biodiversity hotspot, and recent genetic studies of several vertebrate groups have revealed its level of diversity is far higher than previously thought. However, the extent to which this applies to the AMT’s insect fauna, which represents most AMT faunal species, remains unknown. Here we examine the extent of unrecognised diversity in the AMT’s ecologically dominant insect group, ants. We used CO1 barcoding in combination with morphological variation and geographic distribution to explore diversity within seven taxa currently recognised as single species occurring throughout the AMT: one species of Papyrius Shattuck 1992, one of Iridomyrmex Mayr 1862, two from the Cardiocondyla nuda (Mayr 1866) group, and three from the Camponotus novaehollandiae (Mayr 1870) group. We found six of the seven target species each to represent several species, based on a combination of CO1 divergence (ranging up to 13%), morphological differentiation and geographic distribution. Our findings indicate that the levels of diversity and endemism of the AMT ant fauna are far higher than currently realised. We urge the need for further research in insect biodiversity in the AMT, both for a better understanding of the evolution of its remarkable biota, and as a basis for improved conservation planning. Full article
(This article belongs to the Special Issue DNA Barcoding for Biodiversity)
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