Comprehensive DNA barcodes for species identification and discovery of cryptic diversity in mayfly larvae from South Korea: Implications for freshwater ecosystem biomonitoring

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

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Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽

10.1139/g06-025 ◽

2006 ◽

Vol 49 (7) ◽

pp. 851-854 ◽

Cited By ~ 48

Author(s):

Mehrdad Hajibabaei ◽

Gregory AC Singer ◽

Donal A Hickey

Keyword(s):

New Species ◽

Cryptic Species ◽

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Primate Species ◽

Dna Barcodes ◽

Global Biodiversity ◽

Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

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Freshwater Biodiversity Platform (FBP): an Integrated Information Management System of Freshwater Ecosystem for the Conservation and Sustainable Use of Biodiversity

Biodiversity Information Science and Standards ◽

10.3897/biss.2.26490 ◽

2018 ◽

Vol 2 ◽

pp. e26490

Author(s):

Ye-seul Kwan ◽

Gi Cheol Lee ◽

Sang Myeon Park ◽

Ji Hae Lee ◽

Jeong Su Oh

Keyword(s):

South Korea ◽

Management System ◽

Sustainable Use ◽

Information Management System ◽

Freshwater Ecosystem ◽

Freshwater Species ◽

Freshwater Biodiversity ◽

Biodiversity Data ◽

Biological Resources ◽

Integrated Information

Since the Nagoya Protocol on Access to genetic resources and Benefit Sharing (ABS) came into force in 2014, the conservation and assurance of national biodiversity has been internationally stressed. The Government of South Korea is exercising significant efforts to integrate and manage the information pertaining to biological resources in line with this global trend. However, connecting and sharing biodiversity data has certain challenges because the existing databases and information systems are being operated using different standards. In the present study, we established an integrated management system for freshwater biodiversity information, the Freshwater Biodiversity Platform (FBP), to support the conservation and sustainable use of biodiversity. This platform allows the management of various types of biodiversity data, such as occurrences, habitats and genetics, for freshwater species inhabiting South Korea. The data fields are based on a global biodiversity data standard, Darwin Core, and national biodiversity standards of South Korea in order to share our data more efficiently, both nationally and internationally. It is important to note that the platform deals with information related to the utilization of biological resources as well as information representing the national biodiversity. We have collected bibliographical data, such as papers and patents, from databases, including information on the use of biological resources. The data have been refined by applying a national species list of South Korea and ontology terms in (MeSH) to compile valuable information for biological industries. Furthermore, our platform is open source and is compatible with multiple language packs to facilitate the availability of biodiversity data for other countries and institutions. Currently, the Freshwater Biodiversity Platform is being used to collect and standardize various types of existing freshwater biodiversity data to build foundations for data management. Based on these data, we will improve the platform by adding new systems that can analyze and release data for public access. This platform will provide integrated information on freshwater species from the Korean Peninsula to the world and contribute to the conservation and sustainable use of biological resources.

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BarcodingR: an integrated r package for species identification using DNA barcodes

Methods in Ecology and Evolution ◽

10.1111/2041-210x.12682 ◽

2016 ◽

Vol 8 (5) ◽

pp. 627-634 ◽

Cited By ~ 19

Author(s):

Ai‐bing Zhang ◽

Meng‐di Hao ◽

Cai‐qing Yang ◽

Zhi‐yong Shi

Keyword(s):

Species Identification ◽

R Package ◽

Dna Barcodes

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The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2012.07.033 ◽

2012 ◽

Vol 65 (2) ◽

pp. 765-773 ◽

Cited By ~ 12

Author(s):

Melanie Lou ◽

G. Brian Golding

Keyword(s):

Species Identification ◽

Statistical Approach ◽

Dna Barcodes ◽

Subdivided Populations

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Who is biting you? DNA barcodes reveal cryptic diversity in human-biting black flies (Diptera: Simuliidae)

Acta Tropica ◽

10.1016/j.actatropica.2019.05.001 ◽

2019 ◽

Vol 196 ◽

pp. 22-29 ◽

Cited By ~ 2

Author(s):

Panya Jomkumsing ◽

Ubon Tangkawanit ◽

Komgrit Wongpakam ◽

Pairot Pramual

Keyword(s):

Black Flies ◽

Cryptic Diversity ◽

Dna Barcodes

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Using DNA barcodes to assess identity and diversity of Dendropsophus minutus: Failure?

Zootaxa ◽

10.11646/zootaxa.1691.1.3 ◽

2008 ◽

Vol 1691 (1) ◽

pp. 67 ◽

Cited By ~ 3

Author(s):

M. ALEX SMITH

Keyword(s):

Cytochrome C ◽

Small Group ◽

Cytochrome C Oxidase ◽

Species Identification ◽

Mitochondrial Gene ◽

Dna Barcode ◽

Gene Region ◽

Dna Barcodes ◽

Taxonomic Groups

The 5' end (Folmer or Barcode region) of cytochrome c oxidase 1 (CO1) has been proposed as the gene region of choice for a standardized animal DNA barcode (Hebert et al. 2003). Concerns have been raised regarding the decision to utilize this particular mitochondrial gene region as a barcode. Nevertheless, widely divergent taxonomic groups have reported success using CO1 for both species identification and discovery. The utility of CO1 for barcoding amphibians was raised early on (Vences, et al. 2005) and concerns for this group were reported widely (Waugh 2007)—although some considered that the reporting of the concerns outstripped the data that had been analyzed at that point (Smith et al. 2008). Indeed, our analysis of CO1 for a small group of Holarctic amphibians was neither more difficult to generate nor to analyze than for other groups where we have utilized the technique.

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