scholarly journals Imagining Sisyphus happy: DNA barcoding and the unnamed majority

2016 ◽  
Vol 371 (1702) ◽  
pp. 20150329 ◽  
Author(s):  
Mark Blaxter
Keyword(s):  
Dna Barcoding ◽  
Time Frame ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Species Definition ◽  
Operational Taxonomic Units ◽  
The Earth ◽  
Biodiversity Science ◽  
Reasonable Time Frame

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on ‘charismatic megabionts’: larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species. This article is part of the themed issue ‘From DNA barcodes to biomes’.

DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae)

2014 ◽  
Vol 104 (4) ◽  
pp. 486-493 ◽  
Author(s):  
Y.J. Wang ◽  
Z.H. Li ◽  
S.F. Zhang ◽  
Z. Varadínová ◽  
F. Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Morphological Identification ◽  
Pest Species ◽  
Dna Barcodes ◽  
Molecular Approaches ◽  
Worldwide Distribution ◽  
Haplotype Networks ◽  
Stored Product Pest ◽  
The Usa

AbstractSeveral species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.

scholarly journals Contribution to the knowledge of the beetle fauna (Insecta, Coleoptera) of Malta: new records of seven species with supporting DNA barcodes

Check List ◽  
2021 ◽  
Vol 17 (5) ◽  
pp. 1443-1449
Author(s):  
Clare Marie Mifsud ◽  
Noel Vella ◽  
Adriana Vella
Keyword(s):  
Dna Barcoding ◽  
New Records ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Central Mediterranean ◽  
Maltese Islands

We report the presence of seven species of Coleoptera newly found on the Maltese Islands in the central Mediterranean. The first species records from the Maltese Islands include: Ancylopus melanocephalus (Olivier, 1808) (Endomychidae), Aplidia transversa (Fabricius, 1801) (Scarabaeidae), Cercyon quisquilius (Linnaeus, 1761) (Hydrophilidae), Hyperaspis duvergeri Fürsch, 1985 (Coccinellidae), Lebia cruxminor (Linnaeus, 1758) (Carabidae), Smicronyx pauperculus Wollaston, 1864 (Curculionidae), and Oxytelus sculptus Gravenhorst, 1806 (Staphylinidae). The morphological identification of each newly reported species was also confirmed through DNA barcoding.

scholarly journals Unravelling the hidden biodiversity – the establishment of DNA barcodes of fish-parasitizing Acanthocephala Koehlreuther, 1771 in view of taxonomic misidentifications, intraspecific variability and possible cryptic species

Parasitology ◽  
2020 ◽  
Vol 147 (13) ◽  
pp. 1499-1508
Author(s):  
Susanne Reier ◽  
Helmut Sattmann ◽  
Thomas Schwaha ◽  
Hans-Peter Fuehrer ◽  
Elisabeth Haring
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Species Level ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Taxonomic Assignment ◽  
Obligate Parasites ◽  
Intraspecific Variations

AbstractAcanthocephalans are obligate parasites of vertebrates, mostly of fish. There is limited knowledge about the diversity of fish-parasitizing Acanthocephala in Austria. Seven determined species and an undetermined species are recorded for Austrian waters. Morphological identification of acanthocephalans remains challenging due to their sparse morphological characters and their high intraspecific variations. DNA barcoding is an effective tool for taxonomic assignment at the species level. In this study, we provide new DNA barcoding data for three genera of Acanthocephala (Pomphorhynchus Monticelli, 1905, Echinorhynchus Zoega in Müller, 1776 and Acanthocephalus Koelreuter, 1771) obtained from different fish species in Austria and provide an important contribution to acanthocephalan taxonomy and distribution in Austrian fish. Nevertheless, the taxonomic assignment of one species must remain open. We found indications for cryptic species within Echinorhynchus cinctulus Porta, 1905. Our study underlines the difficulties in processing reliable DNA barcodes and highlights the importance of the establishment of such DNA barcodes to overcome these. To achieve this goal, it is necessary to collect and compare material across Europe allowing a comprehensive revision of the phylum in Europe.

scholarly journals Sand fly identification and screening for Leishmania spp. in six provinces of Thailand

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Orawan Phuphisut ◽  
Chanyapat Nitatsukprasert ◽  
Nattaphol Pathawong ◽  
Boonsong Jaichapor ◽  
Arissara Pongsiri ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Distinct Species ◽  
Morphological Characters ◽  
Sand Fly ◽  
Morphological Identification ◽  
Sand Flies ◽  
Operational Taxonomic Units ◽  
Species Complexes ◽  
Human Leishmaniasis ◽  
Leishmania Spp

Abstract Background Phlebotomine sand flies are vectors of Leishmania spp. At least 27 species of sand flies have been recorded in Thailand. Although human leishmaniasis cases in Thailand are mainly imported, autochthonous leishmaniasis has been increasingly reported in several regions of the country since 1999. Few studies have detected Leishmania infection in wild-caught sand flies, although these studies were carried out only in those areas reporting human leishmaniasis cases. The aim of this study was therefore to identity sand fly species and to investigate Leishmania infection across six provinces of Thailand. Methods Species of wild-caught sand flies were initially identified based on morphological characters. However, problems identifying cryptic species complexes necessitated molecular identification using DNA barcoding in parallel with identification based on morphological characters. The wild-caught sand flies were pooled and the DNA isolated prior to the detection of Leishmania infection by a TaqMan real-time PCR assay. Results A total of 4498 sand flies (1158 males and 3340 females) were caught by trapping in six provinces in four regions of Thailand. The sand flies were morphologically classified into eight species belonging to three genera (Sergentomyia, Phlebotomus and Idiophlebotomus). Sergentomyia iyengari was found at all collection sites and was the dominant species at most of these, followed in frequency by Sergentomyia barraudi and Phlebotomus stantoni, respectively. DNA barcodes generated from 68 sand flies allowed sorting into 14 distinct species with 25 operational taxonomic units, indicating a higher diversity (by 75%) than that based on morphological identification. Twelve barcoding sequences could not be assigned to any species for which cytochrome c oxidase subunit I sequences are available. All tested sand flies were negative for Leishmania DNA. Conclusions Our results confirm the presence of several sand fly species in different provinces of Thailand, highlighting the importance of using DNA barcoding as a tool to study sand fly species diversity. While all female sand flies tested in this study were negative for Leishmania, the circulation of Leishmania spp. in the investigated areas cannot be ruled out. Graphical abstract

DNA Barcoding of Simulium asakoae (Diptera: Simuliidae) From Northern Thailand

2020 ◽  
Vol 57 (5) ◽  
pp. 1675-1678 ◽  
Author(s):  
Van Lun Low ◽  
Wichai Srisuka ◽  
Atiporn Saeung ◽  
Tiong Kai Tan ◽  
Zubaidah Ya’cob ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Genetic Divergence ◽  
Species Complex ◽  
Morphological Variability ◽  
Single Species ◽  
Genetic Distances ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Barcode Gap

Abstract Previous studies suggested the presence of species complex in the so-called Simulium asakoae Takaoka & Davies (Diptera: Simuliidae) in Thailand due to its high morphological variability and genetic divergence. To investigate whether the true S. asakoae is present in Thailand, we performed a detailed morphological identification of S. asakoae and compared its DNA barcodes with the morphospecies S. asakoae from Myanmar and the typical S. asakoae from Malaysia. Phylogenetic analysis revealed the Thai materials analyzed in this study were indeed genetically similar with those from Myanmar and Malaysia, though genetic distances 0–2.27% were observed. We tentatively regard this divergence as intraspecific variation, and the automatic barcode gap discovery analysis further supports them as a single species.

Validation of Heterocerus heydeni Kuwert, 1890 based on morphology and DNA barcoding, with notes on the problems of classification of the Heteroceridae (Coleoptera)

Zootaxa ◽  
2019 ◽  
Vol 4614 (1) ◽  
pp. 160
Author(s):  
STANISLAV V. LITOVKIN ◽  
ALEXEY S. SAZHNEV ◽  
FEDOR JR ČIAMPOR
Keyword(s):  
Central Asia ◽  
Dna Barcoding ◽  
Morphological Characters ◽  
European Part ◽  
Junior Synonym ◽  
Data Systems ◽  
Dna Barcodes ◽  
Life Data ◽  
European Part Of Russia

New taxonomic data on mud-loving beetles are provided based on morphological characters and DNA barcoding. Heterocerus heydeni Kuwert, 1890 was previously considered a junior synonym of H. flexuosus Stephens, 1828, but we support the validity of the species and restore the name. H. heydeni is redescribed, based on material from Central Asia and European part of Russia. Specimens of H. hauseri Kuwert, 1893 were also studied, suggesting it as a possible junior synonym of H. heydeni. We provide new DNA barcodes for H. flexuosus and Augyles cf. flavidus and comment on Heterocerus barcode data published in Barcode Of Life Data Systems (BOLD). 

scholarly journals Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue

2012 ◽  
Vol 12 (3) ◽  
pp. 301-308 ◽  
Author(s):  
Luis Anderson Ribeiro Leite
Keyword(s):  
Mitochondrial Dna ◽  
Dna Barcoding ◽  
Nuclear Genome ◽  
Short Sequence ◽  
Dna Barcodes ◽  
Molecular Tools ◽  
Points Of View ◽  
Living Organisms ◽  
As If

Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. When these paralogous sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were orthologous sequences. In this contribution the different points of view regarding the implications of mitochondrial pseudogenes for entomology are reviewed and discussed. A discussion of the problem from a historical and conceptual perspective is presented as well as a discussion of strategies to keep these nuclear mtDNA copies out of sequence analyzes.

Application of DNA Barcoding in the Classification of Grasshoppers (Orthoptera: Acridoidea)—A Case Study of grasshoppers from Hebei Province, China

Zootaxa ◽  
2018 ◽  
Vol 4497 (1) ◽  
pp. 99 ◽  
Author(s):  
LI-PING CHEN ◽  
YA-GE CHANG ◽  
JIAN LI ◽  
JIAN-MEI WANG ◽  
JIN-LIN LIU ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Animal Husbandry ◽  
Hebei Province ◽  
Sequence Difference ◽  
Morphological Identification ◽  
Difference Threshold ◽  
Cox1 Gene ◽  
Operational Taxonomic Units ◽  
Relationship Of ◽  
Barcoding Technology

Grasshoppers (Orthoptera: Acridoidea) are the main pests in agriculture, animal husbandry and forestry, and some species of grasshoppers can cause serious disaster. Taxonomy is the basis of pest control. Traditional morphological identification is time-consuming and laborious. It may be due to the existence of cryptic species or the limited number of morphologists, making the identification extremely unstable. In recent years, with the development of molecular systematics, DNA barcoding technology has been applied to environment, ecology, quarantine and so on. This study focuses on testing the feasibility of DNA barcoding in the species identification for superfamily Acridoidea. Sequences of the cox1 gene were obtained from 245 individuals of 43 species of Acridoidea and one species of Tetrigoidea as outgroup from Hebei Province. Phylogenetic, genetic distance and sequence difference threshold analyses using the Maximum Likelihood (ML), Automatic Barcode Gap Discovery (ABGD) and Molecular Defined Operational Taxonomic Units (MOTU) methods, respectively, were performed for obtained sequences and the 139 additional sequences of 21 species downloaded from GenBank. The results have shown that 40, 33, and 35 species among the 48 species are consistent with the traditional morphological classification based on the phylogenetic tree, ABGD and MOTU results, respectively and the DNA barcoding technology is very efficient and helpful for identifying the species of the superfamily Acridoidea; however, the morphological approach is still playing a key role in the species identifications. It also indicates that the cox1 gene is suitable for the phylogeny of genera and species level, but it is not suitable for the phylogenetic relationship of the advanced taxa such as families. 

scholarly journals Clinical correlates of anti-SARS-CoV-2 antibody profiles in Spanish COVID-19 patients from a high incidence region

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Robert Markewitz ◽  
Antje Torge ◽  
Klaus-Peter Wandinger ◽  
Daniela Pauli ◽  
Andre Franke ◽  
...  
Keyword(s):  
Case Fatality ◽  
Time Frame ◽  
Epidemic Outbreak ◽  
Sample Collection ◽  
Rt Pcr ◽  
High Incidence ◽  
Duration Of Hospitalization ◽  
Reasonable Time Frame ◽  
Support Treatment ◽  
Diagnostic And Prognostic Value

AbstractLaboratory testing for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consists of two pillars: the detection of viral RNA via rt-PCR as the diagnostic gold standard in acute cases, and the detection of antibodies against SARS-CoV-2. However, concerning the latter, questions remain about their diagnostic and prognostic value and it is not clear whether all patients develop detectable antibodies. We examined sera from 347 Spanish COVID-19 patients, collected during the peak of the epidemic outbreak in Spain, for the presence of IgA and IgG antibodies against SARS-CoV-2 and evaluated possible associations with age, sex and disease severity (as measured by duration of hospitalization, kind of respiratory support, treatment in ICU and death). The presence and to some degree the levels of anti-SARS-CoV-2 antibodies depended mainly on the amount of time between onset of symptoms and the collection of serum. A subgroup of patients did not develop antibodies at the time of sample collection. Compared to the patients that did, no differences were found. The presence and level of antibodies was not associated with age, sex, duration of hospitalization, treatment in the ICU or death. The case-fatality rate increased exponentially with older age. Neither the presence, nor the levels of anti-SARS-CoV-2 antibodies served as prognostic markers in our cohort. This is discussed as a possible consequence of the timing of the sample collection. Age is the most important risk factor for an adverse outcome in our cohort. Some patients appear not to develop antibodies within a reasonable time frame. It is unclear, however, why that is, as these patients differ in no respect examined by us from those who developed antibodies.

Is Cauda Equina Syndrome Being Treated Within the Recommended Time Frame?

Neurosurgery ◽  
2011 ◽  
Vol 68 (6) ◽  
pp. 1520-1526 ◽  
Author(s):  
Robert T. Arrigo ◽  
Paul Kalanithi ◽  
Maxwell Boakye
Keyword(s):  
Cauda Equina Syndrome ◽  
Medical Condition ◽  
Cauda Equina ◽  
Time Frame ◽  
Current Guideline ◽  
International Classification Of Disease ◽  
Lumbar Disk ◽  
Urgent Surgery ◽  
Spine Surgeon

Abstract BACKGROUND: Cauda equina syndrome (CES) is a rare but devastating medical condition requiring urgent surgery to halt or reverse neurological compromise. Controversy exists as to how soon surgery must be performed after diagnosis, and clinical and medicolegal factors make this question highly relevant to the spine surgeon. It is unclear from the literature how often CES patients are treated within the recommended time frame. OBJECTIVE: To determine whether CES patients are being treated in compliance with the current guideline of surgery within 48 hours and to assess incidence, demography, comorbidities, and outcome measures of CES patients. METHODS: We searched the 2003 to 2006 California State Inpatient Databases to identify degenerative lumbar disk disorder patients surgically treated for CES. An International Classification of Disease, ninth revision, clinical modification, diagnosis code was used to identify CES patients with advanced disease. RESULTS: The majority (88.74%) of California's CES patients received surgery within the recommended 48-hour window after diagnosis. The incidence of CES in surgically treated degenerative lumbar disk patients was 1.51% with an average of 397 cases per year in California. CES patients had worse outcomes and used more healthcare resources than other surgically treated degenerative lumbar disk patients; this disparity was more pronounced for patients with advanced CES. CES patients treated after 48 hours had 3 times the odds of a nonroutine discharge as patients treated within 48 hours (odds ratio = 3.082; P < .001). CONCLUSION: In California, patients are being treated within the recommended 48-hour time frame.

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