Cyst morphology of large branchiopod crustaceans (Anostraca, Notostraca, Laevicaudata, Spinicaudata) in western Poland

Czyż, Michał; Woliński, Paweł; Gołdyn, Bartłomiej

doi:10.1515/biolet-2017-0006

Cited by 5 publications

(1 citation statement)

References 18 publications

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“…At present, DNA-based community analyses have offered some alternatives to the traditional methods of species identification, and metabarcoding is one of the most promising techniques to understand taxon diversity. This method enables species detection from a bulk of samples, e.g., environmental samples, gut or faecal contents [ 36 ], and it might be a good solution to the problems with proper species identification in the case of cryptic species (e.g., [ 71 ]) or poor species-specificity of cyst morphology and biometry, which is used when no active specimens are present (e.g., [ 72 ]). Metabarcoding is based on PCR amplification followed by deep sequencing of homologous gene regions.…”

Section: Discussionmentioning

confidence: 99%

Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too “universal”?

Mioduchowska¹,

Czyż²,

Gołdyn³

et al. 2018

PLoS ONE

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The cytochrome c oxidase subunit I (cox1) gene is the main mitochondrial molecular marker playing a pivotal role in phylogenetic research and is a crucial barcode sequence. Folmer’s “universal” primers designed to amplify this gene in metazoan invertebrates allowed quick and easy barcode and phylogenetic analysis. On the other hand, the increase in the number of studies on barcoding leads to more frequent publishing of incorrect sequences, due to amplification of non-target taxa, and insufficient analysis of the obtained sequences. Consequently, some sequences deposited in genetic databases are incorrectly described as obtained from invertebrates, while being in fact bacterial sequences. In our study, in which we used Folmer’s primers to amplify COI sequences of the crustacean fairy shrimp Branchipus schaefferi (Fischer 1834), we also obtained COI sequences of microbial contaminants from Aeromonas sp. However, when we searched the GenBank database for sequences closely matching these contaminations we found entries described as representatives of Gastrotricha and Mollusca. When these entries were compared with other sequences bearing the same names in the database, the genetic distance between the incorrect and correct sequences amplified from the same species was c.a. 65%. Although the responsibility for the correct molecular identification of species rests on researchers, the errors found in already published sequences data have not been re-evaluated so far. On the basis of the standard sampling technique we have estimated with 95% probability that the chances of finding incorrectly described metazoan sequences in the GenBank depend on the systematic group, and variety from less than 1% (Mollusca and Arthropoda) up to 6.9% (Gastrotricha). Consequently, the increasing popularity of DNA barcoding and metabarcoding analysis may lead to overestimation of species diversity. Finally, the study also discusses the sources of the problems with amplification of non-target sequences.

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Section: Discussionmentioning

confidence: 99%