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Shen, Y.-Y., Chen, X., & Murphy, R. W. (2013). Assessing dna barcoding as a tool for species identification and data quality control. PLoS ONE, 8(2), e57125. 
Added by: Admin (06 Jan 2014 18:23:10 UTC)
Resource type: Journal Article
BibTeX citation key: Shen2013
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Categories: General
Keywords: Emydidae, Emys orbicularis, Emys trinacris, Genetik - genetics, Geoemydidae, Indotestudo forstenii, Rhinoclemmys diademata, Rhinoclemmys melanosterna, Rhinoclemmys punctularia, Schildkröten - turtles + tortoises, Stigmochelys pardalis, Systematik - taxonomy, Testudinidae, Testudo graeca
Creators: Chen, Murphy, Shen
Collection: PLoS ONE
Views: 3/635
Views index: 17%
Popularity index: 4.25%
Abstract     
Testudinidae In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing. No particular level of divergence can serve to identify species. Rather, such data can point to taxa that need additional study. K2P distances between Rhinoclemmys diademata, R. punctularia, and R. melanosterna range from 1.4% to 2.3%. The low levels of divergence indicate either recent divergences or perhaps a taxon-specific slowing of the molecular clock. More importantly, only one sequence is available for each species and the result indicates a need for further study using more samples. Similarly, newly described Emys trinacris forms an independent lineage that is the sister group of E. orbicularis. However, interspecific divergences are very low (0.7–2.3%) and intraspecific divergences of E. orbicularis range from 0.0 to 2.0%. Many currently recognized taxonomic names are composites of cryptic species complexes . Testudo graeca (six subspecies) and Geochelone pardalis (two subspecies) have complex relationships. Intraspecific divergence in the former species ranges from 0.0 to 8.1% and in the latter from 0.0 to 12.4%. Thus, these two species complexes require further attention as they may be polytypic. DNA barcoding has accelerated the rates of taxonomic discovery and descriptions to meet or exceed rates of biodiversity loss . In contrast to great variation, 16 samples of Indotestudo forstenii share one haplotype. This endangered species has a critically low level of diversity necessitating that greater attention must be paid to its conservation status.
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