Title
Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case
Author
Faculty/Department
Faculty of Sciences. Biology
Publication type
article
Publication
Subject
Biology
Human medicine
Source (journal)
PLoS ONE
Volume/pages
7(2012) :2 , p. e31581,1-e31581,8
ISSN
1932-6203
Article Reference
e31581
Carrier
E-only publicatie
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
Abstract
We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error <0.05. According to the expectations, when we used this threshold for the identification of 188 independently collected tephritids, less than 5% of queries with a distance query-best match below the threshold were misidentified. Ad hoc thresholds can be calculated for each particular reference library of DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.
Full text (open access)
https://repository.uantwerpen.be/docman/irua/9ce8d6/1721.pdf
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