Article

Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case

Royal Museum for Central Africa, Tervuren, Belgium.
PLoS ONE (Impact Factor: 3.23). 02/2012; 7(2):e31581. DOI: 10.1371/journal.pone.0031581
Source: PubMed

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.

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Available from: Massimiliano Virgilio
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    • "It is particularly important to resolve invasive agricultural pest species, because inadequate morphological/molecular characterisation of the species might have serious economic consequences , resulting in inept ecological models and/or pest control strategies (Virgilio et al. 2013, Vaníčková et al. 2014). The need to develop a precise pest-detection technique, diagnostic tools and management strategies for these pest species initiated large scale morphological and genetic studies, the investigation of their evolutionary relationships as well as the characterisation of the variation of cuticular hydrocarbon profiles within and between the species (De Meyer 2001, De Meyer and Freidberg 2006, Virgilio et al. 2012, Delatte et al. 2013, Virgilio et al. 2013, Vaníčková et al. 2014a,b, Vaníčková et al. 2015). The species of the FAR complex can only be identified based on specific small differences between the morphological characters of adult male leg patterns (larvae, pupae and females, are even more difficult to distinguish) (De Meyer and Freidberg 2006). "

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    • "It is particularly important to resolve invasive agricultural pest species, because inadequate morphological/molecular characterisation of the species might have serious economic consequences , resulting in inept ecological models and/or pest control strategies (Virgilio et al. 2013, Vaníčková et al. 2014). The need to develop a precise pest-detection technique, diagnostic tools and management strategies for these pest species initiated large scale morphological and genetic studies, the investigation of their evolutionary relationships as well as the characterisation of the variation of cuticular hydrocarbon profiles within and between the species (De Meyer 2001, De Meyer and Freidberg 2006, Virgilio et al. 2012, Delatte et al. 2013, Virgilio et al. 2013, Vaníčková et al. 2014a,b, Vaníčková et al. 2015). The species of the FAR complex can only be identified based on specific small differences between the morphological characters of adult male leg patterns (larvae, pupae and females, are even more difficult to distinguish) (De Meyer and Freidberg 2006). "
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    • "In these conditions, minibarcodes have proven to be very successful (Sundquist et al. 2007), so we identified potential minibarcodes for feather mites and explored their efficacy. 2 The use of thresholds to differentiate species has been repeatedly discussed in the DNA barcoding literature, finding that no single threshold is optimal for all species (Puillandre et al. 2012; Virgilio et al. 2012; Collins & Cruickshank 2013). Moreover, the accuracy of a threshold-based approach critically depends upon the level of overlap between intra-and interspecific variation across a phylogeny (Meyer & Paulay 2005). "
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