Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case.

PloS One
M VirgilioM DE Meyer

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 identifica...Continue Reading

References

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Citations

Mar 14, 2013·Molecular Ecology Resources·Muhammad AshfaqYusuf Zafar
Jan 7, 2016·Annual Review of Entomology·Sunday EkesiChristian Borgemeister
Jan 3, 2013·Molecular Ecology Resources·R A Collins, R H Cruickshank
Feb 7, 2015·Molecular Ecology Resources·Jorge DoñaRoger Jovani
Apr 30, 2015·PloS One·Rodger A GwiazdowskiPaul D N Hebert
Oct 30, 2016·Genome Génome / Conseil National De Recherches Canada·Jennifer HodgettsNeil Boonham
Dec 2, 2017·Scientific Reports·Junning LiuChenhong Li
Nov 23, 2019·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Chonticha Kunprom, Pairot Pramual
Jun 19, 2016·Journal of Phycology·Maja Łukomska-KowalczykBożena Zakryś
Dec 11, 2019·PloS One·Muhammad Tayyib NaseemPaul D N Hebert
Oct 19, 2016·Genome Génome / Conseil National De Recherches Canada·Muhammad Ashfaq, Paul D N Hebert
Nov 11, 2018·Insects·Narin SontigunAnchalee Wannasan
Dec 5, 2017·Journal of Economic Entomology·Norman B BarrDonald B Thomas
Oct 4, 2017·Genome Génome / Conseil National De Recherches Canada·Jason Gibbs
May 22, 2020·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Dumas DeconinckSofie Derycke
Aug 7, 2021·Scientific Reports·Monica R YoungPaul D N Hebert
Aug 20, 2021·Neotropical Entomology·Adriane Vieira SouzaJanisete Gomes Silva

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Software Mentioned

Barcode of Life
SpeciesIdentifier
OriginPro

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