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Abstract

The current classification of African tephritids is the interim result of a continuous process of minor and major changes that, in the last 20 years, has resulted in the description of more than 60 new species from the seven tephritid genera of main economic relevance in Africa (Bactrocera, Capparimyia, Ceratitis, Dacus, Neoceratitis, Trirhithrum and Zeugodacus). In this context of dynamic change, rapid and accurate fruit fly identification is critical, particularly with respect to the early detection of pest invasions. Valuable resources for fruit fly identification include: the tephritid reference collections and repositories distributed within and outside the African continent; publicly available online databases; and the single- and multi-entry keys for the morphological identification of African tephritids. Identification through DNA barcoding represents a cost effective tool for the molecular diagnosis of African fruit flies and it has proved particularly useful for the identification of immature stages, of damaged specimens and of incomplete specimens. The molecular diagnosis of tephritids also represents a partial solution to the gradual loss of taxonomical expertise on this and other insect groups. In this chapter the advantages and limitations of the available identification tools and resources are discussed.

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References

  • Abuel-Ela RG, Hashem AG, Mohamed SMA (1998) Bactrocera pallidus (Perkin and May) (Diptera: Tephritidae), a new record in Egypt. J Egyptian German Soc Zool Entomol 27:221–229

    Google Scholar 

  • Aluja M, Norrbom AL (1999) Fruit flies (Tephritidae) phylogeny and evolution of behavior. CRC Press, Boca Raton, pp 967

    Book  Google Scholar 

  • Armstrong KF, Ball SL (2005) DNA barcodes for biosecurity: invasive species identification. Phil Trans Roy Soc London Ser B 360:1813–1823

    Article  CAS  Google Scholar 

  • Barr NB, Islam MS, De Meyer M, McPheron BA (2012) Molecular identification of Ceratitis capitata (Diptera: Tephritidae) using DNA sequences of the COI barcode region. Anns Entomol Soc Amer 105:339–350

    Article  CAS  Google Scholar 

  • Boykin LM, Armstrong K, Kubatko L, De Barro P (2012) DNA barcoding invasive insects: database roadblocks. Invertebr System 26:506–514

    Article  CAS  Google Scholar 

  • Cameron S, Rubinoff D, Will K (2006) Who will actually use DNA barcoding and what will it cost? System Biol 55:844–847

    Article  Google Scholar 

  • Collins RA, Cruickshank RH (2013) The seven deadly sins of DNA barcoding. Mol Ecol Res 13:969–975

    CAS  Google Scholar 

  • de Carvalho MR, Bockmann FA, Amorim DS, Brandão CRF, de Vivo M, de Figueiredo JL, Britski HA, de Pinna MCC, Menezes NA, Marques FPL, Papavero N, Cancello EM, Crisci JV, McEachran JD, Schelly RC, Lundberg JG, Gill AC, Britz R, Wheeler QD, Stiassny MLJ, Parenti LR, Page LM, Wheeler WC, Faivovich J, Vari RP, Grande L, Humphries CJ, DeSalle R, Ebach MC, Nelson GJ (2007) Taxonomic impediment or impediment to taxonomy? A commentary on systematics and the cybertaxonomic-automation paradigm. Evol Biol 34:140–143

    Article  Google Scholar 

  • De Meyer M (1996) Revision of the subgenus Ceratitis (Pardalaspis) Bezzi, 1918 (Diptera, Tephritidae, Ceratitini). Syst Entomol 21:15–26

    Article  Google Scholar 

  • De Meyer M (1998) Revision of the subgenus Ceratitis (Ceratalaspis) Hancock (Diptera: Tephritidae). Bull Entomol Res 88:257–290

    Article  Google Scholar 

  • De Meyer M (2000) Systematic revision of the subgenus Ceratitis Macleay s.s. (Diptera, Tephritidae). Zool J Linn Soc 128:439–467

    Article  Google Scholar 

  • De Meyer M (2006) Systematic revision of the fruit fly genus Carpophthoromyia Austen (Diptera, Tephritidae). Zootaxa 1235:1–48

    Google Scholar 

  • De Meyer M (2009) Taxonomic revision of the fruit fly genus Perilampsis Bezzi (Diptera, Tephritidae). J Nat Hist 43:2425–2463

    Article  Google Scholar 

  • De Meyer M, Copeland R (2001) Taxonomic notes on the subgenera Ceratitis (Hoplolophomyia) and Ceratitis (Acropteromma) (Diptera, Tephritidae). Cimbebasia 17:77–84

    Google Scholar 

  • De Meyer M, Freidberg A (2005) Revision of the fruit fly genus Capparimyia (Diptera, Tephritidae). Zool Scripta 34:279–303

    Article  Google Scholar 

  • De Meyer M, Freidberg A (2006) Revision of the subgenus Ceratitis (Pterandrus) Bezzi (Diptera: Tephritidae). Israel J Entomol 36:197–315

    Google Scholar 

  • De Meyer M, Freidberg A (2012) Taxonomic revision of the fruit fly genus Neoceratitis Hendel (Diptera: Tephritidae). Zootaxa 3223:24–39

    Google Scholar 

  • De Meyer M, White IM, Goodger KFM (2013) Notes on the frugivorous fruit fly (Diptera: Tephritidae) fauna of western Africa, with description of a new Dacus species. Europ J Taxon 50:1–17

    Google Scholar 

  • Dowton M, Meiklejohn K, Cameron SL, Wallman J (2014) A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. System Biol 63:639–644

    Article  Google Scholar 

  • Drew RAI, Tsuruta K, White IM (2005) A new species of pest fruit fly (Diptera : Tephritidae : Dacinae) from Sri Lanka and Africa. Afr Entomol 13:149–154

    Google Scholar 

  • Ekesi S, Billah MK (2007) A field guide to the management of economically important tephritid fruit flies in Africa. ICIPE Science Press, Nairobi

    Google Scholar 

  • Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome C oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol & Biotechnol 3:294–299

    CAS  Google Scholar 

  • Frey J, Guillén L, Frey B, Samietz J, Rull J, Aluja M (2013) Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation. BMC Evol Biol 13:1–19

    Article  Google Scholar 

  • Hancock DL, Drew RAI (2006) A revised classification of subgenera and species groups in Dacus Fabricius (Diptera: Tephritidae). Instrumenta Biodiversitatis VII:167–205

    Google Scholar 

  • Hancock DL, White IM (1997) The identity of Tririthrum nigrum (Graham) and some new combinations in Ceratitis MacLeay (Diptera: Tephritidae). The Entomologist 116:192–197

    Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc Roy Soc B 270:313–321

    Article  CAS  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312

    Article  PubMed  PubMed Central  Google Scholar 

  • Hickerson MJ, Meyer CP, Moritz C (2006) DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55:729–739

    Article  PubMed  Google Scholar 

  • Jiang F, Jin Q, Liang L, Zhang AB, Li ZH (2014) Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp. Mol Ecol Res 14:1114–1128

    Article  CAS  Google Scholar 

  • Kvist S (2013) Barcoding in the dark?: a critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge. Mol Phylog Evol 69:39–45

    Article  CAS  Google Scholar 

  • Kwong S, Srivathsan A, Meier R (2012) An update on DNA barcoding: low species coverage and numerous unidentified sequences. Cladistics 28:639–644

    Article  Google Scholar 

  • Meeyen K, Nanork Sopaladawan P, Pramual P (2014) Population structure, population history and DNA barcoding of fruit fly Bactrocera latifrons (Hendel) (Diptera: Tephritidae). Entomol Sci 17:219–230

    Article  Google Scholar 

  • Meier R, Shiyang K, Vaidya G, Ng PKL (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55:715–728

    Article  PubMed  Google Scholar 

  • Meier R, Wong W, Srivathsan A, Foo M (2016) $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics 32:100–110

    Article  Google Scholar 

  • Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422

    Article  PubMed  PubMed Central  Google Scholar 

  • Mitchell A (2015) Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens. Mol Ecol Res 15:1102–1111

    Article  CAS  Google Scholar 

  • Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLoS Biol 2:e35

    Article  Google Scholar 

  • Nagy ZT, Backeljau T, De Meyer M, Jordaens K (2013) DNA barcoding: a practical tool for fundamental and applied biodiversity research. In: ZooKeys p. 410

    Google Scholar 

  • Nielsen R, Matz M (2006) Statistical approaches for DNA barcoding. Syst Biol 55:162–169

    Article  PubMed  Google Scholar 

  • Pečnikar ŽF, Buzan E (2014) 20 years since the introduction of DNA barcoding: from theory to application. J Appl Gen 55:43–52

    Article  Google Scholar 

  • Porter TM, Gibson JF, Shokralla S, Baird DJ, Golding GB, Hajibabaei M (2014) Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier. Mol Ecol Res 14:929–942

    CAS  Google Scholar 

  • Puillandre N, Lambert A, Brouillet S, Achaz G (2011) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol 2:1864–1877

    Google Scholar 

  • Ratnasingham S, Hebert P (2007) BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes 7:355–364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 8:e66213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schutze MK, Aketarawong N, Amornsak W, Armstrong KF, Augustinos AA, Barr N, Bo W, Bourtzis K, Boykin LM, CÁCeres C, Cameron SL, Chapman TA, Chinvinijkul S, ChomiČ A, De Meyer M, Drosopoulou E, Englezou A, Ekesi S, Gariou-Papalexiou A, Geib SM, Hailstones D, Hasanuzzaman M, Haymer D, Hee AKW, Hendrichs J, Jessup A, Ji Q, Khamis FM, Krosch MN, Leblanc LUC, Mahmood K, Malacrida AR, Mavragani-Tsipidou P, Mwatawala M, Nishida R, Ono H, Reyes J, Rubinoff D, San Jose M, Shelly TE, Srikachar S, Tan KH, Thanaphum S, Haq I, Vijaysegaran S, Wee SL, Yesmin F, Zacharopoulou A, Clarke AR (2015) Synonymization of key pest species within the Bactrocera dorsalis species complex (Diptera: Tephritidae): taxonomic changes based on a review of 20 years of integrative morphological, molecular, cytogenetic, behavioural and chemoecological data. Syst Entomol 40:456–471

    Article  Google Scholar 

  • Shokralla S, Gibson JF, Nikbakht H, Janzen DH, Hallwachs W, Hajibabaei M (2014) Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol Ecol Res 14:892–901

    CAS  Google Scholar 

  • Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M (2015) Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Reps 5:9687

    Article  CAS  Google Scholar 

  • Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365:279–305

    Article  Google Scholar 

  • Sonet G, Jordaens K, Nagy ZT, Breman F, de Meyer M, Backeljau T, Virgilio M (2013) Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. ZooKeys 365:329–336

    Article  Google Scholar 

  • Sucher NJ, Hennell JR, Carles MC (2012) DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants. Methods Mol Biol 862:13–22

    Article  CAS  PubMed  Google Scholar 

  • Tanabe AS, Toju H (2013) Two new computational methods for universal dna barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants. PLoS One 8:e76910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Res 12:377–388

    Article  CAS  Google Scholar 

  • Van Houdt JKJ, Breman FC, Virgilio M, De Meyer M (2010) Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes. Mol Ecol Res 10:459–465

    Article  Google Scholar 

  • Virgilio M, Backeljau T, Nevado B, De Meyer M (2010) Comparative performances of DNA barcoding across insect orders. BMC Bioinf 11:206

    Article  Google Scholar 

  • Virgilio M, Backeljau T, Emeleme R, Juakali JL, De Meyer M (2011) A quantitative comparison of frugivorous tephritids (Diptera: Tephritidae) in tropical forests and rural areas of the Democratic Republic of Congo. Bull Entomol Res 101:591–597

    Article  CAS  PubMed  Google Scholar 

  • Virgilio M, Jordaens K, Breman FC, Backeljau T, De Meyer M (2012) Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case. PLoS One 7:e31581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Virgilio M, White IM, De Meyer M (2014) A set of multi-entry identification keys to African frugivorous flies (Diptera, Tephritidae). ZooKeys 428:97–108

    Article  Google Scholar 

  • Virgilio M, Jordaens K, Verwimp C, White IM, De Meyer M (2015) Higher phylogeny of frugivorous flies (Diptera, Tephritidae, Dacini): localised partition conflicts and a novel generic classification. Mol Phylog Evol 85:171–179

    Article  Google Scholar 

  • White IM (2006) Taxonomy of the Dacina (Diptera:Tephritidae) of Africa and the Middle East. Afr Entomol Memoir 2:1–156

    Google Scholar 

  • White IM, Goodger KFM (2009) African Dacus (Diptera: Tephritidae); new species and data, with particular reference to the Tel Aviv University collection. Zootaxa 2127:1–49

    Google Scholar 

  • White I, Copeland R, Hancock D (2003) Revision of the afrotropical genus Trirhithrum (Diptera: Tephritidae). Cimbebasia 18:71–137

    Google Scholar 

  • Zimmermann J, Hajibabaei M, Blackburn D, Hanken J, Cantin E, Posfai J, Evans T (2008) DNA damage in preserved specimens and tissue samples: a molecular assessment. Front in Zool 5:18

    Article  Google Scholar 

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Correspondence to Massimiliano Virgilio .

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Virgilio, M. (2016). Identification Tools for African Frugivorous Fruit Flies (Diptera: Tephritidae). In: Ekesi, S., Mohamed, S., De Meyer, M. (eds) Fruit Fly Research and Development in Africa - Towards a Sustainable Management Strategy to Improve Horticulture. Springer, Cham. https://doi.org/10.1007/978-3-319-43226-7_2

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