Invertebrate Systematics Invertebrate Systematics Society
Systematics, phylogeny and biogeography
RESEARCH ARTICLE

DNA barcoding invasive insects: database roadblocks

Laura M. Boykin A D , Karen Armstrong A , Laura Kubatko B and Paul De Barro C

A Bio-Protection Research Centre, PO Box 84, Lincoln University, Lincoln 7647, New Zealand.

B Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.

C CSIRO Ecosystem Sciences, GPO Box 2583, Brisbane, Qld 4001, Australia.

D Corresponding author. Email: lboykin@mac.com

Invertebrate Systematics 26(6) 506-514 http://dx.doi.org/10.1071/IS12025
Submitted: 13 April 2012  Accepted: 16 September 2012   Published: 19 December 2012

Abstract

This study examines the genetic data coverage and availability in the Barcode of Life Database (BOLD), versions 2.5 and 3.0, and GenBank for the 88 invasive insects listed in the Global Invasive Species Database (http://www.issg.org). No data are recorded in either BOLD or GenBank for seven of those species. As a dedicated repository of curated barcode data BOLD is either missing data or contains inaccessible private data for 37 (42%) of the species while no data are available in GenBank for nine (8%) of the species. An evaluation of the Barcode Identification Number (BIN) scheme in BOLD ver. 3.0 was also evaluated and in 41% of cases the BIN contained more than one species. This essentially arose due to the 1% delimitation thresholds associated with the BINs and would result in misidentifications. Overall, more information is available from GenBank for the 88 invasive species listed on the Global Invasive Species Database, but quality checking is required to ensure that the data extracted from GenBank are of sufficient quality to make it useful. The implications of these results are discussed, with investment in parallel data silos suggested to be both costly and potentially an inefficient use of resources that may lead to loss of data if the means needed to maintain these databases become unavailable.

Additional keywords: Barcode of Life Database (BOLD), Bemisia tabaci Gennadius, CBOL, iBOL, QBOL.


References

Armstrong, K. F., and Ball, S. L. (2005). DNA barcodes for biosecurity: invasive species identification. Philosophical Transactions of the Royal Society of London B Biological Science 360, 1813–1823.
| 1:CAS:528:DC%2BD2MXhtlSjsrjN&md5=0dce2d0f41befae251fda63c6e3a33eeCAS | open url image1

Ashburner, M., and Drysdale, R. (1994). FlyBase – the Drosophila genetic database. Development 120, 2077–2079.
| 1:CAS:528:DyaK2cXltVOmtro%3D&md5=36bf66b3fbc84cdd834fa77b6d7aedbeCAS | open url image1

Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2011). GenBank. Nucleic Acids Research 39, D32–D37.
GenBank.CrossRef | open url image1

Benson, D. A., Karsch-Mizrachi, I., Clark, K., Lipman, D. J., Ostell, J., and Sayers, E. W. (2012). GenBank. Nucleic Acids Research 40, D48–D53.
GenBank.CrossRef | 1:CAS:528:DC%2BC3MXhs12hur3P&md5=230d09e8990e3e1e06e1d26c3efe1844CAS | open url image1

Bonants, P., Groenewald, E., Rasplus, J. Y., Maes, M., Vos, P. D., Frey, J., Boonham, N., Nicolaisen, M., Bertacini, A., Robert, V., Barker, I., Kox, L., Ravnikar, M., Tomankova, K., Caffier, D., Li, M., Armstrong, K., Freitas-Astúa, J., Stefani, E., Cubero, J., and Mostert, L. (2010). QBOL: a new EU project focusing on DNA barcoding of Quarantine organisms. EPPO Bulletin 40, .
QBOL: a new EU project focusing on DNA barcoding of Quarantine organisms.CrossRef | open url image1

Boykin, L. M., Shatters, R. G., Rosell, R. C., McKenzie, C. L., Bagnall, R. A., De Barro, P., and Frohlich, D. R. (2007). Global relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) revealed using Bayesian analysis of mitochondrial COI DNA sequences. Molecular Phylogenetics and Evolution 44, 1306–1319.
Global relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) revealed using Bayesian analysis of mitochondrial COI DNA sequences.CrossRef | 1:CAS:528:DC%2BD2sXpt1amurY%3D&md5=c2d0ba4efbe7b130543b2c356cd39957CAS | open url image1

Boykin, L. M., Armstrong, K. F., Kubatko, L., and De Barro, P. (2012). Species delimitation and global biosecurity. Evolutionary Bioinformatics 8, 1–37. open url image1

Buhay, J. E. (2009). “COI-LIKE” sequences are becoming problematic in molecular systematic and DNA barcoding studies. Journal of Crustacean Biology 29, 96–110.
“COI-LIKE” sequences are becoming problematic in molecular systematic and DNA barcoding studies.CrossRef | open url image1

Cameron, S., Rubinoff, D., and Will, K. (2006). Who will actually use DNA barcoding and what will it cost? Systematic Biology 55, 844–847.
Who will actually use DNA barcoding and what will it cost?CrossRef | open url image1

Clarke, A. R., Armstrong, K. F., Carmichael, A. E., Milne, J. R., Raghu, S., Roderick, G. K., and Yeates, D. K. (2005). Invasive phytophagous pests arising through a recent tropical evolutionary radiation: the Bactrocera dorsalis complex of fruit flies. Annual Review of Entomology 50, 293–319.
Invasive phytophagous pests arising through a recent tropical evolutionary radiation: the Bactrocera dorsalis complex of fruit flies.CrossRef | 1:CAS:528:DC%2BD2MXhtFOqtL0%3D&md5=1307cc776abad7613f114d017a8a87b8CAS | open url image1

De Barro, P., and Ahmed, M. (2011). Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions. PLoS Biology 6, e25579.
| 1:CAS:528:DC%2BC3MXhtlGmtL3L&md5=abe3eb99d1fb6c7e46aea02d74b6a75eCAS | open url image1

De Barro, P. J., Liu, S. S., Boykin, L. M., and Dinsdale, A. B. (2011). Bemisia tabaci: a statement of species status. Annual Review of Entomology 56, 1–19.
Bemisia tabaci: a statement of species status.CrossRef | 1:CAS:528:DC%2BC3MXhtlSiurk%3D&md5=3a0a46cc92f1ffd6d9c541e20b4191cfCAS | open url image1

DeSalle, R., Egan, M. G., and Siddall, M. (2005). The unholy trinity: taxonomy, species delimitation and DNA barcoding. Proceedings of the Royal Society of London. Series B. Biological Sciences 360, 1905–1916.
| 1:CAS:528:DC%2BD2MXhtlSjsrnE&md5=f8c85670f20b6ef60dd4b6cbf03e6aceCAS | open url image1

Dinsdale, A., Cook, L., Riginos, C., Buckley, Y. M., and De Barro, P. (2010). Refined global analysis of Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyroidea) mitochondrial CO1 to identify species level genetic boundries. Annals of the Entomological Society of America 103, 196–208.
Refined global analysis of Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyroidea) mitochondrial CO1 to identify species level genetic boundries.CrossRef | open url image1

Elias, M., Hill, R. I., Willmott, K. R., Dasmahapatra, K. K., Brower, A. V., Mallet, J., and Jiggins, C. D. (2007). Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings. Biological Sciences 274, 2881–2889.
Limited performance of DNA barcoding in a diverse community of tropical butterflies.CrossRef | 1:CAS:528:DC%2BD2sXhtlOhtr%2FF&md5=e4e4d5ee88385893dc50d4d751b8298cCAS | open url image1

Floyd, R., Lima, J., deWaard, J. R., Humble, L. M., and Hanner, R. H. (2010). Common goals: policy implications of DNA barcoding as a protocol for identification of arthropod pests. Biological Invasions 12, 2947–2954.
Common goals: policy implications of DNA barcoding as a protocol for identification of arthropod pests.CrossRef | open url image1

Forster, P. (2003). To err is human. Annals of Human Genetics 67, 2–4.
To err is human.CrossRef | 1:STN:280:DC%2BD3s%2Fks12gtA%3D%3D&md5=60e010f3ccadaa50433c53842b9470a7CAS | open url image1

Frohlich, D. R., Torres-Jerez, I. I., Bedford, I. D., Markham, P. G., and Brown, J. K. (1999). A phylogeographical analysis of the Bemisia tabaci species complex based on mitochondrial DNA markers. Molecular Ecology 8, 1683–1691.
A phylogeographical analysis of the Bemisia tabaci species complex based on mitochondrial DNA markers.CrossRef | open url image1

Galtier, N., Nabholz, B., Glemin, S., and Hurst, G. D. (2009). Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18, 4541–4550.
Mitochondrial DNA as a marker of molecular diversity: a reappraisal.CrossRef | 1:CAS:528:DC%2BD1MXhs1SjsL%2FM&md5=c66971720e3a4c64c448cc7e4f4911fbCAS | open url image1

Gaschen, B., Kuiken, C., Korber, B., and Foley, B. (2001). Retrieval and on-the-fly alignment of sequence fragments from the HIV database. Bioinformatics 17, 415–418.
Retrieval and on-the-fly alignment of sequence fragments from the HIV database.CrossRef | 1:CAS:528:DC%2BD3MXktlyiur4%3D&md5=bc6fa2761edd241434100469808af6dcCAS | open url image1

Gemeinholzer, B., Oberprieler, C., and Bachmann, K. (2006). Using GenBank data for plant identification: possibilities and limitations using the ITS1 of Asteraceae species belonging to the tribes Lactuceae and Anthemidae. Taxon 55, 173–187.
Using GenBank data for plant identification: possibilities and limitations using the ITS1 of Asteraceae species belonging to the tribes Lactuceae and Anthemidae.CrossRef | open url image1

Harris, J. D. (2003). Can you bank on GenBank? Trends in Ecology & Evolution 18, 317–319.
Can you bank on GenBank?CrossRef | open url image1

Hebert, P. D., Cywinska, A., Ball, S. L., and deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B. Biological Sciences 270, 313–321.
Biological identifications through DNA barcodes.CrossRef | 1:CAS:528:DC%2BD3sXktVWiu7g%3D&md5=bacde07336013937477a1e8839a85156CAS | open url image1

Kuiken, C., Yusim, K., Boykin, L., and Richardson, R. (2005). The Los Alamos hepatitis C sequence database. Bioinformatics 21, 379–384.
The Los Alamos hepatitis C sequence database.CrossRef | 1:CAS:528:DC%2BD2MXovVyitw%3D%3D&md5=3ebcb9c982ac10c6541e912416b013fcCAS | open url image1

Liu, S., De Barro, P., Jing, X., Luan, J. B., Zang, L. S., and Ruan, Y. M. (2007). Asymmetric mating interactions drive widespread invasion and displacement in a whitefly. Science 318, 1769–1772.
Asymmetric mating interactions drive widespread invasion and displacement in a whitefly.CrossRef | 1:CAS:528:DC%2BD2sXhsVWhu7bO&md5=4939cdf9813005981fdc31867e715a8eCAS | open url image1

Liu, S. S., Colvin, J., and De Barro, P. (2012). Species concepts as applied to the whitefly Bemisia tabaci systematics: how many species are there? Journal of Integrative Agriculture 11, 176–186.
Species concepts as applied to the whitefly Bemisia tabaci systematics: how many species are there?CrossRef | open url image1

Mack, R. N., Simberloff, D., Lonsdale, W. M.,, Evans, H., Clout, M., and Bazzaz, F. A. (2000). Issues in ecology. Biotic invasions: causes, epidemiology, global consequences, and control. Ecological Applications 10, 689–710.
Issues in ecology. Biotic invasions: causes, epidemiology, global consequences, and control.CrossRef | open url image1

Macken, C., Lu, H., Goodman, J., and Boykin, L. (2001). The value of a database in surveillance and vaccine selection. International Congress Series 1219, 103–106.
The value of a database in surveillance and vaccine selection.CrossRef | open url image1

Pennisi, E. (2008). DNA data. Proposal to ‘Wikify’ GenBank meets stiff resistance. Science 319, 1598–1599.
DNA data. Proposal to ‘Wikify’ GenBank meets stiff resistance.CrossRef | 1:CAS:528:DC%2BD1cXktFWmtrg%3D&md5=71ae41176bc2587de201ad9deba79821CAS | open url image1

Prendini, L. (2005). Identifying spiders through DNA barcodes. Canadian Journal of Zoology 83, 498–504.
Identifying spiders through DNA barcodes.CrossRef | 1:CAS:528:DC%2BD2MXmsFylsrY%3D&md5=e2aef7094f23e641c5ec7a41b693a4f8CAS | open url image1

Ratnasingham, S., and Hebert, P. D. (2007). BOLD: The Barcode of Life Data system (http://www.barcodinglife.org). Molecular Ecology Notes 7, 355–364.
BOLD: The Barcode of Life Data system (http://www.barcodinglife.org).CrossRef | 1:CAS:528:DC%2BD2sXntVyksbc%3D&md5=53cd40598900a88b3cc1c91ad7b9427cCAS | open url image1

Ross, H. A., Murugan, S., and Li, W. L. (2008). Testing the reliability of genetic methods of species identification via simulation. Systematic Biology 57, 216–230.
Testing the reliability of genetic methods of species identification via simulation.CrossRef | open url image1

Rubinoff, D., Cameron, S., and Will, K. (2006). A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. The Journal of Heredity 97, 581–594.
A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification.CrossRef | 1:CAS:528:DC%2BD28XhtlCru7jL&md5=f56101a94f8a21efa442294774f30254CAS | open url image1

Song, H., Buhay, J. E., Whiting, M. F., and Crandall, K. A. (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences of the United States of America 105, 13486–13491.
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified.CrossRef | 1:CAS:528:DC%2BD1cXhtFChs7vP&md5=3a04f63265faa303944ae4d7dc4d61fdCAS | open url image1

Taylor, H. R., and Harris, W. E. (2012). An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology Resources 12, 377–388.
An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding.CrossRef | 1:STN:280:DC%2BC38vjvVynug%3D%3D&md5=e2f38a9b9e6979e684f791bfb2a2f41eCAS | open url image1

Tixier, M. S., Hernandes, F. A., Guichou, S., and Kreiter, S. (2011). The puzzle of DNA sequences of Phytoseiidae (Acari: Mesostigmata) in the public Genbank database. Invertebrate Systematics 25, 389–406.
The puzzle of DNA sequences of Phytoseiidae (Acari: Mesostigmata) in the public Genbank database.CrossRef | 1:CAS:528:DC%2BC38XisVygurg%3D&md5=44c341df4b2602c37795ed369dfcc0d8CAS | open url image1

Virgilio, M., Backeljau, T., Nevado, B., and De Meyer, M. (2010). Comparative performances of DNA barcoding across insect orders. BMC Bioinformatics 11, 206.
Comparative performances of DNA barcoding across insect orders.CrossRef | open url image1

Virgilio, M., Jordaens, K., Breman, F. C., Backeljau, T., and De Meyer, M. (2012). Identifying insects with incomplete DNA barcode libraries, african fruit flies (Diptera: Tephritidae) as a test case. PLoS ONE 7, e31581.
Identifying insects with incomplete DNA barcode libraries, african fruit flies (Diptera: Tephritidae) as a test case.CrossRef | 1:CAS:528:DC%2BC38Xjt1Sjsb0%3D&md5=2ff151c6161d59a5fadc5dcb639f1edbCAS | open url image1

Will, K. W., Mishler, B. D., and Wheeler, Q. D. (2005). The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54, 844–851.
The perils of DNA barcoding and the need for integrative taxonomy.CrossRef | open url image1



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