Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry
Autoři:
Mary J. L. Madden aff001; Robert G. Young aff001; John W. Brown aff002; Scott E. Miller aff002; Andrew J. Frewin aff001; Robert H. Hanner aff001
Působiště autorů:
Department of Integrated Biology, University of Guelph, Guelph, Ontario, Canada
aff001; Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
aff002
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222291
Souhrn
Interception of potential invasive species at ports-of-entry is essential for effective biosecurity and biosurveillance programs. However, taxonomic assessment of the immature stages of most arthropods is challenging; characters for identification are often dependent on adult morphology and reproductive structures. This study aims to strengthen the identification of such specimens through DNA barcoding, with a focus on microlepidoptera. A sample of 241 primarily immature microlepidoptera specimens intercepted at U.S. ports-of-entry from 2007 to 2011 were selected for analysis. From this sample, 201 COI-5P sequences were generated and analyzed for concordance between morphology-based and DNA-based identifications. The retrospective analysis of the data over 10 years (2009 to 2019) using the Barcode of Life Data (BOLD) system demonstrates the importance of establishing and growing DNA barcode reference libraries for use in specimen identification. Additionally, analysis of specimen identification using public data (43.3% specimens identified) vs. non-public data (78.6% specimens identified) highlights the need to encourage researchers to make data publicly accessible. DNA barcoding surpassed morphological identification with 42.3% (public) and 66.7% (non-public) of the sampled specimens achieving a species-level identification, compared to 38.3% species-level identification by morphology. Whilst DNA barcoding was not able to identify all specimens in our dataset, its incorporation into border security programs as an adjunct to morphological identification can provide secondary lines of evidence and lower taxonomic resolution in many cases. Furthermore, with increased globalization, database records need to be clearly annotated for suspected specimen origin versus interception location.
Klíčová slova:
Biology and life sciences – Molecular biology – Molecular biology techniques – DNA barcoding – Evolutionary biology – Evolutionary systematics – Molecular systematics – Taxonomy – Genetics – DNA – DNA libraries – Biochemistry – Nucleic acids – Research and analysis methods – Database and informatics methods – Biological databases – Bioinformatics – Sequence analysis – Sequence databases – Storage and handling – Specimen storage – Computer and information sciences – Data management – Metadata – Ecology and environmental sciences – Species colonization – Invasive species
Zdroje
1. Caffrey JM, Baars JR, Barbour JH, Boets P, Boon P, Davenport K, et al. Tackling invasive alien species in Europe: the top 20 issues. Manage Biol Invasions. 2014;5(1): 1–20. doi: 10.3391/mbi.2014.5.1.01
2. Oerke EC. Crop losses to pests. J Agri Sci. 2006;144(1): 31–43. doi: 10.1017/S0021859605005708
3. Augustin S, Boonham N, De Kogel WJ, Donner P, Faccoli M, Lees DC, et al. A Review of Pest Surveillance Techniques for Detecting Quarantine Pests in Europe. EPPO Bulletin. 2012;42: 515–551. doi: 10.1111/epp.2600
4. Oliveira CM, Auad AM, Mendes SM, Frizzas MR. Crop losses and the economic impact of insect pests on Brazilian agriculture. Crop Prot. 2014;56: 50–54. doi: 10.1016/j.cropro.2013.10.022
5. Westphal MI, Browne M, MacKinnon K, Noble I. The link between international trade and the global distribution of invasive alien species. Biol Invasions. 2008;10(4): 391–398. doi: 10.1007/s10530-007-9138-5
6. Navia D, Ochoa R, Welbourn C, Ferragut F. Adventive eriophyoid mites: a global review of their impact, pathways, prevention and challenges. Exp Appl Acarol. 2010;51(1–3): 225–55. doi: 10.1007/s10493-009-9327-2 19844795
7. Lenda M, Skorka P, Knops JMH, Moron D, Sutherland WJ, Kuszewska K et al. Effect of the internet commerce on dispersal modes of invasive alien species. Plos One 2014;9:7. doi: 10.1371/journal.pone.0099786 24932498
8. Suffert M, Wilstermann A, Petter F, Schrader G, Grousset F. Identification of new pests likely to be introduced into Europe with the fruit trade. EPPO Bulletin, 2018;48(1): 144–154. doi: 10.1111/epp.12462
9. Moser WK, Barnard EL, Billings RF, Crocker SJ, Dix M, Gray AN, et al. Impacts of Nonnative Invasive Species on US Forests and Recommendations for Policy and Management. J Forest, 2009;107(6): 320–327. doi: 10.1093/jof/107.6.320
10. Bacon SJ, Bacher S, Aebi A. Gaps in Border Controls Are Related to Quarantine Alien Insect Invasions in Europe. PLoS ONE, 2012;7(10). doi: 10.1371/journal.pone.0047689 23112835
11. Kenis M, Rabitsch W, Auger-Rozenberg MA, Roques A. How can alien species inventories and interception data help us prevent insect invasions? Bull Entomol Res. 2007;97(5): 489–502. doi: 10.1017/S0007485307005184 17916267
12. Harwood TD, Xu X, Pautasso M, Jeger MJ, Shaw MW. Epidemiological risk assessment using linked network and grid based modelling: Phytophthora ramorum and Phytophthora kernoviae in the UK. Ecol Model. 2009;220: 3353–3361. doi: 10.1016/j.ecolmodel.2009.08.014
13. Moslonka-Lefebvre M, Finley A, Dorigatti I, Dehnen-Schmutz K, Harwood T, Jeger MJ, et al. Networks in plant epidemiology: From genes to landscapes, countries, and continents. Phytopathology. 2011;101: 392–403. doi: 10.1094/PHYTO-07-10-0192 21062110
14. Whittle PJL, Stoklosa R, Barrett S, Jarrad FC, Majer JD, Martin PAJ, et al. A method for designing complex biosecurity surveillance systems: detecting non-indigenous species of invertebrates on Barrow Island. Divers and Distrib. 2013;19: 629–639. doi: 10.1111/ddi.12056
15. Vanninen I, Worner S, Huusela-Veistola E, Tuovinen T, Nissinen A, Saikkonen K. Recorded and potential alien invertebrate pests in Finnish agriculture and horticulture. Agri Food Sci. 2011;20: 96–113. doi: 10.2137/145960611795163033
16. Schachat SR. The wing pattern of Moerarchis Durrant, 1914 (Lepidoptera: Tineidae) clarifies transitions between predictive models. R Soc Open Sci. 2017;4(3), 1–12. doi: 10.1098/rsos.161002 28405390
17. Sweeney BW, Battle JM, Jackson JK, Dapkey T. Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? J N Am Benthol Soc. 2011;30(1): 195–216. doi: 10.1899/10-016.1
18. Stehr FW, editors. Immature insects. Vol. 1. Dubuque: Kendall Hunt Publishing Co; 1987. np.
19. Gilligan TM, Goldstein PZ, Timm AE, Farris R, Ledezma L, Cunningham AP. Identification of Heliothine (Lepidoptera: Noctuidae) Larvae Intercepted at U.S. Ports of Entry from the New World. J Econ Entomol. 2019;1–13. doi: 10.1093/jee/toy247
20. Ko HL, Wang YT, Chiu TS, Lee MA, Leu MY, Chang KZ, et al. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. Plos One 2013;8: doi: 10.1371/journal.pone.0053451 23382845
21. McCullough DG, Work TT, Cavey JF, Liebhold AM, Marshall D. Interceptions of nonindigenous plant pests at US ports of entry and border crossings over a 17-year period. Biol Invasions. 2006;8: 611–630. doi: 10.1007/s10530-005-1798-4
22. Worner SP, Gevrey M. Modelling global insect pest species assemblages to determine risk of invasion. J Appl Ecol. 2006;43: 858–867. doi: 10.1111/j.1365-2664.2006.01202.x
23. Brasier M. The biosecurity threat to the UK and global environment from international trade in plants. Plant Pathol. 2008;57(5): 792–808. doi: 10.1111/j.1365-3059.2008.01886.x
24. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc R Soc B. 2003;270: 313–321. doi: 10.1098/rspb.2002.2218 12614582
25. Frewin A, Scott-Dupree C, Hanner R. DNA barcoding for plant protection: applications and summary of available data for arthropod pests. CAB Rev. 2013;8(18): 1–13. doi: 10.1079/PAVSNNR20138018
26. Wilson JRU, Ivey P, Manyama P, Naenni I. A new national unit for invasive species detection, assessment and eradication planning. S Afr J Sci. 2013;109: 33–45. doi: 10.1590/sajs.2013/20120111
27. Serrao NR, Steinke D, Hanner RH. Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species. Plos One 2014;9(6):e99546. doi: 10.1371/journal.pone.0099546 24915194
28. Wilson AD, Schiff NM. Identification of Sirex noctilio and Native North American Woodwasp Larvae using DNA Barcode. J Entomol. 2010;7: 60–79. doi: 10.3923/je.2010.60.79
29. Brabrand A, Bremnes T, Koestler AG, Marthinsen G, Pavels H, Rindal E, et al. Mass occurrence of bloodsucking blackflies in a regulated river reach: Localization of oviposition habitat of Simulium truncatum using DNA barcoding. River Res Appl. 2014;30: 602–608. doi: 10.1002/rra.2669
30. Mastrangelo T, Paulo DF, Bergamo LW, Morais EGF, Silva M, Bezerra-Silva G, et al. Detection and genetic diversity of a heliothine invader (Lepidoptera: Noctuidae) from north and northeast of Brazil. J Econ Entomol. 2014;107: 970–980. doi: 10.1603/ec13403 25026655
31. Pramual P, Wongpakam K. Association of black fly (Diptera: Simuliidae) life stages using DNA barcode. J Asia-Pac Entomol. 2014;17: 549–554. doi: 10.1016/j.aspen.2014.05.006
32. Ratnasingham S, Hebert PDN. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes. 2007;7: 355–364. doi: 10.1111/j.1471-8286.2007.01678.x 18784790
33. Borisenko AV, Sones JE, Hebert PD. The front-end logistics of DNA barcoding: Challenges and prospects. Mol Ecol Resour. 2009;9: 27–34. doi: 10.1111/j.1755-0998.2009.02629.x 21564961
34. Hanner R. 2009. Data Standards for BARCODE Records in INSDC (BRIs). https://github.com/SIBarcodeNetwork/SIBarcodeNetwork/blob/master/BARCODE%20Data%20Standards%20v2.4.pdf
35. Curry C. J., Gibson J. F., Shokralla S., Hajibabaei M., & Baird D. J. (2018). Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?. Freshwater Science, 37(1), 178–189.
36. Porter T. M., & Hajibabaei M. Over 2.5 million COI sequences in GenBank and growing. PloS one. 2018; 13(9), e0200177. doi: 10.1371/journal.pone.0200177 30192752
37. Blaxter M.L. The promise of a DNA taxonomy. Philos.Trans. R. Soc. B Biol. Sci. 2004; 359(1444): 669–679. doi: 10.1098/rstb.2003.1447 15253352
38. Ratnasingham S, Hebert PDN. A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. Plos One 2013;8: doi: 10.1371/journal.pone.0066213 23861743
39. Zahiri RJ, Lafontaine D, Schmidt BC, deWaard JR, Zakharov EV, Hebert PDN. A transcontinental challenge—A test of DNA barcode performance for 1,541 species of Canadian Noctuoidea (Lepidoptera). Plos One. 2014;9(3): e92797. doi: 10.1371/journal.pone.0092797 24667847
40. Castalanelli MA, Severtson DL, Brumley CJ, Szito A, Foottit RG, Grimm M, et al. A rapid non-destructive DNA extraction method for insects and other arthropods. J Asia-Pac Entomol. 2012;13(3): 243–248. doi: 10.1016/j.aspen.2010.04.003
41. Wilson JJ. DNA Barcodes for Insects. Method Mol Biol, 2012;858: 17–46. doi: 10.1007/978-1-61779-591-6_3
42. Ivanova NV, Borisenko AV, Hebert PDN. Express barcodes: racing from specimen to identification. Mol Ecol Resour. 2009;9(s1). doi: 10.1111/j.1755-0998.2009.02630.x 21564962
43. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA. 2004;101(41): 14812–14817. doi: 10.1073/pnas.0406166101 15465915
44. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD. DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences. 2006; 103(4):968–71.
45. Hulme PE. Trade, transport and trouble: managing invasive species pathways in an era of globalization. J Appl Ecol. 2009;46(1): 10–18. doi: 10.1111/j.1365-2664.2008.01600.x
46. Early R, Bradley BA, Dukes JS, Lawler JJ, Olden JD, Blumenthal DM, et al. Global threats from invasive alien species in the twenty-first century and national response capacities. Nat Commun. 2016;7: 12485. doi: 10.1038/ncomms12485 27549569
47. Watts C, Dopheide A, Holdaway R, Davis C, Wood J, Thornburrow D, et al. DNA metabarcoding as a tool for invertebrate community monitoring: A case study comparison with conventional techniques. Austral Entomol. 2019;8(7): e1000417. doi: 10.1111/aen.12384
48. Bonants PJM. Results of the EU Project QBOL, Focusing on DNA Barcoding of Quarantine Organisms, Added to an International Database (Q-Bank) on Identification of Plant Quarantine Pathogens and Relatives. In: Gullino M, Bonants P, editors. Detection and Diagnostics of Plant Pathogens. Plant Pathology in the 21st Century (Contributions to the 9th International Congress). Dordrecht: Springer; 2014. pp. 119–133.
49. Phillips JD, Gillis DJ, Hanner RH. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol, 2019;9(5), 2996–3010. doi: 10.1002/ece3.4757 30891232
50. Padial JM, Miralles A, De la Riva I, Vences M. The integrative future of taxonomy. Front Zool. 2010;7: 1–14. doi: 10.1186/1742-9994-7-1
51. Janzen DH, Hajibabaei M, Burns JM, Hallwachs W, Remigio E, Hebert PDN. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philos Trans R Soc Lond B Biol Sci. 2005;360: 1835–1845. doi: 10.1098/rstb.2005.1715 16214742
52. Janzen DH, Hallwachs W, Harvey DJ, Darrow K, Rougerie R, Hajibabaei M, et al. What happens to the traditional taxonomy when a well-known tropical saturniid moth fauna is DNA barcoded? Invertebr Syst. 2012;26(6): 478–505. doi: 10.1071/IS12038
53. Smith AM, Fernández-Triana JL, Eveleigh E, Gómez J, Guclu C, Hallwachs W, et al. DNA barcoding and the taxonomy of Microgastrinae wasps (Hymenoptera, Braconidae): impacts after 8 years and nearly 20 000 sequences. Mol Ecol Resour 2012;13: 168–176. doi: 10.1111/1755-0998.12038 23228011
54. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2005. GenBank. Nucleic Acids Res, 2005;33(Database issue): D34–8. doi: 10.1093/nar/gki063 15608212
55. Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, et al. A ranking system for reference libraries of DNA barcodes: Application to marine fish species from Portugal. Plos One. 2012;7(4): doi: 10.1371/journal.pone.0035858 22558244
56. Meyer CP, Paulay G (2005) DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLOS Biology 3(12): e422. doi: 10.1371/journal.pbio.0030422 16336051
57. Wiemers M., & Fiedler K. (2007). Does the DNA barcoding gap exist?–a case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in zoology, 4(1), 8.
58. Puillandre N., Macpherson E., Lambourdière J., Cruaud C., Boisselier-Dubayle M. C., & Samadi S. (2011). Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda: Eumunididae). Invertebrate Systematics, 25(4), 322–333.
59. Liu Z, Ci X, Li L, Li H, Conran JG, Li J. DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. Plos One, 2017;12(4). doi: 10.1371/journal.pone.0175788 28414813
60. Vernooy R, Haribabu E, Muller MR, Vogel JH, Hebert PDN, Schindel DE, et al. Barcoding life to conserve biological diversity: Beyond the taxonomic imperative. PLoS Biol 2010;8: e1000417. doi: 10.1371/journal.pbio.1000417 20644709
61. Milić D, Radenković S, Ačanski J, Vujić A. The importance of hidden diversity for insect conservation: a case study in hoverflies (the Merodon atratus complex, Syrphidae, Diptera). J Insect Conserv. 2019;23(1): 29–44. doi: 10.1007/s10841-018-0111-7
62. Levesque-Beaudin V., Rosati M. E., Silverson N., Warne C. P., Brown A., Telfer A. C., Sobel C. N., Miskie R. N., Miller M. E., Sones J. E., Miller S. E., and de Waard J. R. 2017. Museum harvesting in major natural history collections. Genome 60(11):962. doi: 10.1139/gen-2017-0178
63. Hebert PDN, deWaard JR, Landry JF. DNA barcodes for 1/1000 of the animal kingdom. Biol Lett 2009;6: 359–362. doi: 10.1098/rsbl.2009.0848 20015856
64. deWaard JR, Hebert PDN, Humble LM. A comprehensive DNA barcode library for the looper moths (Lepidoptera: Geometridae) of British Columbia, Canada. Plos One. 2011;6: doi: 10.1371/journal.pone.0018290 21464900
65. Hebert PDN, deWaard JR, Zakharov EV, Prosser SWJ, Sones JE, McKeown JTA, et al. A DNA 'barcode blitz': Rapid digitization and sequencing of a natural history collection. Plos One 2013;8(7). doi: 10.1371/journal.pone.0068535 23874660
66. Prosser S, Martínez-Arce A, Elías-Gutiérrez M. A new set of primers for COI amplification from freshwater microcrustaceans. Mol. Ecol. Resour. 2013;13(6): 1151–1155. doi: 10.1111/1755-0998.12132 23795700.
Článek vyšel v časopise
PLOS One
2019 Číslo 9
- Proč jsou nemocnice nepřítelem spánku? A jak to změnit?
- Dlouhodobá ketodieta může poškozovat naše orgány
- „Jednohubky“ z klinického výzkumu – 2024/42
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- MUDr. Jana Horáková: Remise již dosahujeme u více než 80 % pacientů s myastenií