DNA Barcoding of Invasive Species

Fifty Years of Invasion Ecology: The Legacy of Charles Elton

Volumn , Issue , 2010, Pages 289-299

  Cross, Hugh B ^a,b   Lowe, Andrew J ^a,b   Gurgel, Frederico D ^a,b,c  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b State Herbarium of South Australia   (Australia)

^c SOUTH AUSTRALIAN RESEARCH AND DEVELOPMENT INSTITUTE   (Australia)

Author keywords

Consortium on the Barcoding of Life (CBOL); DNA barcoding of invasive species; DNA barcoding, a universal standard molecular marker to identify all species around the world; DNA barcoding, an international initiative beginning in 2003; DNA barcoding, lingua franca identifying positively all specimens of a species; Early and rapid identification of invasive species; Genetic identification above and below species level; Greatest challenges in handling what Elton termed 'ecological explosions'; New international initiative transforming research, into invasive species; Ultimate goal of DNA barcoding research into invasive species and monitoring development of a handheld device, 'DNA barcorder'

Indexed keywords

EID: 84886063667     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781444329988.ch22     Document Type: Chapter

References (60)

1. Armstrong, K.F. & Ball, S.L.(2005)DNA barcodes for biosecurity: invasive species identification. Philosophical Transactions of the Royal Society B, 360, 1813-1823.
2. Chen, S., Yao, H., Han, J., et al.(2010)Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE, 5, e8613.
3. Cho, G.Y., Choi, D.W., Kim, M.S. & Boo, S.M.(2009)Sequence repeats enlarge the internal transcribed spacer 1 region of the brown alga Colpomenia sinuosa (Scytosiphonaceae, Phaeophyceae). Phycological Research, 57, 242-250.
4. Chown, S., Sinclair, B. & van Vuuren, B.(2008)DNA barcoding and the documentation of alien species establishment on sub-Antarctic Marion Island. Polar Biology, 31, 651-655.
5. Cooper, A. & Poinar, H.(2000)Ancient DNA: do it right or not at all. Science, 289, 1139.
6. Darling, J.A. & Blum, M.J.(2007)DNA-based methods for monitoring invasive species: a review and prospectus. Biological Invasions, 9, 751-765.
7. Elton, C.S.(1958)The ecology of invasions by animals and plants. Methuen, London.
8. Fazekas, A.J., Burgess, K.S., Kesanakurti, P.R., et al.(2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE, 3, e2802.
9. Gomez, A., Wright, P.J., Lunt, D.H., Cancino, J.M., Carvalho, G.R. & Hughes, R.N.(2007)Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of Royal Society London B, 274, 199-207.
10. Gurgel, C.F.D. & Fredericq, S.(2004)Systematics of the Gracilariaceae (Gracilariales, Rhodophyta): a critical assessment based on rbc L sequence analysies. Journal of Phycology, 40, 138-159.
11. Gurgel C.F.D., Fredericq S. & Norris, J.N.(2004) Phylogeography of Gracilaria tikvahiae (Gracilariaceae, Rhodophyta): a study of genetic discontinuity in a continuously distributed species. Journal of Phycology, 40, 748-758.
12. Hajibabaei, M., Singer, G.A., Hebert, P.D. & Hickey, D.(2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 23, 167-172.
13. Hajibabaei, M., Smith, M., Janzen, D. H., Rodriguez, J., Whitfield, J. & Hebert, P.(2006)A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6, 959-964.
14. Hall, N.(2007)Advanced sequencing technologies and their wider impact in microbiology. Journal of Experimental Biology, 210, 1518-1525.
15. Hebert, P. & Gregory, T.(2005)The promise of DNA barcoding for taxonomy. Systematic Biology, 54, 852-859.
16. Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003a)Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B, 270, 313-321.
17. Hebert, P.D.N., Ratnasingham, S. and deWaard, J.R.(2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Royal Society of London B, 270(Supplement), S96-S99.
18. Hebert, P.D.N., Penton, E.H., Burns, J.M., Janzen, D.H. & Hallwachs, W.(2004)Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfiy Astraptes fulgerator. Proceedings of the National Academy of Sciences of the USA, 101, 14812-14817.
19. Holland, B.S., Dawson, M.N., Crow, G.L. & Hofmann, D.K. (2004)Global phylogeography of Cassiopea (Scyphozoa: Rhizostomeae): molecular evidence for cryptic species and multiple invasions of the Hawaiian Islands. Marine Biology, 145, 1119-1128.
20. Ivanova, N., Borisenko, A. & Hebert, P.D.N.(2009)Express barcodes: racing from specimen to identification. Molecular Ecology Resources, 9, 35-41.
21. Janzen, D.H.(2004)Now is the time. Philosophical transactions of the Royal Society of London B, 359, 731-732.
22. Janzen, D.H., Hajibabaei, M., Burns, J.M., Hallwachs, W., Remigio, E. & Hebert, P.D.N.(2005)Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society B, 360, 1835-1845.
23. Kang, M., Buckley, Y. & Lowe, A.J.(2007)Testing the role of genetic factors across multiple independent invasions of the shrub Scotch broom(Cytisus scoparius). Molecular Ecology, 16, 4662-4673.
24. Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A. & Janzen, D.H.(2005)Use of DNA barcodes to identify fiowering plants. Proceedings of the National Academy of Sciences of the USA, 102, 8369-8374.
25. Kress, W.J. & Erickson, D.L.(2008)DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the USA, 105, 2761-2762.
26. Kress, W., Erickson, D. & Shiu, S.(2007)A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE, 2, e508.
27. Lane, C., Lindstrom, S. & Saunders, G.(2007)A molecular assessment of northeast Pacific Alaria species (Laminariales,Phaeophyceae) with reference to the utility of DNA barcoding. Molecular Phylogenetics and Evolution, 44, 634-648.
28. Margulies, M., Egholm, M., Altman, W., et al.(2005)Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
29. Meusnier, I., Singer, G.A.C., Landry, J.-F., Hickey, D.A., Hebert, P.D.N. & Hajibabaei, M.(2008)A universal DNA mini-barcode for biodiversity analysis. BMC Genomics, 9, 214.
30. Noor, M. & Feder, J.(2006)Speciation genetics: evolving approaches. Nature Reviews
31. Okuyama, Y., Fujii, N., Wakabayashi, M., et al.(2005) Nonuniform concerted evolution and chloroplast capture: heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (Saxifragaceae). Molecular Biology and Evolution, 22, 285-296.
32. Porter, T., Skillman, J. & Moncalvo, J.(2008)Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Molecular Ecology, 17, 3037-3050.
33. Plant Working Group(2009)A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the USA, 106, 12794-12797.
34. Prentis, P.J., Sigg, D.P., Raghu, S., Dhileepan, K. & Lowe, A.J. (2009)Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management. Diversity and Distributions, 15, 822-830.
35. Prentis, P., Wilson, J.R.U., Dormontt, E.E., Richardson, D.M & Lowe, A.J.(2008)Adaptive evolution in invasive species. Trends in Plant Sciences, 13, 288-294.
36. Pringle, A., Adams, R.I., Cross, H.B. & Bruns, T.D.(2009)The ectomycorrhizal fungus Amanita phalloides was introduced and is expanding its range on the west coast of North America. M olecular Ecology, 1 8, 817-833.
37. Provan, J., Booth, D., Todd, N.P., Beatty, G.E. & Maggs, C.A. (2008). Tracking biological invasions in space and time: elucidating the invasive history of the green alga Codium fragile using old DNA. Diversity and Distributions, 14, 343-354.
38. Quince, C., Lanzén, A., Curtis, T., et al.(2009)Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 1-6.
39. Rokas, A. & Abbot, P.(2009)Harnessing genomics for evolutionary insights. Trends in Ecology & Evolution, 24, 192-200.
40. Rubinoff, D.(2006)Utility of mitochondrial DNA barcodes in species conservation. Conservation Biology 20, 1026-1033.
41. Santana, Q.C., Coetzee, M., Steenkamp, E.T., Mlonyeni, O.X., Hammond, G.N.A. & Wingfield, B. D.,(2009)Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques, 46, 217-223.
42. Saunders, G.W.(2005)Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philosophical Transactions of the Royal Society B, 360, 1879-1888.
43. Saunders, G.W.(2009)Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia. Molecular Ecology Resources, 9, 140-150.
44. Scheffer, S.J., Lewis, M.L. & Joshi, R.C.(2006)DNA barcoding applied to invasive leafminers (Diptera: Agromyzidae) in the Philippines. Annals of the Entomological Society of America, 99, 204-210.
45. Seifert, K.(2009)Progress towards DNA barcoding of fungi. Molecular Ecology Resources, 9, 83-89.
46. Singh, J., Behal, A., Singla, N., et al.(2009)Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnology Journal, 4, 480-494.
47. Sogin, M., Morrison, H., Huber, J., et al.(2006)Microbial diversity in the deep sea and the underexplored ' rare biosphere '. Proceedings of the National Academy of Sciences of the USA, 103, 12115-12120.
48. Swaminathan, K., Varala, K. & Hudson, M.(2007)Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics, 8, 132.
49. Taberlet, P., Coissac, E., Pompanon, F., et al.(2007)Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, e14.
50. Tomaru, N., Takahashi, M., Tsumura, Y., Takahashi, M. & Ohba, K.(1998)Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA. American Journal of Botany, 85, 629-636.
51. Thomsen, M.S., Gurgel, C.F.D., Fredericq, S. & McGlathery, K.J..(2006)G racilaria vermiculophylla (Rhodophyta, Gracilariales) in Hog Island Bay, Virginia: a cryptic alien invasive macroalga and taxonomic correction. Journal of Phycology, 42, 139-141.
52. van de Wiel, C., Van Der Schoot, J., Van Valkenburg, J., Duistermaat, H. & Smulders, M.(2009)DNA barcoding discriminates the noxious invasive plant species, fioating pennywort(Hydrocotyle ranunculoides L.f.), from non-invasive relatives. Molecular Ecology Resources, 9, 1086-1091.
53. van Orsouw, N., Hogers, R., Janssen, A., et al.(2007) Complexity reduction of polymorphic sequences (CRoPS ™): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE, 2, 1-10.
54. van Geel, B., Aptroot, A., Baittinger, C., et al.(2008)The ecological implications of a Yakutian mammoth's last meal. Quaternary Research, 69, 361-376.
55. Venter, J.C., Remington, K., Heidelberg, J.F., et al.(2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.
56. Verbruggen, H., Tyberghein, L., Pauly, K., et al.(2009) Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda. Global Ecology and Biogeography, 18, 393-405.
57. Vialle, A., Feau, N., Allaire, M., et al.(2009)Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Molecular Ecology Resources, 9, 99-113.
58. White, T., Bruns, T.D., Lee, S. & Taylor, J.(1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications (ed. M.D. Innis, D. Gelfand, J. Sninsky and T. White), pp. 315-322. Academic Press, San Diego.
59. Willerslev, E., Cappellini, E., Boomsma, W., et al.(2007) Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science, 317, 111-114.
60. Wilson, J.R.U., Dormontt, E.E., Prentis, P.J., Lowe, A.J. & Richardson, D.M.(2009)Something in the way you move: dispersal pathways affect invasion success. Trends in Ecology & Evolution, 24, 136-144.