Mitochondrial pseudogenes in insect DNA barcoding: Differing points of view on the same issue;Pseudogenes mitocondriais no DNA barcoding em insetos: Diferentes pontos de vista sobre a mesma questão

Biota Neotropica

Volumn 12, Issue 3, 2012, Pages 301-308

  Leite, Luis Anderson Ribeiro ^a  

^a FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

Author keywords

COI; Molecular; NUMTS

Indexed keywords

EID: 84873954451     PISSN: 16786424     EISSN: 16760611     Source Type: Journal    
DOI: 10.1590/S1676-06032012000300029     Document Type: Article

References (74)

1. Arthofer, W., Avtzis, D.N., Riegler, M. & Stauffer, C. 2010. Mitochondrial phylogenies in the light of pseudogenes and Wolbachia: re-assessment of a bark beetle dataset. Zookeys 56:269-280. http://dx.doi. org/10.3897/zookeys.56.531
2. Bensasson, D., Zhang, X., Hartl, D.L. & Hewitt, G.M. 2011a. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16:314-321. PMid:11369110
3. Bensasson, D., Zhang, X. & Hewitt, G.M. 2011b. Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Mol. Biol. Evol. 17:406-415.
4. Blanchard, J.L. & Schmidt, G.W. 1996. Mitochondrial DNA Migration Events in Yeast and Humans: Integration by a Common End-joining Mechanism and Alternative Perspectives on Nucleotide Substitution Pattern. J. Mol. Evol. 13:537-548. PMid:8754225
5. Borisenko, A.V., Sones, J.E. & Hebert, P.D.N. 2009. The front- end logistics of DNA barcoding: challenges and prospects. Mol. Ecol. Resour. 9:27-34. http://dx.doi.org/10.1111/j.1755-0998.2009.02629.x
6. Bravo, J.P., Silva, J.L.C., Munhoz, R.E.F. & Fernandez, M.A. 2008. DNA barcode information for the sugar cane moth borer Diatraea saccharalis. Genet. Mol. Res. 7:741-748. PMid:18767242.
7. Brower, A.V.Z. 2006. Problems with DNA barcodes for species delimitation: 'ten species' of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Syst. Biodivers. 4:127-132. http://dx.doi.org/10.1017/ S147720000500191X
8. Buhay, J.E. 2009. 'COI-like' sequences are becoming problematic in molecular systematic and DNA barcoding studies. J. Crustacean Biol. 29:96-110. http://dx.doi.org/10.1651/08-3020.1
9. Burns, J.M., Janzen, D.H., Hajibabaei, M., Hallwachs, W. & Hebert, P.D.N. 2007. DNA barcodes of closely related (but morphologically and ecologically distinct) species of skipper butterfies (Hesperiidae) can differ by only one to three nucleotides. J. Lep. Soc. 61:138-153.
10. Calvignac, S., Konecny, L., Malard, F. & Douady, C.J. 2011. Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts). Mitochondrion. 11:246-254. PMid:21047564.
11. Clare, E.L., Fraser, E.E., Braid, H.E., Fenton, M.B. & Hebert, P.D.N. 2009. Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): using a molecular approach to detect arthropod prey. Mol. Ecol. 18:2532-2542. PMid:19457192.
12. Craft, K.J., Pauls, S.U., Darrow, K., Miller, S.E., Hebert, P.D.N., Helgen, L. E., Novotny, V. & Weiblen, G.D. 2010. Population genetics of ecological communities with DNA barcodes: an example from New Guinea Lepidoptera. P. Natl. Acad. Sci. 11:5041-5046. http:// dx.doi.org/10.1073/pnas.0913084107
13. Dasmahapatra, K.K., Elias, M., Hill, R.I., Hoffman, J.I. & Mallet, J. 2010. Mitochondrial DNA barcoding detects some species that are real, and some that are not. Mol. Ecol. Resour. 10:264-273. http:// dx.doi.org/10.1111/j.1755-0998.2009.02763.x
14. D'errico, I., Gadaleta, G. & Saccone, C. 2004. Pseudogenes in metazoa: Origin and features. Brief. Funct. Gen. Prot. 3:157-167. PMid:15355597.
15. Decaëns, T. & Rougerie, R. 2008. Descriptions of two new species of Hemileucinae (Lepidoptera: Saturniidae) from the region of Muzo in Colombia - evidence from morphology and DNA barcodes. Zootaxa. 1944:34-52.
16. Ekrem, T., Willassen, E. & Stur, E. 2007. A comprehensive DNA sequence library is essential for Identification with DNA barcodes. Mol. Phylogenet. Evol. 43:530-542. http://dx.doi.org/10.1016/j. ympev.2006.11.021
17. Emery, V.J., Landry, J.F. & Eckert, C.G. 2009. Combining DNA barcoding and morphological analysis to identify specialist floral parasites (Lepidoptera:Coleophoridae: Momphinae: Mompha). Mol. Ecol. Resour. 9:217-223. http://dx.doi.org/10.1111/j.1755-0998.2009.02647.x
18. Foottit, R.G., Maw, H.E.L., Havill, N.P., Ahern, R.G. & Montgomery, E. 2009. DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea). Mol. Ecol. Resour. 9:188-195. PMid:21564978.
19. Frézal, L. & Leblois, R. 2009. Four years of DNA barcoding: Current advances and prospects. Infect. Genet. Evol. 8:727-736. PMid:18573351.
20. Geraci, C.J., Mohammed, A.A. & Zhou, X. 2011. DNA barcoding facilitates description of unknown faunas: a case study on Trichoptera in the headwaters of the Tigris River, Iraq. J. N. Am. Benthol. Soc. 30:163-173. http://dx.doi.org/10.1899/10-011.1
21. Gellisen, G., Bradfield, J.Y., White, B.N. & Wyatt, G.R. 1983. Mitochondrial DNA sequences in the nuclear genome of a locust. Nature. 301:631-634. http://dx.doi.org/10.1038/301631a0
22. Gerstein, M. & Zheng, D. 2006. The real life of pseudogenes. Sci. Am. 295:48-55. PMid:16866288.
23. Greenstone, M.H., Rowley, D.L., Heimbach, U., Lundgren, G., Pfannenstiel, R.S. & Rehner, S.A. 2005. Barcoding generalist predators by polymerase chain reaction: carabids and spiders. Mol. Ecol. 14:3247-3266. PMid:16101789.
24. Greenstone, M.H. 2006. Molecular methods for assessing insect parasitism. B. Entomol. Res. 96:1-13. http://dx.doi.org/10.1079/ BER2005402
25. Greenstone, M.H., Vandenberg, N.J. & Hu, J.H. 2011. Barcode haplotype variation in north American agroecosystem lady beetles (Coleoptera: Coccinellidae). Mol. Ecol. Resour. 11:629-637. http://dx.doi. org/10.1111/j.1755-0998.2011.03007.x
26. Hajibabaei, M., Dewaard, J.R., Ivanova, N.V., Ratnasingham, S., Dooh, R.T., Kirk, S.L., Mackie, P.M. & Hebert, P.D.N. 2005. Critical factors for assembling a high volume of DNA barcodes. Philos T. R. Soc. B. 360:1959-1967. PMid:16214753.
27. Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W. & Hebert, P.D.N. 2006. DNA barcodes distinguish species of tropical Lepidoptera. P. Natl. Acad. Sci. USA. 103:968-971. http://dx.doi. org/10.1073/pnas.0510466103
28. Hajibabaei, M., Singer, G.A.C., Hebert, P.D.N. & Hickey, D.A. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23:167-172. PMid:17316886.
29. Harrison, P.M., Milburn, D., Zhang, Z., Bertone, P. & Gerstein, M. 2003. Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res. 31:1033-1037. PMid:12560500.
30. Hausmann, A., Haszprunar, G. & Hebert, P.D.N. 2011. DNA Barcoding the Geometrid Fauna of Bavaria (Lepidoptera): Successes, Surprises, and Questions. PLoS ONE. 6:e17134. http://dx.doi. org/10.1371/journal.pone.0017134
31. Hazkani-Covo, E., Zeller, R. M. & Martin, W. 2010. Molecular poltergeists: Mitochondrial DNA copies in sequenced nuclear genomes. PLoS Genet. 6:1-11. http://dx.doi.org/10.1371/journal.pgen.1000834
32. Hebert, P.D.N., Cywinska, A., Ball, S.L. & Dewaard, J.R. 2003a. Biological identifications through DNA barcodes. P. Roy. Soc. Lond. B. 270:313-321. http://dx.doi.org/10.1098/rspb.2002.2218
33. Hebert, P.D.N., Ratnasingham, S. & Dewaard, J.R. 2003b. Barcoding animal life:cytochrome c oxidase subunit 1 divergences among closely related species. P. Roy. Soc. Lond. B. 270:S96-S99. http://dx.doi. org/10.1098/rsbl.2003.0025
34. 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 butterfy Astraptes fulgerator. P. Natl. Acad. Sci. USA. 101:14812-14817. http://dx.doi.org/10.1073/ pnas.0406166101
35. Hlaing, T., Tun-Lin, W., Somboon, P., Socheat, D., Setha, T., Min, S., Chang, M.S. & Walton, C. 2009. Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies. BMC Genet. 10:11. http://dx.doi. org/10.1186/1471-2156-10-11
36. Hrcek, J., Miller, S.E., Quicke, D.L.J. & Smith, M.A. 2011. Molecular detection of trophic links in a complex insect host-parasitoid food web. Mol. Ecol. Resour. 11(5):786-94. http://dx.doi.org/10.1111/ j.1755-0998.2011.03016.x
37. Hulcr, J., Miller, S.E., Setliff, G.P., Darrow, K., Mueller, M.D., Hebert, P.D.N. & Weiblen, G.D. 2007. DNA barcoding confrms polyphagy in a generalist moth, Homona mermerodes (Lepidoptera: Tortricidae). Mol. Ecol. Notes 7:549-57. http://dx.doi.org/10.1111/j.1471- 8286.2007.01786.x
38. Ivanova, N.V., Borisenko, A.V. & Hebert, P.D.N. 2009. Express barcodes: racing from specimen to Identification. Mol. Ecol. Resour. 9:35-41. ttp://dx.doi.org/10.1111/j.1755-0998.2009.02630.x
39. 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. Philo. T. Roy. Soc. B. 360:1835-45. http://dx.doi.org/10.1098/rstb.2005.1715
40. Janzen, D.H., Hallwachs, W., Blandin, P., Burns, J.M., Cadiou, J-M., Chacon, I., Dapkey, T., Deans, A.R., Epstein, M.E., Espinoza, B., Franclemont, J.G., Haber, W.A., Hajibabaei, M., Hall, J.P.W., Hebert, P.D.N., Gauld, I.D., Harvey, D.J., Hausmann, A., Kitching, I.J., Lafontaine, D., Landry, J-F., Lemaire, C., Miller, J.Y., Miller, J.S., Miller, L., Miller, S.E., Montero, J., Munroe, E., Green, S.R., Ratnasingham, S., Rawlins, J.E., Robbins, R.K., Rodriguez, J.J., Rougerie, R., Sharkey, M.J., Smith, M.A., Solis, M.A., Sullivan, J.B., Thiaucourt, P., Wahl, D.B., Weller, S.J., Whitfield, J.B., Willmott, K.R., Wood, D.M., Woodley, N.E. & Wilson, J.J. 2009. Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Mol. Ecol. Resour. 9:1-26. http://dx.doi. org/10.1111/j.1755-0998.2009.02628.x
41. Jinbo, U., Kato, T. & Ito, M. 2011. Current progress in DNA barcoding and future implications for entomology. Entomol. Sci. 14(2):107-24. http://dx.doi.org/10.1111/j.1479-8298.2011.00449.x
42. Jurado-Rivera, J.A., Vogler, A.P., Reid, C.A.M., Petitpierre, E. & Gómez-Zurita, J. 2009. DNA barcoding insect-host plant associations. P. Roy. Soc. B-Biol. Sci. 276:639-648. http://dx.doi. org/10.1098/rspb.2008.1264
43. Lee, W., Kim, H., Lim, J., Choi, H-R., Kim, Y., Kim, Y-S., Ji, J-Y., Foottit, R.G. & Lee, S. 2010. Barcoding aphids (Hemiptera:Aphididae) of the Korean Peninsula: updating the global data set. Mol. Ecol. Resour. 11(1):32-7. http://dx.doi.org/10.1111/j.1755-0998.2010.02877.x
44. Lukhtanov, V.A., Sourakov, A., Zakharov, E.V. & Hebert, P.D.N. 2009. DNA barcoding Central Asian butterflies: increasing geographical dimension does not signifcantly reduce the success of species Identification. Mol. Ecol. Resour. 9:1302-1310. PMid:21564901.
45. Magnacca, K.N. & Brown, M.J.F. 2010. Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae). BMC Evol. Biol. 10:174. http://dx.doi. org/10.1186/1471-2148-10-174
46. Miller, K.B., Alarie, Y., Wolfe, G.W. & Whiting, M.F. 2005. Association of insect life stages using DNA sequences: the larvae of Philodytes umbrinus (Motschulsky) (Coleoptera: Dytiscidae). Syst. Entomol. 30:499-509. http://dx.doi.org/10.1111/j.1365- 3113.2005.00320.x
47. Moulton, M.J., Song, H. & Whiting, M.F. 2010. Assessing the effects of primer specificity on eliminating numt coamplification inDNAbarcoding: a case study from Orthoptera (Arthropoda: Insecta). Mol. Ecol. Resour. 10:615-627. PMid:21565066.
48. Packer, L., Gibbs, J., Sheffield, C. & Hanner, R. 2009. DNA barcoding and the mediocrity of morphology. Mol. Ecol. Resour. 9:42-50. PMid:21564963.
49. Pamilo, P., Viljakainen, L. & Vihavainen, A. 2007. Exceptionally high density of NUMTs in the honeybee genome. Mol. Biol. Evol. 24:1340-1346. ttp://dx.doi.org/10.1093/molbev/msm055
50. Pfenninger, M., Nowak, C., Kley, C., Steinke, D. & Streit, B. 2007. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Mol. Ecol. 16(9):1957-68. http://dx.doi.org/10.1111/ j.1365-294X.2006.03136.x
51. Ratnasingham, S. & Hebert, P.D.N. 2007. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Notes. 7:355-64. ttp://dx.doi.org/10.1111/j.1471-8286.2007.01678.x
52. Raupach, M.J., Astrin, J.J., Hanning, K., Peters, M.K., Stoeckle, M.Y. & Wägele, J-W. 2010. Molecular species Identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes. Front. Zool. 7:26. http://dx.doi.org/10.1186/1742-9994-7-26
53. Richly, E. & Leister, D. 2004. NUMTs in Sequenced Eukaryotic Genomes. Mol Biol. Evol. 21:1081-1084. http://dx.doi.org/10.1093/ molbev/msh110
54. Rivera, J. & Currie, D.C. 2009. Identification of Nearctic black fies using DNA Barcodes (Diptera: Simuliidae). Mol. Ecol. Resour. 9:224-236. PMid:21564982.
55. Salokannel, J., Rantala, M.J. & Whalberg, N. 2010. DNA- barcoding clarifes species defnitions of Finnish Apatania (Trichoptera: Apataniidae). Entomol. Fennica 21:1-11.
56. Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K. & Lane, R. 2005. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philos. T. Roy. Soc. B. 360:1805-1811. http://dx.doi. org/10.1098/rstb.2005.1730
57. Sheffield, K.A., Hebert, P.D.N., Kevan, P.G. & Packer, L. 2009. DNA Barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies. Mol. Ecol. Resour. 9:196-207. http:// dx.doi.org/10.1111/j.1755-0998.2009.02645.x
58. Shufran, K.A. & Puterka, G.J. 2011. DNA Barcoding to Identify All Life Stages of Holocyclic Cereal Aphids (Hemiptera: Aphididae) on Wheat and Other Poaceae. Ann. Entomol. Soc. Am. 104:39-42. http:// dx.doi.org/10.1603/AN10129
59. Smith, M.A., Fisher, B.L. & Hebert, P.D.N. 2005. DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philos. T. Roy. Soc. B. 360:1825-1834. http://dx.doi. org/10.1098/rstb.2005.1714
60. Smith, M.A., Woodley, N.E., Janzen, D.H., Hallwachs, W. & Hebert, P.D.N. 2006. DNA barcodes reveal cryptic host-specifcity within the presumed polyphagous members of a genus of parasitoid fies (Diptera: Tachinidae). P. Natl. Acad. Sci. USA. 103:3657-3662. http:// dx.doi.org/10.1073/pnas.0511318103
61. Smith, M.A, Fernandez-Triana, J., Roughley, R. & Hebert, P.D.N. 2009. DNA barcode accumulation curves for understudied taxa and areas. Mol. Ecol. Resour. 9:208-216.
62. Song, H., Buhay, J.E., Whiting, M.F. & Crandall, K.A. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplifed. P. Natl. Acad. Sci. USA. 105:13468-13491. PMid:21564980
63. Sorenson, M.D. & Quinn, T.W. 1998. Numts: a challenge for avian systematics and population biology. The Auk. 115:214-221.
64. Strugnell, J.M. & Lindgren, A.R. 2007. A barcode of life database for the Cephalopoda? Considerations and concerns. Rev. Fish Biol. Fisher. 17:337-344. http://dx.doi.org/10.1007/s11160-007-9043-0
65. Strutzenberger, P., Brehm, G. & Fiedler, K. 2010. DNA barcoding-based species delimitation increases species count of Eois (Geometridae) moths in a well-studied tropical mountain forest by up to 50%. Insect Sci. 18:349-362. http://dx.doi.org/10.1111/j.1744- 7917.2010.01366.x
66. Sunnucks, P., HALES, D.F. 1996. Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol. Biol. Evol. 13:510-523.
67. Timmis, J.N., Ayliffe, M.A., Huang, C.Y. & Martin, W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5:123-135. PMid:14735123.
68. Vaglia, T., Haxaire, J., Kitching, I.J., Meusnier, I. & Rougerie, R. 2008. Morphology and DNA barcoding reveal three cryptic species within the Xylophanes neoptolemus and loelia species-groups (Lepidoptera: Sphingidae). Zootaxa. 1923:18-36.
69. Wheat, C.W. & Watt, W.B. 2008. A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterfies (Lepidoptera, Pieridae). Mol. Phylogenet. Evol. 47:893-902. PMid:18442929.
70. Williams, S.T. & Knowlton, N. 2001. Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp Genus Alpheus. Mol. Biol. Evol. 18:1484-1493.
71. Wilson, J.J. 2010. Assessing the Value of DNA Barcodes and Other Priority Gene Regions for Molecular Phylogenetics of Lepidoptera. PloS ONE 5:e10525. http://dx.doi.org/10.1371/journal.pone.0010525
72. Yoshitake, H., Kato, T., Jinbo, U. & Ito, M. 2008. A new Wagnerinus (Coleoptera: Curculionidae) from northern Japan: description including a DNA barcode. Zootaxa. 1740:15-27.
73. Zhang, D.X. & Hewitt, G.M. 1996. Nuclear integrations: Challenges for mitochondrial DNA markers. Trends Ecol. Evol. 11:247-251. http:// dx.doi.org/10.1016/0169-5347(96)10031-8
74. Zhou, X., Robinson, J.L., Geraci, C.J., Parker, C.R., Flint, J.R.O.S., Etnier, D.A., Ruiter, D., Dewalt, R.E., Jacobus, L.M., Hebert, P.D.N. 2011. Accelerated construction of a regional DNA-barcode reference library: caddisfies (Trichoptera) in the great smoky mountains national park. J. N. Am. Benthol. Soc. 30:131-162.