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“COI-like” Sequences Are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies

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Abstract The cytochrome c oxidase subunit I (COI) gene plays a pivotal role in a global effort to document biodiversity and continues to be a gene of choice in phylogenetic and phylogeographic studies. Due to increased attention on this gene as a species' barcode, quality control and sequence homology issues are re-emerging. Taylor and Knouft (2006) attempted to examine gonopod morphology in light of the subgeneric classification scheme within the freshwater crayfish genus Orconectes using COI sequences. However, their erroneous analyses were not only based on supposed mitochondrial sequences but also incorporated many questionable sequences due to the possible presence of numts and manual editing or sequencing errors. In fact, 22 of the 86 sequences were flagged as “COI-like” by GenBank due to the presence of stop codons and indels in what should be the open reading frame of a conservative protein-coding gene. A subsequent search of “COI-like” accessions in GenBank turned up a multitude of taxa across Crustacea from published and unpublished studies thereby warranting this illustrated discussion about quality control, pseudogenes, and sequence composition.

Affiliations: 1: University of South Carolina, Belle W. Baruch Institute of Marine and Coastal Sciences, Columbia, South Carolina 29208, U.S.A. and IAP World Services, NOAA, 705 Convent Avenue, Pascagoula, Mississippi 39567, U.S.A. (

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    • Publication Date : 22 May 2013
    • DOI : 10.1651/08-3020.1_001
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1. Arctander P. 1995 "Comparison of a mitochondrial gene and a corresponding nuclear pseudogene." Proceedings of the Royal Society of London, Series B, Biological Sciences Vol 262 13 19
2. Bensasson D. , Zhang D. , Hartl D. L. , Hewitt G. M. 2001 "Mitochondrial pseudogenes: evolution's misplaced witnesses." Trends in Ecology and Evolution Vol 16 314 321
3. Blankenship L. E. , Yayanos A. A. 2005 "Universal primers and PCR of gut contents to study marine invertebrate diets." Molecular Ecology Vol 14 891 899
4. Buhay J. E. , Crandall K. A. 2005 "Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes." Molecular Ecology Vol 14 4259 4273
5. Buhay J. E. , Crandall K. A. 2008 "Taxonomic revision of cave crayfish in the genus Orconectes, subgenus Orconectes (Decapoda: Cambaridae) along the Cumberland Plateau, including a description of a new species - Orconectes barri." Journal of Crustacean Biology Vol 28 57 67
6. Clark E. 1936 "The freshwater and land crayfishes of Australia." Memoirs of the National Museum of Victoria Vol 10 5 58
7. Collins T. M. , Wimberger P. H. , Naylor G. J P. 1994 "Compositional Bias, Character-State Bias, and Character-State Reconstruction Using Parsimony." Systematic Biology Vol 43 482 496
8. Cope E. D. 1872 "On the Wyandotte Cave and its fauna." American Naturalist Vol 6 406 422
9. Costa F. O. , deWaard J. R. , Boutillier J. , Ratnasingham S. , Dooh R. , Hajibabaei M. , Hebert P. D N. 2007 "Biological identifications through DNA barcodes: the case of the Crustacea." Canadian Journal of Fisheries and Aquatic Sciences Vol 64 272 295
10. Cracraft J. , Felsenstein J. , Vaughn J. , Helm-Bychowski K. 1998 "Sorting out tigers (Panthera tigris): Mitochondrial sequences, nuclear inserts, systematics, and conservation genetics." Animal Conservation Vol 1 139 150
11. Cracraft J. , Fitzpatrick J. F. Jr. 1996 "Crayfish molecular systematics: using a combination of procedures to estimate phylogeny." Systematic Biology Vol 45 1 26
12. Cracraft J. , Rudolph E. H. 2007 "A new species of burrowing crayfish Virilastacus retamali (Decapoda: Parastacidae) from the southern Chile peatland." Journal of Crustacean Biology Vol 27 502 512
13. Dayrat B. 2005 "Towards integrative taxonomy." Biological Journal of the Linnean Society Vol 85 407 415
14. Edgar R. C. 2004 "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Research Vol 32 1792 1797
15. Fetzner J. W. Jr. 1996 "Biochemical systematics and evolution of the crayfish genus Orconectes (Decapoda: Cambaridae)." Journal of Crustacean Biology Vol 16 111 141
16. 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." Molecular Marine Biology and Biotechnology Vol 3 294 299
17. Griffiths C. S. 1997 "Correlation of Functional Domains and Rates of Nucleotide Substitution in Cytochrome b." Molecular Phylogenetics and Evolution Vol 7 352 365
18. Hall T. A. 1999 "BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT." Nucleic Acids Symposium Series Vol 41 95 98
19. Hansen B. , Smolenski A. J. 2002 "A preliminary examination of the molecular relationships of some crayfish species from the genus Parastacoides (Decapoda: Parastacidae), pp. 547-554." In, G. J. Whisson and B. Knott (eds.), Freshwater Crayfish 13: Proceedings of the 13th symposium of the International Association of Astacology
20. Hazkani-Covo E. , Graur D. 2007 "A comparative analysis of numt evolution in human and chimpanzee." Molecular Biology and Evolution Vol 24 13 18
21. Hebert P. D N. , Cywinska A. , Ball S. L. , de Waard J. R. 2003a "Biological identifications through DNA barcodes." Proceedings of the Royal Society B Vol 270 313 322
22. Hebert P. D N. , Ratnasingham S. , deWaard J. R. 2003b "Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species." Proceedings of the Royal Society of London B Vol 270 596 599
23. Hebert P. D N. , Penton E. H. , Burns J. M. , Janzen D. H. , Hallwachs W. 2004a "Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator." Proceedings of the National Academy of Sciences USA Vol 101 14812 14817
24. Hebert P. D N. , Stoeckle M. Y. , Zemlak T. S. , Francis C. M. 2004b "Identification of birds through DNA barcodes." PLoS Biology Vol 2 1657 1663
25. Hogg I. D. , Hebert P. D N. 2004 "Biological identification of springtails (Collembola: Hexapoda) from the Canadian Arctic, using mitochondrial DNA barcodes." Canadian Journal of Zoology Vol 82 749 754
26. Huelsenbeck J. P. , Ronquist F. 2001 "MrBayes: Bayesian inference of phylogeny." Bioinformatics Vol 17 754 755
27. Lopez J. V. , Yuhki N. , Masuda R. , Modi W. , O'Brien S. J. 1994 "Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat." Journal of Molecular Evolution Vol 39 174 190
28. Maddison W. P. , Maddison D. R. 2002 "MacClade: Analysis of Phylogeny and Character Evolution. Version 4.0." Sinauer: Sunderland, Massachusetts
29. Meyer C. P. , Paulay G. 2005 "DNA Barcoding: Error Rates Based on Comprehensive Sampling." PLoS Biology Vol 3 e422
30. Miller A. D. , Nguyen T. T T. , Burridge C. P. , Austin C. M. 2004 "Complete mitochondrial DNA sequences of the Australian freshwater, Cherax destructor (Crustacea: Decapoda: Parasticidae): a novel gene order revealed." Gene Vol 331 65 72
31. Moritz C. , Cicero C. 2004 "DNA barcoding: promise and pitfalls." PLoS Biology 2, e354
32. Nguyen T. T T. , Murphy N. P. , Austin C. M. 2002 "Amplification of multiple copies of mitochondrial Cytochrome b gene fragments in the Australian freshwater crayfish, Cherax destructor Clark (Parastacidae: Decapoda)." Animal Genetics Vol 33 304 308
33. Olsen L. E. , Yoder A. D. 2002 "Using secondary structure to identify ribosomal numts: cautionary examples from the human genome." Molecular Biology and Evolution Vol 19 93 100
34. Paquin P. , Hedin M. 2004 "The power and perils of molecular taxonomy: a case study of eyeless and endangered Cicurina (Araneae: Dictynidae) from Texas caves." Molecular Ecology Vol 13 3239 3255
35. Posada D. , Crandall K. A. 1998 "MODELTEST: Testing the model of DNA substitution." Bioinformatics Vol 14 817 818
36. Rhoades R. 1941 "Notes on some crayfishes from Alabama cave, with the description of a new species and a new subspecies." Proceedings of the United States National Museum Vol 91 141 148
37. Richly E. , Leister D. 2004 "NUMTs in sequenced eukaryotic genomes." Molecular Biology and Evolution Vol 21 1081 1084
38. Ronquist F. , Huelsenbeck J. P. 2003 "MRBAYES 3: Bayesian phylogenetic inference under mixed models." Bioinformatics Vol 19 1572 1574
39. Rozas J. , Sanchez-DelBarrio J. C. , Messeguer X. , Rozas R. 2003 "DnaSP, DNA polymorphism analyses by the coalescent and other methods." Bioinformatics Vol 19 2496 2497
40. Rubinoff D. 2006 "DNA Barcoding Evolves into the Familiar." Conservation Biology Vol 20 1548 1549
41. Schneider-Broussard R. , Neigel J. E. 1997 "A large subunit mitochondrial ribosomal DNA sequence translocated to the nuclear genomes of two stone crabs." Molecular Biology and Evolution Vol 14 156 165
42. Schneider-Broussard R. , Felder D. L. , Chlan C. A. , Neigel J. E. 1998 "Tests of phylogeographic models with nuclear and mitochondrial DNA sequence variation in the stone crabs, Menippe adina and M. mercenaria." Evolution Vol 52 1671 1678
43. Sharp P. M. , Li W. H. 1987 "The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications." Nucleic Acids Research Vol 15 1281 95
44. Sinclair E. A. , Fetzner J. W. Jr. , Buhay J. E. , Crandall K. A. 2004 "Proposal to complete a phylogenetic taxonomy and systematic revision for freshwater crayfish (Astacidae)." Freshwater Crayfish Vol 14 21 29
45. Sites J. W. Jr. , Marshall J. C. 2004 "Operational criteria for delimiting species." Annual Review of Ecology, Evolution, and Systematics Vol 35 199 227
46. 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 coamplified." Proceedings of the National Academy of Sciences U.S.A Vol 105 13486 13491
47. Sorenson M. D. , Quinn T. W. 1998 "Numts: A Challenge for Avian Systematics and Population Biology." Auk Vol 155 214 221
48. Sueoka N. 1999 "Two aspects of DNA base composition: GC content and translation-coupled deviation from intra-strand rule of A T and G C." Journal of Molecular Evolution Vol 49 49 62
49. Swofford D. L. 2001 "PAUP: Phylogenetic Analysis Using Parsimony (and other methods). Version 4." Sinauer Associates, Sunderland, Massachusetts
50. Tang B. , Zhou K. , Song D. , Yang G. , Dai A. 2003 "Molecular systematics of the Asian mitten crabs, genus Eriocheir (Crustacea: Brachyura)." Molecular Phylogenetics and Evolution Vol 29 309 316
51. Taylor C. A. , Sabaj M. H. 1998 "A new crayfish of the genus Orconectes from the Blood River drainage of western Kentucky and Tennessee (Decapoda: Cambaridae)." Proceedings of the Biological Society of Washington Vol 111 645 652
52. Taylor C. A. , Hardman M. 2002 "Phylogenetics of the crayfish subgenus Crockerinus, genus Orconectes (Decapoda: Cambaridae), based on cytochrome oxidase I." Journal of Crustacean Biology Vol 22 874 881
53. Taylor C. A. , Knouft J. H. 2006 "Historical influences on genital morphology among sympatric crayfishes: systematics and gonopod evolution in the genus Orconectes (Cambaridae)." Biological Journal of the Linnean Society Vol 89 1 12
54. Vestheim H. , Edvardsen B. , Kaartvedt S. 2005 "Assessing feeding of a carnivorous copepod using species-specific PCR." Marine Biology Vol 147 381 385
55. Wan X-F. , Xu D. , Kleinhofs A. , Zhou J. 2004 "Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes." BMC Evolutionary Biology Vol 4 19
56. Ward R. D. , Zemlak T. S. , Innes B. H. , Last P. R. , Hebert P. D N. 2005 "DNA barcoding Australia's fish species." Philosophical Transactions of the Royal Society B Vol 360 1847 1857
57. Williams S. T. , Knowlton N. 2001 "Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus." Molecular Biology and Evolution Vol 18 1484 1493
58. Woodward S. R. , Weyand N. J. , Bunnell M. 1994 "DNA sequence from Cretaceous period bone fragments." Science Vol 266 1229 1232
59. Zhang D-X. , Hewitt G. M. 1996 "Highly conserved nuclear copies of the mitochondrial control region in the desert locust Schistocerca gregaria: some implications for population studies." Molecular Ecology Vol 5 295 300
60. Zischler H. , Hoss M. , Handt O. , von Haeseler A. , van der Kuyl A. C. , Goudsmit J. 1995 "Detecting dinosaur DNA." Science Vol 268 1192 1193

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