Potential efficacy of mitochondrial genes for animal DNA barcoding: A case study using eutherian mammals

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Luo, Arong ^a,b   Zhang, Aibing ^c   Ho, Simon Y W ^d   Xu, Weijun ^e   Zhang, Yanzhou ^a   Shi, Weifeng ^f   Cameron, Stephen L ^g   Zhu, Chaodong ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c CAPITAL NORMAL UNIVERSITY   (China)

^d UNIVERSITY OF SYDNEY   (Australia)

^e NANJING NORMAL UNIVERSITY   (China)

^f UNIVERSITY COLLEGE DUBLIN   (Ireland)

^g CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL PROTEIN; CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

ARTICLE; CASE STUDY; CONTROLLED STUDY; CYTOCHROME OXIDASE 1 GENE; DNA BARCODING; DNA DETERMINATION; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; MAMMAL; MITOCHONDRIAL GENE; MITOCHONDRIAL GENOME; NUCLEOTIDE SEQUENCE; SPECIES IDENTIFICATION; TAXONOMY; ANIMAL; CLASSIFICATION; GENETICS; METHODOLOGY;

ANIMALIA; EUTHERIA;

ANIMALS; DNA BARCODING, TAXONOMIC; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; GENOME, MITOCHONDRIAL; MAMMALS;

EID: 79251584049     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-84     Document Type: Article

References (73)

1. Ebach MC, Holdrege C. DNA barcoding is no substitute for taxonomy. Nature 2005, 434:697. 10.1038/434697b, 15815602.
2. Gregory TR. DNA barcoding does not compete with taxonomy. Nature 2005, 434:1067. 10.1038/4341067b, 15858548.
3. Cameron S, Rubinoff D, Will K. Who will actually use DNA barcoding and what will it cost?. Syst Biol 2006, 55:844-847. 10.1080/10635150600960079, 17060204.
4. Hickerson MJ, Meyer CP, Moritz C. DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 2006, 55:729-739. 10.1080/10635150600969898, 17060195.
5. Rubinoff D, Cameron S, Will K. A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. J Hered 2006, 97:581-594. 10.1093/jhered/esl036, 17135463.
6. Barcode of Life: Identifying Species with DNA Barcoding. , http://www.barcodeoflife.org/
7. Hebert PD, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 2003, 270:313-321.
8. Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, Kirk SL, Mackie PM, Hebert PD. Critical factors for assembling a high volume of DNA barcodes. Philos Trans R Soc Lond B Biol Sci 2005, 360:1959-1967. 10.1098/rstb.2005.1727, 1609220, 16214753.
9. Hebert PD, Gregory TR. The promise of DNA barcoding for taxonomy. Syst Biol 2005, 54:852-859. 10.1080/10635150500354886, 16243770.
10. Hebert PD, 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, 101:14812-14817. 10.1073/pnas.0406166101, 522015, 15465915.
11. Hebert PD, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes. PLoS Biol 2004, 2:e312. 10.1371/journal.pbio.0020312, 518999, 15455034.
12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
13. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
14. Kelly RP, Sarkar IN, Eernisse DJ, Desalle R. DNA barcoding using chitons (genus Mopalia). Mol Ecol Notes 2007, 7:177-183.
15. Abdo Z, Golding GB. A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst Biol 2007, 56:44-56. 10.1080/10635150601167005, 17366136.
16. Zhang AB, Sikes DS, Muster C, Li SQ. Inferring species membership using DNA sequences with back-propagation neural networks. Syst Biol 2008, 57:202-215. 10.1080/10635150802032982, 18398766.
17. Waugh J. DNA barcoding in animal species: progress, potential and pitfalls. Bioessays 2007, 29:188-197. 10.1002/bies.20529, 17226815.
18. CBOL Plant Working Group A DNA barcode for land plants. Proc Natl Acad Sci USA 2009, 106:12794-12797. 10.1073/pnas.0905845106, 2722355, 19666622, CBOL Plant Working Group.
19. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 2005, 102:8369-8374. 10.1073/pnas.0503123102, 1142120, 15928076.
20. Moore WS. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 1995, 49:718-726.
21. Nichols R. Gene trees and species trees are not the same. Trends Ecol Evol 2001, 16:358-364. 10.1016/S0169-5347(01)02203-0, 11403868.
22. Richly A, Leister D. NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 2004, 21:1081-1084. 10.1093/molbev/msh110, 15014143.
23. Song H, Buhay JE, Whiting MF, Crandall KA. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci USA 2008, 105:13486-13491. 10.1073/pnas.0803076105, 2527351, 18757756.
24. Xu J. The inheritance of organelle genes and genomes: patterns and mechanisms. Genome 2005, 48:951-958. 10.1139/g05-082, 16391664.
25. Wares JP, Cunningham CW. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 2001, 55:2455-2469.
26. Trontelj P, Machino Y, Sket B. Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences. Mol Phylogenet Evol 2005, 34:212-226. 10.1016/j.ympev.2004.09.010, 15579394.
27. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 1994, 3:294-299.
28. Roe AD, Sperling FA. Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding. Mol Phylogenet Evol 2007, 44:325-345. 10.1016/j.ympev.2006.12.005, 17270468.
29. Meier R, Shiyang K, Vaidya G, Ng PK. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 2006, 55:715-728. 10.1080/10635150600969864, 17060194.
30. Hebert PD, Ratnasingham S, deWaard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci 2003, 270:S96-S99.
31. Mueller RL. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst Biol 2006, 55:289-300. 10.1080/10635150500541672, 16611600.
32. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. A plea for DNA taxonomy. Trends Ecol Evol 2003, 18:70-74.
33. Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool 2005, 2:5. 10.1186/1742-9994-2-5, 555853, 15771783.
34. Vences M, Thomas M, Bonett RM, Vieites DR. Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philos Trans R Soc Lond B Biol Sci 2005, 360:1859-1868. 10.1098/rstb.2005.1717, 1609216, 16221604.
35. Aliabadian M, Kaboli M, Nijman V, Vences M. Molecular identification of birds: performance of distance-based DNA barcoding in three genes to delimit parapatric species. PLoS One 2009, 4:e4119. 10.1371/journal.pone.0004119, 2612741, 19127298.
36. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessiere J, Taberlet P, Pompanon F. An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010, 11:434. 10.1186/1471-2164-11-434, 20637073.
37. Nijman V, Aliabadian M. Performance of distance-based DNA barcoding in the molecular identification of primates. C R Biol 2010, 333:11-16. 10.1016/j.crvi.2009.10.003, 20176330.
38. Zardoya R, Meyer A. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol Biol Evol 1996, 13:933-942.
39. da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A. The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics 2008, 9:119. 10.1186/1471-2164-9-119, 2375446, 18318906.
40. Vialle A, Feau N, Allaire M, Didukh M, Martin F, Moncalvo J, Hamelin RC. Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Mol Ecol Resour 2009, 9:99-113.
41. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120. 10.1007/BF01731581, 7463489.
42. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818. 10.1093/bioinformatics/14.9.817, 9918953.
43. Luo A, Qiao H, Zhang Y, Shi W, Ho SY, Xu W, Zhang A, Zhu C. Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol 2010, 10:242. 10.1186/1471-2148-10-242, 2925852, 20696057.
44. Wildman DE, Uddin M, Opazo JC, Liu G, Lefort V, Guindon S, Gascuel O, Grossman LI, Romero R, Goodman M. Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci USA 2007, 104:14395-14400. 10.1073/pnas.0704342104, 1958817, 17728403.
45. Awadalla P, Eyre-Walker A, Smith JM. Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 1999, 286:2524-2525. 10.1126/science.286.5449.2524, 10617471.
46. Rokas A, Ladoukakis E, Zouros E. Animal mitochondrial DNA recombination revisited. Trends Ecol Evol 2003, 18:411-417.
47. Hanner R. Data standards for barcode records in INSDC (BRIs). 2005, http://www.barcoding.si.edu/PDF/DWG_data_standards-Final.pdf
48. Min XJ, Hickey DA. DNA barcodes provide a quick preview of mitochondrial genome composition. PLoS One 2007, 2:e325. 10.1371/journal.pone.0000325, 1828616, 17389916.
49. Nijman IJ, Otsen M, Verkaar EL, de Ruijter C, Hanekamp E, Ochieng JW, Shamshad S, Rege JE, Hanotte O, Barwegen MW, Sulawati T, Lenstra JA. Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites. Heredity 2003, 90:10-16. 10.1038/sj.hdy.6800174, 12522420.
50. Halbert ND, Derr JN. A comprehensive evaluation of cattle introgression into US federal bison herds. J Hered 2007, 98:1-12. 10.1093/jhered/esl051, 17172633.
51. Talbot SL, Shields GF. Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Mol Phylogenet Evol 1996, 5:477-494. 10.1006/mpev.1996.0044, 8744762.
52. Shields GF, Adams D, Garner G, Labelle M, Pietsch J, Ramsay M, Schwartz C, Titus K, Williamson S. Phylogeography of mitochondrial DNA variation in brown bears and polar bears. Mol Phylogenet Evol 2000, 15:319-326. 10.1006/mpev.1999.0730, 10837161.
53. Swofford DL. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0 b 10. 2002, Sunderland, MA: Sinauer Associates.
54. Rubinoff D, Cameron S, Will K. Are plant DNA barcodes a search for the Holy Grail?. Trends Ecol Evol 2006, 21:1-2. 10.1016/j.tree.2005.10.019, 16701459.
55. Barrett RD, Hebert PD. Identifying spiders through DNA barcodes. Can J Zool 2005, 83:481-491.
56. Kuiken C, Hraber P, Thurmond J, Yusim K. The hepatitis C sequence database in Los Alamos. Nucleic Acids Res 2008, 36:D512-D516. 10.1093/nar/gkm962, 2238885, 18025038.
57. Nei M, Kumar S. Molecular Evolution and Phylogenetics. 2000, New York: Oxford University Press.
58. Nucleotide Home of NCBI. , http://www.ncbi.nlm.nih.gov/nuccore
59. NCBI Reference Sequence (RefSeq). , http://www.ncbi.nlm.nih.gov/RefSeq/
60. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
61. Maddison WP, Maddision DR. Mesquite: a modular system for evolutionary analysis, version 2.6. 2009, http://mesquiteproject.org
62. Levesque R. SPSS Programming and Data Management, 4th Edition: A Guide for SPSS and SAS Users. 2007, SPSS Inc., Chicago: SPSS Inc.
63. Rozas J, Rozas R. DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data. Comput Appl Biosci 1995, 11:621-625.
64. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452. 10.1093/bioinformatics/btp187, 19346325.
65. Krause J, Unger T, Nocon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW, Bray SC, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol 2008, 8:220. 10.1186/1471-2148-8-220, 2518930, 18662376.
66. Nei M. Molecular Evolutionary Genetics. 1987, New York: Columbia University Press.
67. Nei M, Miller JC. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 1990, 125:873-879. 1204113, 1975792.
68. Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 1979, 76:5269-5273. 10.1073/pnas.76.10.5269, 413122, 291943.
69. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 2001, 294:2348-2351. 10.1126/science.1067179, 11743200.
70. Gower JC. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 1966, 53:325-338.
71. Higgins DG. Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets. Comput Appl Biosci 1992, 8:15-22.
72. Felsenstein J. PHYLIP - phylogeny inference package (version 3.2). Cladistics 1989, 5:164-166.
73. Galtier N, Enard D, Radondy Y, Bazin E, Belkhir K. Mutation hot spots in mammalian mitochondrial DNA. Genome Res 2006, 16:215-222. 10.1101/gr.4305906, 1361717, 16354751.