Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 36, 2008, Pages 13486-13491

  Song, Hojun ^a   Buhay, Jennifer E ^a,b   Whiting, Michael F ^a   Crandall, Keith A ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Cytochrome c oxidase I; Decapoda; Orthoptera

Indexed keywords

MITOCHONDRIAL DNA; NUCLEOTIDE;

ARTHROPOD; ARTICLE; CRAYFISH; DNA BARCODING; DNA SEQUENCE; GENE AMPLIFICATION; GENE CONTROL; GENETIC VARIABILITY; GRASSHOPPER; NONHUMAN; NUCLEAR MITOCHONDRIAL PSEUDOGENE; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; PSEUDOGENE; QUALITY CONTROL; SPECIES DIFFERENTIATION; STOP CODON;

ANIMALS; ASTACOIDEA; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENE AMPLIFICATION; GRASSHOPPERS; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGENY; PSEUDOGENES;

ARTHROPODA; ASTACOIDEA; EUKARYOTA; ORTHOPTERA;

EID: 51649110939     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0803076105     Document Type: Article

References (34)

1. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397-423.
2. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc London Ser B: 270:313-322.
3. Rubinoff D, Cameron S, Will K (2006) A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. J Hered 97:581-594.
4. Campbell NJH, Barker SC (1999) The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: Fivefold tandem repetition of a coding region Mol Biol Evol 16:732-740.
5. Frey JE, Frey B (2004) Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): Mitochondrial heteroplasmy or nuclear integration? Hereditas 140:92-98.
6. Hurst GDD, Jiggins FM (2005) Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proc R Soc London Ser B: 272:1525-1534.
7. Zhang D-X, Hewitt GM (1996) Nuclear integrations: Challenge for mitochondrial DNA markers. Trends Ecol Evol 11:247-251.
8. Bensasson D, Zhang D-X, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: Evolution's misplaced witnesses. Trends Ecol Evol 16:314-321.
9. Whitworth TL, Dawson RD, Magalon H, Baudry E (2007) DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proc R Soc London Ser B: 274:1731-1739.
10. Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081-1084.
11. Gellissen G, Bradfield JY, White BN, Wyatt GR (1983) Mitochondrial DNA sequences in the nuclear genome of a locust. Nature 301:631-634.
12. Lopez JV, Yuhki N, Masuda R, Modi W, O'Brien SJ (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39:174-190.
13. Pamilo P, Viljakainen L, Vihavainen A (2007) Exceptionally high density of NUMTs in the honeybee genome. Mol Biol Evol 24:1340-1346.
14. 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. Mol Mar Biol Biotechnol 3:294-299.
15. Simon C, et al. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87:651-701.
16. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812-14817.
17. Bensasson D, Zhang D-X, Hewitt GM (2000) Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Mol Biol Evol 17:406-415.
18. Williams ST, Knowlton N (2001) Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Mol Biol Evol 18:1484-1493.
19. Nguyen TTT, Murphy NP, Austin CM (2002) Amplification of multiple copies of mitochondrial cytochrome b gene fragments in the Australian freshwater crayfish, Cherax destructor Clark (Parastacidae; Decapoda). Anim Genet 33:304-308.
20. Mirol PM, Mascheretti S, Searle JB (2000) Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, Rodentia) with either great similarity to or high divergence from the true mitochondrial sequence. Heredity 84:538-547.
21. Bensasson D, Petrov DA, Zhang D-X, Hartl DL, Hewitt GM (2001) Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol Biol Evol 18:246-253.
22. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852-859.
23. Lopez JV, Culver M, Stephens JC, Johnson WE, O'Brien SJ (1997) Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol Biol Evol 14:277-286.
24. Brower AVZ (2006) Problems with DNA barcodes for species delimitation: 'Ten species' of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Syst Biodivers 4:127-132.
25. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312.
26. Pereira SL, Baker AJ (2004) Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: Implications for molecular inference of population history and phylogenetics. BMC Evol Biol 4:17.
27. Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L (2004) Unreliable mtDNA data due to nuclear insertions: A cautionary tale from analysis of humans and other great apes. Mol Ecol 13:321-335.
28. Burns JM, Janzen DH, Hajibabaei M, Hallwachs W, Hebert PDN (2007) DNA barcodes of closely related (but morphologically and ecologically distinct) species of skipper butterflies (Hesperiidae) can differ by only one to three nucleotides. J Lepid Soc 61:138-153.
29. Sun CW, Callis J (1993) Recent stable insertion of mitochondrial DNA into an Arabidopsis polyubiquitin gene by nonhomologous recombination. Plant Cell 5:97-107.
30. Sorenson MD, Quinn TW (1998) Numts: A challenge for avian systematics and population biology. Auk 115:214-221.
31. Podnar M, Haring E, Pinsker W, Mayer W (2007) Unusual origin of a nuclear pseudogene in the Italian wall lizard: Intergenomic and interspecific transfer of a large section of the mitochondrial genome in the genus Podacris (Lacertidae). J Mol Evol 64:308-320.
32. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163.
33. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
34. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.