How many loci does it take to DNA barcode a crocus?

PLoS ONE

Volumn 4, Issue 2, 2009, Pages

  Seberg, Ole ^a   Petersen, Gitte ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CROCUS; DNA BARCODING; GENE LOCUS; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLANT TAXONOMY; PLASTID; SEQUENCE ANALYSIS; SPECIES IDENTIFICATION;

ANIMALIA; CROCUS; EMBRYOPHYTA;

EID: 80053328730     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004598     Document Type: Article

References (39)

1. Blaxter ML (2004) The promise of a DNA taxonomy. Philo Trans R Soc Lond B Biol Sci 359: 669-679.
2. Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. Bioessays 29: 188-197.
3. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, et al. (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360: 1889-1895.
4. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102: 8369-8374.
5. Newmaster SG, Fazekas AJ, Ragupathy S (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot 84: 335-341.
6. Cowan RS, Chase MW, Kress WJ, Savolainen V (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55: 611-616.
7. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, et al. (2008) Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well. PLoS ONE 3: e2802.
8. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, et al. (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A 26: 2923-2928.
9. Muse SV (2000) Examining rates and patterns of nucleotide substitution in plants. Plant Mol Biol 42: 25-43.
10. Wendel JF, Schnabel A, Seelanan T (1995) Bidirctional interlocus concereted eolution following allopolyploid speciciation in cotton ( Gossypium). Proc Natl Acad Sci U S A 92: 280-284.
11. Kane NC, Cronk QCB (2008) Meeting Review: Botany without borders: barcoding in focus. Mol Ecol 17: 5175-5176.
12. Kress WJ, Erickson DL (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.
13. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, et al. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35: e14.
14. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madriñán S, et al. (2007) A proposal for a standarised protocol to barcode all land plants. Taxon 56: 295-299.
15. Pennisi E (2007) Wanted: A barcode for plants. Science 318: 190-191.
16. Edwards D, Horn A, Taylor D, Savolainen V, Hawkins JA (2008) DNA barcoding of a large genus, Aspalathus L. (Fabaceae). Taxon 57: 1317-1327.
17. Presting GG (2006) Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Can J Bot 84: 1434-1443.
18. Petersen G, Seberg O, Thorsø S, Jørgensen T, Mathew B (2008) A phylogeny of the genus Crocus (Iridaceae) based on sequence data from five plastid regions. Taxon 57: 487-499.
19. Syring J, Farrell K, Businsky R, Cronn R, Liston A (2007) Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus. Syst Biol 56: 163-181.
20. Funk DJ, Omland KE (2003) Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA. Annu Rev Ecol Syst 34: 397-423.
21. Meyer CP, Paulay G (2005) DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLoS Biology 3: 2229-2238.
22. Costa FO, DeWaard JR, Boutillier J, Ratnasingham S, Dooh RT, et al. (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64: 272-295.
23. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103: 968-971.
24. Hillis DM, Bull JJ (1993) An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis. Syst Biol 42: 182-192.
25. Davies TJ, Barraclough TG, Chase MW, Soltis PS, Soltis DE, et al. (2004) Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc Natl Acad Sci USA 101: 1904-1909.
26. Helfenbein KG, DeSalle R (2005) Falsifications and corroborations: Karl Popper's influence on systematics. Mol Phylogenet Evol 35: 271-280.
27. Little DP, Stevenson DW (2007) A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23: 1-21.
28. Kress WJ, Erickson DL (2008) DNA barcodes: Genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105: 2761-2762.
29. Sass C, Little DP, Stevenson DW, Specht CD (2007) DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS ONE 2: e1154.
30. Rubinoff D, Cameron S, Will K (2006) Are plant DNA barcodes a search for the Holy Grail? Trends Ecol Evol 21: 1-2.
31. Mathew B (1982) The Crocus. Portland, OR: Timber Press. 127 p.
32. Olmstead RG, Sweere JA (1994) Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the Solanaceae. Syst Biol 43: 467-481.
33. Kress WJ, Liu AZ, Newman M, Li QJ (2005) The molecular phylogeny of Alpinia (Zingiberaceae): A complex and polyphyletic genus of gingers. Amer J Bot 92: 167-178.
34. Sang T, Donoghue MJ, Zhang D (1997) Evolution of alcohol dehydrogenase genes in peonies (Paeonia); phylogenetic relationships of putative nonhybrid species. Mol Biol Evol 14: 994-1007.
35. Tate JA, Simpson BB (2003) Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploidy species. Syst Bot 28: 723-737.
36. Swofford DL (2001) PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), version 4.0b8 [computer program]. Sunderland, Mass.: Sinauer Associates.
37. Maddison WP, Maddison DR (2000) MacClade, version 4.08 [computer program]. Sunderland, Massachusetts: Sinauer Associates.
38. Nixon KC (2002) WinClada, version 1.00.08 [computer program]. Ithaca, NY.: The Author.
39. Goloboff PA (1999) NONA (NO NAME), version 2 [computer program]. Tucumán, Argentina: The Author.