Assessing the value of DNA barcodes and other priority gene regions for molecular phylogenetics of Lepidoptera

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Wilson, John James ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 18S; DNA;

ARTICLE; DNA BARCODING; GENE AMPLIFICATION; GENE DUPLICATION; GENE LOCATION; GENE SEQUENCE; GENUS; LEPIDOPTERA; MOLECULAR SYSTEMATICS; NONHUMAN; PHYLOGENY; SCORING SYSTEM; SPECIES DIVERSITY; TAXONOMIC RANK; ANIMAL; CLASSIFICATION; DNA SEQUENCE; GENE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

LEPIDOPTERA;

ANIMALS; BASE SEQUENCE; DNA; GENES, INSECT; LEPIDOPTERA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 77956284971     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010525     Document Type: Article

References (55)

1. Solis MA, Pogue MG (1999) Lepidoptera biodiversity: patterns and estimators. American Entomologist 45: 206-212.
2. Scoble MJ (1992) Lepidoptera: Form Function and Diversity. Oxford: Oxford University Press. 404 p.
3. Wahlberg N (2006) Lepidoptera evolution, taxonomy and systematics. Scientific report, ESF LESC Exploratory Workshop, Stockholm, Sweden, 26-29 April 2006.
4. Wahlberg N, Braby MF, Brower AVZ, de Jong R, Lee MM, et al. (2005) Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proceedings of the Royal Society BBiological Sciences 272: 1577-1586.
5. Regier JC, Cook CP, Mitter C, Hussey A (2008) A phylogenetic study of the 'bombycoid complex' (Lepidoptera) using five protein-coding nuclear genes, with comments on the problem of macrolepidopteran phylogeny. Systematic Entomology 33: 175-189.
6. Warren AD, Ogawa JR, Brower AVZ (2008) Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea). Cladistics 24: 642-676.
7. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 37: D5-D15.
8. Driskell AC, Ané C, Burleigh JG, McMahon MM, O'Meara BC, et al. (2004) Prospects for building the tree of life from large sequence databases. Science 306: 1172-1174.
9. Heath TA, Zwickl DJ, Kim J, Hillis DM (2008) Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology 57: 160-166.
10. Gatesy J, DeSalle R, Wahlberg N (2007) How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Systematic Biology 56: 355-363.
11. Mitchell A, Mitter C, Regier JC (2000) More taxa or more characters revisited: Combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Systematic Biology 49: 202-224.
12. Mitchell A (2008) DNA barcoding demystified. Australian Journal of Entomology 47: 169-173.
13. Regier JC, Grant MC, Mitter C, Cook CP, Peigler RS, et al. (2008) Phylogenetic relationships of wild silkmoths (Lepidoptera: Saturniidae) inferred from four protein-coding nuclear genes. Systematic Entomology 33: 219-228.
14. Caterino MS, Cho S, Sperling FAH (2001) The current state of insect molecular systematics: A thriving tower of Babel. Annual Review of Entomology 45: 1-54.
15. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series BBiological Sciences 270: 313-321.
16. Floyd R, Wilson JJ, Hebert PDN (2009) DNA barcodes and insect biodiversity. In: Foottit RG, Adler PH, eds. Insect Biodiversity: Science and Society. Oxford: Blackwell Publishing. pp 417-431.
17. Regier JC, Zwick A, Cummings MP, Kawahara AY, Cho S, et al. (2009) Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evolutionary Biology 9: 280.
18. Whinnett A, Zimmermann M, Willmott KR, Herrera N, Mallarino R, et al. (2005) Strikingly variable divergence times inferred across an Amazonian butterfly 'suture zone'. Proceedings of the Royal Society of London Series BBiological Sciences 272: 2525-2533.
19. Wortley AH, Scotland RW (2006) Determining the potential utility of datasets for phylogeny reconstruction. Taxon 55: 431-442.
20. Baker RH, Wilkinson GS, DeSalle R (2001) Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Systematic Biology 50: 87-105.
21. Nazari V, Zakharov EV, Sperling FAH (2007) Phylogeny, historical biogeography, and taxonomic ranking of Parnassiinae (Lepidoptera, Papilionidae) based on morphology and seven genes. Molecular Phylogenetics and Evolution 42: 131-156.
22. Sperling FA (2003) Butterfly molecular systematics: from species definitions to higher-level phylogenetics. In: Boggs CL, Watt WB, Ehrlich PR, eds. Butterflies: Ecology and Evolution Taking Flight. Chicago: The University of Chicago Press. pp 431-458.
23. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R (2005) Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences 360: 1805-1811.
24. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences USA 106: 12794-12797.
25. Cameron SL, Whiting MF (2008) The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insect: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408: 112-123.
26. Feil EJ (2004) Small change: keeping pace with microevolution. Nature Reviews Microbiology 2: 483-495.
27. Brower AV (2000) Phylogenetic relationships among the Nymphalidae (Lepidoptera) inferred from partial sequences of the wingless gene. Proceedings of the Royal Society of London Series B-Biological Sciences 267: 1201-1211.
28. Rosenberg MS, Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52: 119-124.
29. Kitching IJ, Forey PL, Humphries CJ, Williams DM (1998) Cladistics: The Theory and Practice of Parsimony Analysis 2nd Edition. Oxford: Oxford University Press. 228 p.
30. Bapteste E, Philippe H (2002) The potential value of indels as phylogenetic markers: position of Trichomonads as a case study. Molecular Biology and Evolution 19: 972-977.
31. Monaghan MT, Inward DJG, Hunt T, Vogler AP (2007) A molecular phylogenetic analysis of the Scarabaeinae (dung beetles). Molecular Phylogenetics and Evolution 45: 674-692.
32. Vane-Wright RI (2003) Evidence and identity in butterfly systematics. In Boggs CL, Watt WB, Ehrlich PH, eds. Butterflies: Ecology and Evolution Taking Flight. Chicago: University of Chicago Press. pp 477-513.
33. Brower AVZ, DeSalle R, Vogler A (1996) Gene trees, species trees, and systematics: A cladistic perspective. Annual Review of Ecology and Systematics 27: 423-450.
34. Wahlberg N, Wheat CW (2008) Genomic outposts serve the phylogenomic pioneers: Designing novel nuclear markers for genomic DNA extractions of Lepidoptera. Systematic Biology 57: 231-242.
35. Lunt DH. Zhang DX, Szymura JM, Hewitt GM (1996) The insect cytochrome oxidase I gene: evolutionary patterns and conserved primers for phylogenetic studies. Insect Molecular Biology 5: 153-165.
36. Shull VL, Vogler AP, Baker MD, Maddison DR, Hammond PM (2001) Sequence alignment of 18S ribosomal RNA and the basal relationships of adephagan beetles: evidence for monophyly of aquatic families and the placement of Trachypachindae. Systematic Biology 50: 945-969.
37. Kandul NP, Lukhtanov VA, Dantchenko AV, Coleman JWS, Sekercioglu CH, et al. (2004) Phylogeny of Agrodiaetus Hübner 1822 (Lepidoptera: Lycaenidae) inferred from mtDNA sequences of COI and COII and nuclear sequences of Ef- 1a: karyotype diversification and species radiation. Systematic Biology 53: 278-298.
38. Wenzel JW, Siddal ME (1999) Noise. Cladistics 15: 51-64.
39. Phillips AJ (2006) Homology assessment and molecular sequence alignment. Journal of Biomedical Informatics 39: 18-33.
40. Purvis A, Quicke DLJ (1997) Building phylogenies: Are the big easy? Trends in Ecology & Evolution 12: 49-50.
41. Zhang M, Cao T, Zhong Y, Ren Z, Guo Y, et al. (2008) Molecular phylogenetic analysis of the main lineages of Nymphalinae (Nymphalidae: Lepidoptera) based on the partial mitochondrial COI gene. Agricultural Sciences in China 7: 731-739.
42. Janzen D, Hallwachs W, Blandin P, Burns JM, Cadiou J-M, et al. (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Molecular Ecology Resources 9: 1-25.
43. Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, et al. (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B-Biological Sciences 360: 1959-1967.
44. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
45. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony Version 4.0b2a. Sunderland: Sinauer.
46. Goloboff PA, Catalano SA, Mirande JM, Szumik CA, Arias JS, et al. (2009) Phylogenetic analysis of 73060 taxa corroborates major eukaryotic groups. Cladistics 25: 211-230.
47. Cho SW, Mitchell A, Regier JC, Mitter C, Poole RW, et al. (1995) A highly conserved nuclear gene for low-level phylogenetics- elongation factor-1-alpha recovers the morphology-based tree for heliothine moths. Molecular Biology and Evolution 12: 650-656.
48. Mitchell A, Cho S, Regier JC, Mitter C, Poole RW, et al. (1997) Phylogenetic utility of elongation factor-1 alpha in Noctuoidea (Insecta: Lepidoptera): The limits of synonymous substitution. Molecular Biology and Evolution 14: 381-390.
49. Regier JC, Fang QQ, Mitter C, Peigler RS, Friedlander TP, et al. (1998) Evolution and phylogenetic utility of the period gene in Lepidoptera. Molecular Biology and Evolution 15: 1172-1182.
50. Pogue MG (2009) Biodiversity of Lepidoptera. In: Foottit RG, Adler PH, eds. Insect Biodiversity: Science and Society. Oxford: Blackwell Publishing. pp 263-293.
51. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of USA 103: 968-971.
52. Reed RD, Sperling FA (1999) Interaction of process partitions in phylogenetic analysis: an example from the swallowtail butterfly genus Papilio. Molecular Biology and Evolution 16: 286-297.
53. Brower AVZ, DeSalle R (1998) Patterns of mitochondrial versus nuclear DNA sequence divergence among nymphalid butterflies the utility of wingless as a source of characters for phylogenetic inference. Insect Molecular Biology 7: 73-82.
54. Wiegmann BM, Mitter C, Regier JC, Friedlander TP, Wagner DM, et al. (1999) Nuclear genes resolve Mesozoic-aged divergences in the insect order Lepidoptera. Molecular Phylogenetics and Evolution 15: 242-259.
55. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes;doi: 10.1111/ j.1471-8286.2007.01748.x.