The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding

Molecular Phylogenetics and Evolution

Volumn 57, Issue 2, 2010, Pages 509-517

  Yassin, Amir ^a   Markow, Therese A ^b   Narechania, Apurva ^a   O'Grady, Patrick M ^c   DeSalle, Rob ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

COI; Integrative taxonomy; Introgression; Phylogenetic species concept; Speciation

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; DNA BARCODING; DROSOPHILA; GENETICS; METHODOLOGY; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; DNA BARCODING, TAXONOMIC; DROSOPHILA; PHYLOGENY; SPECIES SPECIFICITY;

EID: 78049382780     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.08.020     Document Type: Article

References (59)

1. Abdo Z., Golding G.B. A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst. Biol. 2007, 56:44-56.
2. Ayala F.J., Dobzhansky T. A new subspecies of Drosophila pseudoobscura (Diptera: Drosophilidae). Pan-Pac. Entomol. 1975, 50:211-219.
3. Ballard J.W.O. Comparative genomics of mitochondrial DNA in Drosophila simulans. J. Mol. Evol. 2000, 51:64-75.
4. Bull V., Beltrán M., Jiggins C.D., McMillan W.O., Bermingham E., Mallet J. Polyphyly and gene flow between non-sibling Heliconius species. BMC Biol. 2006, 4:11.
5. Burns J.M., Janzen D.H., Hajibabaei M., Hallwachs W., Hebert P.D.N. DNA barcodes of closely related (but morphologically and ecologically distinct species of butterflies (Hesperiidae) can differ by only one to three nucleotides. J. Lepidopt. Soc. 2007, 61:138-153.
6. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulous J., Bealer K., Madden T.L. BLAST plus: architecture and applications. BMC Bioinf. 2009, 10:421.
7. Dayrat B. Towards integrative taxonomy. Biol. J. Linn. Soc. 2005, 85:407-415.
8. DeSalle R. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conserv. Biol. 2006, 20:1545-1547.
9. DeSalle R. Phenetic and DNA taxonomy; a comment on Waugh. BioEssays 2007, 29:1289-1290.
10. DeSalle R., Amato G. The expansion of conservation genetics. Nat. Rev. Genet. 2004, 5:702-712.
11. DeSalle R., Grimaldi D.A. Morphological and molecular systematics of the Drosophilidae. Ann. Rev. Ecol. Syst. 1991, 22:447-475.
12. DeSalle R., Egan M.G., Siddall M. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Phil. Trans. R. Soc. Lond. B 2005, 360:1905-1916.
13. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
14. Dobzhansky T., Epling C. Taxonomy, geographic distribution, and ecology of Drosophila pseudoobscura and its relatives. Carnegie Inst. Washington Publ. 1944, 554:1-46.
15. Dyer K.A., Jaenike J. Evolutionary stable infection by a male-killing endosymbiont in Drosophila innubila: molecular evidence from the host and parasite genomes. Genetics 2004, 168:1443-1455.
16. Fazekas A.J., Kesanakurti P.R., Burgess K.S., Percy D.M., Graham S.W., Barrett S.C.H., Newmaster S.G., Hajibabaei M., Husband B.C. Are plant species inherently arder than animal species using DNA barcoding markers?. Mol. Ecol. Resour 2009, 9:130-139.
17. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Syst. 2003, 34:397-423.
18. Hebert P.D.N., Cywinska A., Ball S.L., deWaard J.R. Biological identification through DNA barcodes. Proc. R. Soc. Lond. B 2003, 270:S96-S99.
19. Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Nat. Acad. Sci. USA 2004, 101:14812-14817.
20. Hudson R.R., Coyne J.A. Mathematical consequences of the genealogical species concept. Evolution 2002, 56:1557-1565.
21. Knowles L.L., Carstens B.C. Delimiting species without monophyletic gene trees. Syst. Biol. 2007, 56:887-895.
22. Kopp A., Barmina O. Evolutionary history of the Drosophila bipectinata species complex. Genet. Res. 2005, 85:23-46.
23. Kumar S., Dudley J., Nei M., Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 2008, 9:299-306.
24. Lachaise D., Cariou M.-L., David J.R., Lemeunier F., Tsacas L., Ashburner M. Historical biogeography of the Drosophila melanogaster species subgroup. Evol. Biol. 1988, 22:159-225.
25. Lahaye R., Van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S., Barraclough T.G., Savolainen V. DNA barcoding the floras of biodiversity hotspots. Proc. Nat. Acad. Sci. USA 2008, 105:2923-2928.
26. Lou M., Golding G.B. Assigning sequences to species in the absence of large interspecific differences. Mol. Phyl. Evol. 2010, 56:187-194.
27. Lukhtanov V.A., Sourakov A., Zakharov E.V., Hebert P.D.N. DNA barcoding Central Asian butterflies: increasing geographical dimension does not successfully reduce the success of species identification. Mol. Ecol. Resour. 2009, 9:1302-1310.
28. Machado C.A., Hey J. The causes of phylogenetic conflict in a classic Drosophila species group. Proc. R. Soc. Lond. B. 2003, 270:1193-1202.
29. Maddison, W. P., Maddison, D. R., 2009. MESQUITE: a modular system for evolutionary analysis (). http://mesquiteproject.org.
30. Mallet J. What has Drosophila genetics revealed about speciation?. TREE 2006, 21:386-393.
31. Markow T.A., O'Grady P.M. Drosophila: a Guide to Species Identification and Use 2006, Elsevier, Amsterdam.
32. McDermott S.R., Kliman R.M. Estimation of isolation times in the Drosophila simulans complex. PLoS ONE 2008, 3:e2442.
33. Meier, R. 2008. DNA Sequences in Taxonomy: Opportunities and Challenges. Pages 95-128 in The New Taxonomy Systematics Association Special Volume Q. Wheeler, ed.
34. Meier R., Kwong S., Vaidya G., Ng P.K.L. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 2006, 55:715-728.
35. Meier R., Zhang G., Ali F. The use of mean instead of smallest interspecific distances exaggerates the size of the " barcoding gap" and leads to misidentification. Syst. Biol. 2008, 57:809-813.
36. Meyer C.P., Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 2005, 3:2229-2238.
37. Munch K., Boomsma W., Huelsenbeck J.P., Willerslev E., Nielsen R. Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst. Biol. 2008, 57:750-757.
38. Munch K., Boomsma W., Willerslev E., Nielsen R. Fast phylogenetic DNA barcoding. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008, 363:3997-4002.
39. Nielsen R., Matz M. Statistical approaches for DNA barcoding. Syst. Biol. 2006, 55:162-169.
40. O'Grady P.M., Lapoint R.T., Bennett G.M. The potential and peril of the supertree approach: a response to van der Linde and Houle. Insect Syst. Evol. 2008, 39:269-280.
41. Papadopoulou A., Bergsten J., Fujisawa T., Monaghan M.T., Barraclough T.G., Vogler A.P. Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete clusters. Phil. Trans. R. Soc. B 2008, 363:2987-2996.
42. Pons J., Barraclough T.G., Gomez-Zurita J., Cardoso A., Duran D.P., Hazell S., Kamoun S., Sumlin W.D., Vogler A.P. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 2006, 55:595-609.
43. Rach J., DeSalle R., Sarkar I.N., Schierwater B., Hadrys H. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proc. R. Soc. Lond. B 2008, 275:237-247.
44. Ratnasingham S., Hebert P.D.N. BOLD: the Barcode of Life Data system (www.barcodinglife.org). Mol. Ecol. Notes 2007, 7:355-364.
45. Robinson E.A., Blagoev G.A., Hebert P.D.N., Adamowicz S.J. Prospects for using DNA barcoding to identify spiders in species-rich genera. Zookeys 2009, 16:27-46.
46. Rubinoff D. DNA barcoding evolves into the familiar. Conserv. Biol. 2006, 20:1548-1549.
47. Rubinoff D. Utility of mitochondrial DNA barcodes in species conservation. Conserv. Biol. 2006, 20:1026-1033.
48. Sarkar I.N., Planet P.J., DeSalle R. CAOS software for use in character-based DNA barcoding. Mol. Ecol. Res. 2008, 8:1256-1259.
49. Savolainen V., Cowan R.S., Vogler A.P., Roderick G.K., Lane R. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Phil. Trans. R. Soc. Lond. B 2005, 360:1805-1811.
50. Shoemaker D.D., Katju V., Jaenike J. Wolbachia and the evolution of reproductive isolation between Drosophila recens and Drosophila subquinaria. Evolution 1999, 53:1157-1164.
51. Solignac M., Monnerot M. Race formation, speciation, and introgression within Drosophila simulans, D. Mauritiana, and D. sechellia inferred from mitochondrial DNA analysis. Evolution 1986, 40:531-539.
52. Sturtevant A.H. On the subdivision of the genus Drosophila. Proc. Nat. Acad. Sci. USA 1939, 25:137-141.
53. Tan S.H.D., Ali F., Kutty S.N., Meier R. The need for specifying species concepts: how many species of silvered langurs (Trachypithecus cristatus group) should be recognized?. Mol. Phylogen. Evol. 2008, 49:688-689.
54. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res. 1994, 22:4673-4680.
55. Trewick S.A. DNA barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 2008, 24:240-254.
56. Verheyen E., Salzburger W., Snoeks J., Meyer A. Origin of the superflock of cichlid fishes from Lake Victoria, East Africa. Science 2003, 300:325-329.
57. Wild A.L. Evolution of the Neotropical ant genus Linepithema. Syst. Ent. 2009, 34:49-62.
58. Yassin A., Capy P., Madi-Ravazzi L., Ogereau D., David J.R. DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianus. Mol. Ecol. Res. 2008, 8:491-501.
59. Yassin A., Amédégnato C., Cruaud C., Veuille M. Molecular taxonomy and species delimitation in Andean Schistocerca (Orthoptera: Acrididae). Mol. Phyl. Evol. 2009, 53:404-411.