Identifying earthworms through DNA barcodes

Pedobiologia

Volumn 51, Issue 4, 2007, Pages 301-309

  Huang, Jian ^a   Xu, Qin ^b   Sun, Zhen Jun ^a   Tang, Gui Lan ^a   Su, Zi You ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b Beijing Institute of Education   (China)

Author keywords

COI; DNA barcode; Earthworms; mtDNA; Taxonomy

Indexed keywords

DNA; EARTHWORM; SOIL FAUNA; SPECIES DIVERSITY; SUBSPECIES; SUCCESSION; TAXONOMY;

EISENIA FETIDA;

EID: 34548633511     PISSN: 00314056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pedobi.2007.05.003     Document Type: Article

References (54)

1. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard University Press, Cambridge
2. Ball S.L., and Armstrong K.F. DNA barcodes for insect pest identification: a testcase with tussock moths (Lepidoptera: Lymantriidae). Can. J. For. Res. 36 (2006) 337-350
3. Barrett R.D.H., and Hebert P.D.H. Identifying spiders through DNA barcodes. Can. J. Zool. 83 (2005) 481-491
4. Beddard F.E. A monograph of the Order of Oligochaeta (1895), Oxford, Clarendon Press pp. 370
5. Bely A.E., and Wray G.A. Molecular phylogeny of naidid worms (Annelida; Clitellata) based on cytochrome c oxidase I. Mol. Phylogenet. Evo. 30 (2004) 50-63
6. Boore J.L., and Brown W.M. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics 141 (1995) 305-319
7. Brown W.M., George M.J., and Wilson A.C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA. 76 (1979) 1967-1971
8. Chang C.H., and Chen J.H. Taxonomic status and intraspecific phylogeography of two sibling species of Metaphire (Oligochaeta: Megascolecidae) in Taiwan. Pedobiologia 49 (2005) 591-600
9. Coyne J.A., and Orr H.A. Patterns of speciation in Drosophila. Evolution 43 (1989) C362-C381
10. Edwards C.A. The importance of earthworms as key representatives of soil fauna. In: Edwards C.A. (Ed). Earthworm Ecology. second ed (2004), CRC Press, Boca Raton 3-11
11. Farris J.S. Methods for computing Wagner trees. Syst. Zool. 19 (1970) 83-92
12. Ferguson J.W.H. On the use of genetic divergence for identifying species. Biol. J. Linn. Soc. 75 (2002) C509-C516
13. Folmer O., Black M., Hoeh W., Lutz R., and Virjenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotech. 3 (1994) 294-299
14. Gleason J.M., and Ritchie M.G. Evolution of courtship song and reproductive isolation in the Drosophila willistoni species complex: do sexual signals diverge the most quickly?. Evolution 52 (1998) 1493-1500
15. Hajibabaei M., Janzen D.H., Burns J.M., Hallwachs W., and Hebert P.D.N. DNA barcodes distinguish species of tropical Lepidoptera. PNAS 103 (2006) 968-971
16. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
17. Hebert P.D.N., Cywinska A., Ball S.L., and deWaard J.R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B Biol. Sci. 270 (2003) 313-321
18. Hebert P.D.N., Ratnasingham S., and dewaard J.R. Barcoding animal life: cytochrome c oxidase I divergences among closely related species. Proc. R. Soc. Lond. B Biol. Sci. 270 suppl. (2003) S596-S599
19. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., and Francis C.M. Identification of birds through DNA barcodes. PLoS Biol. 2 (2004) 1657-1663
20. Heethoff M., Etzold K., and Scheu S. Mitochondrial COII sequences indicate that the parthenogenetic earthworm Octolasion tyrtaeum (Savigny, 1826) constitutes of two lineages differing in body size and genotype. Pedobiologia 48 (2004) 9-13
21. Heethoff M., Domes K., Laumann M., Maraun M., Norton R.A., and Scheu S. High genetic divergences indicate ancient separation of parthenogenetic lineages of the oribatid mite Platynothrus peltifer (Acari, Oribatida). J. Evol. Biol. 1 (2007) 392-402
22. Hogg I.D., and Hebert P.D.N. Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Can. J. Zool. 82 (2004) 749-754
23. Huang J., Xu Q., Sun Z.J., Wang C., and Zhen D.M. Research on earthworm resources of China: I. Checklist and distribution. J. China Agr. Univ. 11 (2006) 9-20
24. Huelsenbeck, J.P., 2000. MrBayes: Bayesian inference of phylogeny, version 2.01. Distributed by the author.
25. Huelsenbeck J.P., and Rannala B. Frequentist properties of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53 (2004) 904-913
26. Huelsenbeck J.P., and Ronquist F.R. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
27. Kumar S., Tamura K., and Nei M. MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 (2004) 150-163
28. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
29. Lipscomb D., Platnick N., and Wheeler Q. The intellectual content of taxonomy: a comment on DNA taxonomy. Trends Ecol. Evol. 18 (2003) 65-66
30. Michaelsen W. Oligochaeta. Das Tierreich 10 (1900) 1-575
31. Mindell D.P., Sorenson M.D., Huddleston C., Miranda H.C., and Knight A. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. In: Mindell D.P. (Ed). Avian Molecular Evolution and Systematics (1997), New York, Academic Press 214-217
32. Moore W.S. Inferring phylogenies from mtDNA variation: mitochondrial gene trees versus nuclear gene trees. Evolution 49 (1995) 718-726
33. Mršic, N., 1991. Monograph on earthworms (Lumbricidae) of the Balkans. Academia Scientiarum et Atrium Slovenica, Historia naturalis, Ljubljana 31, vol. 1-355, II, pp. 356-757.
34. Nardi F., Spinsanti G., Boore J.L., Carapelli A., Dallai R., and Frati F. Hexapod origins: monophyletic or paraphyletic?. Science (Wash., D.C.) 299 (2003) 1887-1889
35. Palumbi S.R., Martin A., Romano S., McMillan W.O., Stice L., and Grabowski G. The Simple Fool's Guide to PCR (1991), University of Hawaii Press, Honolulu
36. Palumbi S.R., and Cipriano F. Speices identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation. J. Hered. 89 (1998) 459-464
37. Pérez-Losada M., Eiroa J., and Mato S. Phylogenetic species delimitation of the earthworm Eisenia fetida (Savingy, 1826) and Eisenia andrei Bouché, 1972 (Oligocheta, Lumbricidae) based on mitochondrial nuclear DNA sequences. Pedobiologia 49 (2005) 317-324
38. Pop A.A., Wink M., and Pop V.V. Use of 18S, 16S rDNA and cytochrome c oxidase sequences in earthworm taxonomy (Oligochaeta, Lumbricidae). Pedobiologia 47 (2003) 428-433
39. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinofrmatics 14 (1998) 817-818
40. Qiu J.P. Earthworms and their application in environment protection. I. Earthworms and their functions in ecosystem. J. Shanghai Agri. Coll. 17 (1999) 227-232
41. Qiu J.P., and Bouché M.B. Revision des taxons supraspécifiques de Lumbricoidea. Doc. pedozoologiques et Integrologiques, Montpellier 3 (1998) 179-216
42. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
43. Sasa M.M., Chippendale P.T., and Johnson N.A. Patterns of postzygotic isolation in frogs. Evolution 52 (1998) C1811-C1820
44. Scheffer S.J., Lewis M.L., and Joshi R.C. DNA barcoding applied to invasive Leafminers (Diptera: Agromyzidae) in the Philipines. Ann. Entomol. Soc. Am. 99 (2006) 204-210
45. Shen H.P., Tsai C.F., and Tsai S.C. Six new earthworms of the genus Amynthas (Oligochaeta: Megascolecidae) from central Taiwan. Zool. Stud. 42 (2003) 479-490
46. Sperling F. DNA barcoding: deuset machine. Newsl. Biol. Surv. Canada (Terr. Arthropods) 22 (2003) 50-53
47. Stephenson J. The Oligochaeta (1930), Oxford, Clarendon Press pp. 1-978
48. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) (2002), Sinauer Associates, Sunderland, MA
49. Symondson W.O.C. Molecular identification of prey in predator diets. Mol. Ecol. 11 (2002) 627-641
50. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The Clustal X windows interface; flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
51. Tischler W. Agrarökologie (1965), Gustav Fischer, Jena p. 499
52. Tsai C.F., Tsai S.C., and Liaw G.J. Two new species of protandric pheretimoid earthworms belonging to the genus Metaphire (Megascolecidae: Oligochaeta) from Taiwan. J. Nat. Hist. 34 (2000) 1731-1741
53. Will K.W., and Rubinoff D. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20 (2004) 47-55
54. Zhong Y.H., Xu X.Y., and Wand D.Z. On a new species of the earthworm genus Pheretima and its reproductive organ polymorphism. Acta Zootaxon. Sin. 9 (1984) 356-360