A critique of earthworm molecular phylogenetics

Pedobiologia

Volumn 54, Issue SUPPL., 2011, Pages

  Chang, Chih Han ^a   James, Samuel ^b,c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b UNIVERSITY OF KANSAS   (United States)

^c UNIVERSITY OF IOWA   (United States)

Author keywords

Biogeography; DNA barcoding; Earthworm systematics; Molecular phylogeny; Taxonomy

Indexed keywords

DISCRIMINANT ANALYSIS; DIVERGENCE; EARTHWORM; FUNCTIONAL MORPHOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC VARIATION; IDENTIFICATION METHOD; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETICS; RECONSTRUCTION; SPECIATION (BIOLOGY); TAXONOMY;

EID: 84855344480     PISSN: 00314056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pedobi.2011.07.015     Document Type: Article

References (76)

1. Admassu B., Juen A., Traugott M. Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system. Soil Biol. Biochem. 2006, 38:1308-1315.
2. Blakemore R.J. Tasmanian Earthworms, Monograph with Review of World Families 2000, VermEcology, Kippax, Canberra, CD-ROM.
3. Blakemore R.J. A provision list of valid names of Lumbricoidea (Oligochaeta) after Easton, 1983. Avances en taxonomia de lombrices de tierra/Advances in earthworm taxonomy (Annelida: Oligochaeta) 2004, 75-120. Editorial Complutense, Madrid, Spain. A. Moreno, S. Borges (Eds.).
4. Blakemore R.J. A series of searchable texts on earthworm biodiversity, ecology and systematics from various regions of the world. COE Soil Ecology Research Group 2006, Yokohama National University, Japan, CD-ROM. 2nd ed. N. Kaneko, M.T. Ito (Eds.).
5. Blakemore R.J. Unravelling some Kinki earthworms (Annelida: Oligochaeta: Megadrili: Moniligastridae). Part II. Opusc. Zool. Budapest 2010, 41:191-206.
6. Blakemore R.J., Kupriyanova E.K. Unravelling some Kinki worms (Annelida: Oligochaeta: Megadrili: Moniligastridae). Part I. Opusc. Zool. Budapest 2010, 41:3-18.
7. Blakemore R.J., Ito M.T., Kaneko N. Alien earthworms in the Asia/Pacific region with a checklist of species and the first records of Eukerria saltensis (Oligochaeta: Ocnerodrilidae) and Eiseniella tetraedra (Lumbricidae) from Japan, and Pontoscolex corethrurus (Glossoscolecidae) from Okinawa. Assessment and Control of Biological Invasion Risks 2007, 173-181. Shoukadoh Book Sellers/IUCN, Kyoto, Japan/Gland, Switzerland. F. Koike, M.N. Clout, M. Kawamichi, M. De Poorter, K. Iwatsuki (Eds.).
8. Blakemore R.J., Kupriyanova E.K., Grygier M.J. Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to the 'Can of Worms' theory of cryptic species. ZooKeys 2010, 41:1-29.
9. Boyer S., Wratten S.D. Using molecular tool to identify New Zealand endemic earthworms in a mine restoration project (Oligochaeta: Acanthodrilidae, Lumbricidae, Megascolecidae). Advances in Earthworm Taxonomy IV (Annelida: Oligochaeta) 2010, 31-40. Kasparek Verlag, Heidelberg, Germany. T. Pavlicek, P. Cardet, Y. Coskun, C. Csuzdi (Eds.).
10. Buckley T.R., James S., Allwood J., Bartlam S., Howitt R., Prada D. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity. Mol. Phylogenet. Evol. 2011, 58:85-96.
11. Briones M.J.I., Moran P., Posada D. Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?. Soil Biol. Biochem. 2009, 41:2257-2271.
12. Cameron E.K., Bayne E.M., Coltman D.W. Genetic structure of invasive earthworms Dendrobaena octaedra in the boreal forest of Alberta: insights into introduction mechanisms. Mol. Ecol. 2008, 17:1189-1197.
13. Cech G., Csuzdi C., Marialigeti K. Remarks on the molecular phylogeny of the genus Dendrobaena (sensus Pop 1941) based on the investigation of 18S rDNA sequences. Advances in Earthworm Taxonomy II (Annelida: Oligochaeta) 2005, 85-98. Cluj University Press, Cluj-Napoca, Romania. V.V. Pop, A.A. Pop (Eds.).
14. Chang C.-H., Chen J.-H. Taxonomic status and intraspecific phylogeography of two sibling species of Metaphire (Oligochaeta: Megascolecidae) in Taiwan. Pedobiologia 2005, 49:591-600.
15. Chang C.-H., Chuang S.-C., Chen Y.-R., Chen J.-H. NADH dehydrogenase subunit 1 gene of the earthworm Amynthas gracilis (Kinberg, 1867) (Oligochaeta: Megascolecidae), with the discussion on inferring the megascolecid phylogeny using DNA sequences. Taiwania 2005, 50:71-79.
16. Chang C.-H., Lin Y.-H., Chen I.-H., Chuang S.-C., Chen J.-H. Taxonomic re-evaluation of the Taiwanese montane earthworm Amynthas wulinensis Tsai, Shen and Tsai, 2001 (Oligochaeta: Megascolecidae): Polytypic species or species complex?. Org. Divers. Evol. 2007, 7:231-240.
17. Chang C.-H., Lin S.-M., Chen J.-H. Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellatam, Megascolecidae). Mol. Phylogenet. Evol. 2008, 49:958-968.
18. Chang C.-H., Rougerie R., Chen J.-H. Identifying earthworms through DNA barcodes: Pitfalls and promise. Pedobiologia 2009, 52:171-180.
19. Csuzdi C., Zicsi A. Earthworms of Hungary (Annelida: Oligochaeta, Lumbricidae). Pedozoologica Hungarica No. 1 2003, 271. Hungarian Natural History Museum & Systematic Zoology Research Group of HAS, Budapest. C. Csuzdi, S. Mahunka (Eds.).
20. Csuzdi C., Pop A.A., Pop V.V., Wink M., Zicsi A. Revision of the Dendrobaena alpine (Rosa, 1884) species group (Oligochaeta, Lumbricidae) by morphological and molecular methods. Advances in Earthworm Taxonomy II (Annelida: Oligochaeta) 2005, 119-128. Cluj University Press, Cluj-Napoca, Romania. V.V. Pop, A.A. Pop (Eds.).
21. Dayrat B. Towards integrative taxonomy. Biol. J. Linnean Soc. 2005, 85:407-415.
22. Dupont L., Lazrek F., Porco D., King R.A., Rougerie R., Symondson W.O.C., Livet A., Richard B., Decaëns T., Butt K.R., Mathieu J. New insight into the genetic structure of the Allolobophora chlorotica aggregate in Europe using microsatellite and mitochondrial data. Pedobiologia 2011, 54:217-224.
23. Erseus C. Phylogeny of oligochaetous Clitellata. Hydrobiologia 2005, 535/536:357-372.
24. Erseus C., Kallersjo M. 18S rDNA phylogeny of Clitellata (Annelida). Zool. Scr. 2004, 33:187-196.
25. Erseus C., Prestegaard T., Kallersjo M. Phylogenetic analysis of Tubificidae (Annelida, Clitellata) based on 18S rDNA sequences. Mol. Phylogenet. Evol. 2000, 15:381-389.
26. Fernández R., Almodóvar A., Novo M., Gutiérrez M., Díaz Cosín D.J. A vagrant clone in a peregrine species: Phylogeography, high clonal diversity and geographical distribution in the earthworm Aporrectodea trapezoides (Dugès, 1828). Soil Biol. Biochem. 2011, 43:2085-2093.
27. Fernández R., Bergmann P., Almodóvar A., Díaz Cosín D.J., Heethoff M. Ultrastructural and molecular insights into three populations of Aporrectodea trapezoides (Dugès, 1828) (Oligochaeta, Lumbricidae) with different reproductive modes. Pedobiologia 2011, 10.1016/j.pedobi.2011.04.003.
28. Gates G.E. Burmese Earthworms, an introduction to the systematics and biology of megadrile oligochaetes with special reference to South-East Asia. T. Am. Philos. Soc. 1972, 62(7):1-326.
29. Halanych K.M., Janosik A.M. A review of molecular markers used for Annelid phylogenetics. Integr. Comp. Biol. 2006, 46:533-543.
30. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Res. Symp. Ser. 1999, 41:95-98.
31. Harper G.L., King R.A., Dodd C.S., Harwood J.D., Glen D.M., Bruford M.W., Symondson W.O.C. Rapid screening of invertebrate predators for multiple prey DNA targets. Mol. Ecol. 2005, 14:819-827.
32. Hebert P.D.N., Cywinska A., Ball S.L., deWaard J.R. Biological identifications through DNA barcodes. Proc. R. Soc. B 2003, 270:313-321.
33. Hebert P.D.N., Ratnasingham S., deWaard J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. B 2003, 270(Suppl.):S96-S99.
34. Heethoff M., Etzold K., 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 2004, 48:9-13.
35. Huang J., Sun Z.J., Tang G.L., Su Z.Y. Identifying earthworms through DNA barcodes. Pedobiologia 2007, 51:301-309.
36. James S.W. Planetary processes and their interactions with earthworm distributions and ecology. Earthworm Ecology 2004, 53-62. CRC Press, Florida, USA. 2nd ed. C.A. Edwards (Ed.).
37. James S.W. Preliminary molecular phylogeny in the Pheretima group of genera (Crassiclitellata: Megascolecidae) using Bayesian analysis. Advances in Earthworm Taxonomy II (Annelida: Oligochaeta) 2005, 129-142. Cluj University Press, Cluj-Napoca, Romania. V.V. Pop, A.A. Pop (Eds.).
38. James S.W., Porco D., Decaëns T., Richard B., Erseus C. DNA barcoding reveals cryptic diversity in Lumbricus terrestris L., 1758 (Clitellata): resurrection of L. herculeus Savigny, 1826. PLoS One 2010, 5:e15629.
39. Jamieson B.G.M. On the phylogeny and higher classification of the Oligochaeta. Cladistics 1988, 4:367-410.
40. Jamieson B.G.M., Tillier S., Tillier A., Justine J.L., Ling E., James S., McDonald K., Hugall A.F. Phylogeny of the Megascolecidae and Crassiclitellata (Annelida, Oligochaeta): combined versus partitioned analysis using nuclear (28S) and mitochondrial (12S, 16S) rDNA. Zoosystema 2002, 24:707-734.
41. King R.A., Tibble A.L., Symondson W.O.C. Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms. Mol. Ecol. 2008, 17:4684-4698.
42. King R.A., Vaughan I.P., Bell J.R., Bohan D.A., Symondson W.O.C. Prey choice by carabid beetles feeding on an earthworm community analysed using species- and lineage-specific PCR primers. Mol. Ecol. 2010, 19:1721-1732.
43. Knott K.E., Haimi J. High mitochondrial DNA sequence diversity in the parthenogenetic earthworm Dendrobaena octaedra. Heredity 2010, 105:341-347.
44. 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.
45. Martin P., Kaygorodova I., Sherbakov D.Y., Verheyen E. Rapid evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida). Mol. Phylogenet. Evol. 2000, 15:355-368.
46. Mawkawa K., Kon M., Araya K., Matsumoto T. Phylogeny and biogeography of wood-feeding cockroaches, genus Salganea Stal (Blaberidae: Panesthiinae), in Southeast Asia based on mitochondrial DNA sequences. J. Mol. Evol. 2001, 53:651-659.
47. McHugh D. Molecular phylogeny of Annelida. Can. J. Zool. 2000, 78:1873-1884.
48. McHugh D. Molecular phylogenetic analyses indicate a rapid radiation of polychaete annelids. Am. Zool. 2001, 41:1520-1521.
49. Michaelsen W. Das Tierreich 10: Oligochaeta 1900, Friedländer & Sohn, Berlin, 575 pp.
50. Minamiya Y., Yokoyama J., Fukuda T. A phylogeographic study of the Japanese earthworm, Metaphire sieboldi (Horst, 1883) (Oligochaeta: Megascolecidae): Inferences from mitochondrial DNA sequences. Eur. J. Soil Biol. 2009, 45:423-430.
51. Minamiya Y., Hayakawa H., Ohga K., Shimano S., Ito M.T., Fukuda T. Variability of sexual organ possession rates and phylogenetic analyses of a parthenogenetic Japanese earthworm, Amynthas vittatus (Oligochaeta: Megascolecidae). Genes Genet. Syst. 2011, 86:27-35.
52. Novo M., Almodovar A., Diaz-Cosin D.J. High genetic divergence of hormogastrid earthworms (Annelida, Oligochaeta) in the central Iberian Peninsula: evolutionary and demographic implications. Zool. Scr. 2009, 38:537-552.
53. Novo M., Almodovar A., Fernandez R., Trigo D., Diaz Cosin D.J. Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data. Mol. Phylogenet. Evol. 2010, 56:507-512.
54. Novo M., Almodovar A., Fernandez R., Giribet G., Diaz Cosin D.J. Understanding the biogeography of a group of earthworms in the Mediterranean Basin - the phylogenetic puzzle of Hormogastridae (Clitellata: Oligochaeta). Mol. Phylogenet. Evol. 2011, 61:125-135.
55. Omodeo P. Evolution and biogeography of megadriles (Annelida, Clitellata). It. J. Zool. 2000, 67:179-201.
56. Pérez-Losada M., Eiroa J., Mato S., Domínguez J. Phylogenetic species delimitation of the earthworms Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché, 1972 (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA sequences. Pedobiologia 2005, 49:317-324.
57. Pérez-Losada M., Ricoy M., Marshall J.C., Domínguez J. Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta: Lumbricidae) based on mitochondrial and nuclear DNA sequences. Mol. Phylogenet. Evol. 2009, 52:293-302.
58. Pop V.V. On speciation in the genus Octodrilus Omodeo, 1956 (Oligochaeta, Lumbricidae). Mitteilungen aus dem Hamburgischen Zoologischen Museum und Institut 1994, 89:37-46.
59. Pop A.A., Wink M. Molecular taxonomy and phylogeny of earthworms (Oligochaeta, Lumbricidae): 16S rDNA and COI gene corroborate numerical taxonomy in the genus Octodrilus Omodeo, 1956. Avances en Taxonomia de Lombrices de Tierra/Advances in Earthworm Taxonomy (Annelida: Oligochaeta) 2004, 347-360. Editorial Complutense, Madrid, Spain. A. Moreno, S. Borges (Eds.).
60. Pop A.A., Wink M., Pop V.V. Use of 18S, 16S rDNA and cytochrome c oxidase sequences in earthworm taxonomy (Oligochaeta, Lumbricidae). Pedobiologia 2003, 47:428-433.
61. Pop A.A., Csuzdi C., Wink M. Remarks on the molecular phylogeny of Crassiclitellata families using the mitochondrial 16S rDNA gene (Oligochaeta, Opisthopora). Advances in Earthworm Taxonomy II (Annelida: Oligochaeta) 2005, 143-154. Cluj University Press, Cluj-Napoca, Romania. V.V. Pop, A.A. Pop (Eds.).
62. Pop A.A., Csuzdi C., Wink M., Pop V.V. An attempt to reconstruct the molecular phylogeny of the genus Allolobophora Eisen, 1874 (sensus lato, Pop, 1941) using 16S rDNA and COI sequences (Oligochaeta, Lumbricidae). Advances in Earthworm Taxonomy II (Annelida: Oligochaeta) 2005, 155-164. Cluj University Press, Cluj-Napoca, Romania. V.V. Pop, A.A. Pop (Eds.).
63. Pop A.A., Cech G., Wink M., Csuzdi C., Pop V.V. Application of 16S, 18S rDNA and COI sequences in the molecular systematics of the earthworm family Lumbricidae (Annelida, Oligochaeta). Eur. J. Soil Biol. 2007, 43:S43-S52.
64. Pop A.A., Csuzdi C., Wink M., Pop V.V. Molecular taxonomy and phylogeny of the genera Octolasion Orley, 1885, Octodrilus Omodeo, 1956 and Octodriloides Zicsi, 1986 (Oligochaeta, Lumbricidae) based on nucleotide sequences of mitochondrial 16S rDNA and COI genes. Advances in Earthworm Taxonomy III (Annelida: Oligochaeta) 2008, 109-125. The Environment of Service of the Ministry of Agriculture, Natural Resources and Environment of Cyprus, Nicosia, Cyprus. T. Pavlicek, P. Cardet (Eds.).
65. Pop A.A., Wink M., Csuzdi C. Progress in systematics of terrestrial Oligochaeta by using molecular data. Advances in Earthworm Taxonomy III (Annelida: Oligochaeta) 2008, 203-224. The Environment of Service of the Ministry of Agriculture, Natural Resources and Environment of Cyprus, Nicosia, Cyprus. T. Pavlicek, P. Cardet (Eds.).
66. Pop A.A., Pop V.V., Csuzdi C. Significance of the Apuseni Mountains (the Carpathians) in the origin and distribution of Central European earthworm fauna. Advances in Earthworm Taxonomy IV (Annelida: Oligochaeta) 2010, 89-110. Kasparek Verlag, Heidelberg, Germany. T. Pavlicek, P. Cardet, Y. Coskun, C. Csuzdi (Eds.).
67. Qiu J.P., Bouché M.B. Revision des taxons supraspécifiques de Lumbricoidea. Doc. Pedozoologiques et Integrologiques. Montpellier 1998, 3:179-216.
68. Reynolds J.W., Cook D.G. Nomenclatura oligochaetologica Supplementum tertium. New Brunswick Mus. Monogr. Ser. (Nat. Sci.) 1993, 9:1-33.
69. Richard B., Decaëns T., Rougerie R., James S.W., Porco D., Hebert P.D.N. Re-integrating earthworm juveniles into soil biodiversity studies: species identification through DNA barcoding. Mol. Ecol. Res. 2010, 10:606-614.
70. Rougerie R., Decaëns T., Deharveng L., Porco D., James S.W., Chang C.-H., Richard B., Hebert P.D.N. DNA barcodes for soil animal taxonomy: transcending the final frontier. Pesqui. Agropecu. Bras. 2009, 44:789-801.
71. Siddall M.E., Apakupakul K., Burreson E.M., Coates K.A., Erseus C., Kallersjo M., Gelder S.R., Trapido-Rosenthal H. Validating Livanow: molecular data agree that leeches, branchiobdellidans and Acanthobdella peledina are a monophyletic group of oligochaetes. Mol. Phylogenet. Evol. 2001, 21:346-351.
72. Sims R.W. A classification and the distribution of earthworms, suborder Lumbricina (Haplotaxida: Oligochaeta). B. Brit. Mus. Nat. Hist. Zool. 1980, 39:103-124.
73. Struck T.H., Schult N., Kusen T., Hickman E., Bleidorn C., McHugh D., Halanych K.M. Annelid phylogeny and the status of Sipuncula and Echiura. BMC Evol. Biol. 2007, 7:57.
74. Su Z., Imura Y., Osawa S. Evolutionary discontinuity of the Carabine ground beetles. J. Mol. Evol. 2001, 53:517-529.
75. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
76. Voua Otomo P., Jansen van Vuuren B., Reinecke S.A. Usefulness of DNA barcoding in ecotoxicological investigations: resolving taxonomic uncertainties using Eisenia Malm 1877 as an example. Bull. Environ. Contam. Toxicol. 2009, 82:261-264.